From 69d5b63f5382d6d5f170426bfd1e6412e2bbf0fc Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Fri, 10 Nov 2023 22:57:07 -0500
Subject: [PATCH 01/19] Add test for cli

---
 molSimplify/__main__.py                       |  2 +-
 tests/test_cli.py                             | 22 ++++++++++++++++
 .../fe_oct_2_water_6_s_5_conf_1.molinp        | 22 ++++++++++++++++
 .../fe_oct_2_water_6_s_5_conf_1.report        | 26 +++++++++++++++++++
 .../test_cli/fe_oct_2_water_6_s_5_conf_1.xyz  | 21 +++++++++++++++
 5 files changed, 92 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_cli.py
 create mode 100644 tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.molinp
 create mode 100644 tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.report
 create mode 100644 tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.xyz

diff --git a/molSimplify/__main__.py b/molSimplify/__main__.py
index 87e98e8d..c1ee70ca 100644
--- a/molSimplify/__main__.py
+++ b/molSimplify/__main__.py
@@ -166,7 +166,7 @@ def main(args=None):
             parser = argparse.ArgumentParser(description=DescString_basic,
                                              formatter_class=argparse.RawDescriptionHelpFormatter)
             parseinputs_basic(parser)
-        exit()
+        return
     # ## run with gui ###
     elif gui and len(args) == 0:
         print('molSimplify is starting!')
diff --git a/tests/test_cli.py b/tests/test_cli.py
new file mode 100644
index 00000000..76e78b4a
--- /dev/null
+++ b/tests/test_cli.py
@@ -0,0 +1,22 @@
+import pytest
+from molSimplify.__main__ import main
+
+
+def test_main_empty(tmpdir, resource_path_root):
+    main(args=[f"-rundir {tmpdir}"])
+    with open(tmpdir / "fe_oct_2_water_6_s_5" /
+              "fe_oct_2_water_6_s_5_conf_1" /
+              "fe_oct_2_water_6_s_5_conf_1.report", "r") as fin:
+        lines = fin.readlines()
+    with open(resource_path_root / "refs" / "test_cli" /
+              "fe_oct_2_water_6_s_5_conf_1.report", "r") as fin:
+        lines_ref = fin.readlines()
+    assert lines == lines_ref
+
+
+@pytest.mark.skip("Test for help not working yet.")
+def test_help(capsys):
+    main(args=["--help",])
+    captured = capsys.readouterr()
+    print(captured.out)
+    assert "Welcome to molSimplify. Only basic usage is described here." in captured.out
diff --git a/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.molinp b/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.molinp
new file mode 100644
index 00000000..a3d404bc
--- /dev/null
+++ b/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.molinp
@@ -0,0 +1,22 @@
+# Input file generated from molSimplify at 11/10/2023 22:28
+-checkdirb True
+-core Fe
+-oxstate 2
+-coord 6
+-geometry oct
+-lig water
+-ligocc 6
+-spin 5
+-keepHs auto
+-rundir /private/var/folders/l6/1j71dcgj4j7c_vc466yjsq3r0000gn/T/pytest-of-ralf/pytest-5/test_main0
+-ffoption N
+-nconfs 1
+-charge 2
+-calccharge True
+-distort 0
+-qccode terachem
+-runtyp energy
+-method b3lyp
+-basis lacvps_ecp
+-jsched sge
+-bcharge 0
diff --git a/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.report b/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.report
new file mode 100644
index 00000000..c41a7d0e
--- /dev/null
+++ b/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.report
@@ -0,0 +1,26 @@
+Bad structure?, False
+Min_dist (A), 1000
+Was ANN used?, True
+geo_label, 1
+geo_prob, 0.830863893032074
+geo_LSE, 0.056454913968045105
+geo_label_trust, very high
+sc_label, 1
+sc_prob, 0.7422247529029846
+sc_LSE, 0.0010312223992481981
+sc_label_trust, very high
+split, -24.547232997490973
+split_dist, 3.5700187674544474e-15
+This spin, 5
+ANN_ground_state, 5
+homo, -14.943396781167465
+gap, 4.31362875686047
+homo_dist, 0.17068386
+gap_dist, 0.0
+ANN_bondl, [2.1664019408351636, 2.1664019408351636, 2.1664019408351636, 2.1664019408351636, 2.134863201844001, 2.1218319126203653]
+homo_trust, high
+gap_trust, high
+split_trust, high
+Was Catalytic ANN used?, False
+Catalytic ANN reason, False
+ML-bl (database, A), 2.12
diff --git a/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.xyz b/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.xyz
new file mode 100644
index 00000000..10514dcc
--- /dev/null
+++ b/tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.xyz
@@ -0,0 +1,21 @@
+19
+11/10/2023 22:23, XYZ structure generated by mol3D Class, molSimplify
+Fe 	0.000000	0.000000	0.000000
+O 	0.000000	2.120000	0.000000
+H 	0.685027	2.726198	-0.379294
+H 	-0.685027	2.726184	0.379294
+O 	2.120000	0.000000	0.000000
+H 	2.726198	-0.671373	-0.402970
+H 	2.726184	0.671373	0.402970
+O 	0.000000	-2.120000	0.000000
+H 	-0.656900	-2.726198	-0.426155
+H 	0.656900	-2.726184	0.426155
+O 	-2.120000	0.000000	0.000000
+H 	-2.726198	0.641627	-0.448821
+H 	-2.726184	-0.641627	0.448821
+O 	0.000000	0.000000	2.120000
+H 	-0.470940	0.625573	2.726198
+H 	0.470940	-0.625573	2.726184
+O 	0.000000	0.000000	-2.120000
+H 	0.492486	0.608756	-2.726198
+H 	-0.492486	-0.608756	-2.726184

From 4528a42cb2e559a3f6c69df8d51773b134b86b82 Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Fri, 10 Nov 2023 22:57:37 -0500
Subject: [PATCH 02/19] Add io tests

---
 molSimplify/Scripts/io.py |  9 +-----
 tests/test_io.py          | 65 ++++++++++++++++++++++++++++++++++++++-
 2 files changed, 65 insertions(+), 9 deletions(-)

diff --git a/molSimplify/Scripts/io.py b/molSimplify/Scripts/io.py
index 6dd5eac6..1b5f9198 100644
--- a/molSimplify/Scripts/io.py
+++ b/molSimplify/Scripts/io.py
@@ -115,12 +115,6 @@ def readdict(fname):
 
 
 def readdict_sub(fname):
-    # Constructor
-    #  @param self The object pointer
-    #  @param subname The name of the substrate
-    class substrate:
-        def __init__(self, subname):
-            self.subname = subname
     d = dict()
     with open(fname, 'r') as f:
         txt = f.read()
@@ -137,8 +131,7 @@ def __init__(self, subname):
                     vv.append(vvs)
                 else:
                     vv += vvs
-            # dict keys are instances of the substrate class
-            d[substrate(key)] = vv
+            d[key] = vv
     return d
 
 # Get ligands in dictionary
diff --git a/tests/test_io.py b/tests/test_io.py
index 0ab41b46..8b2a58c2 100644
--- a/tests/test_io.py
+++ b/tests/test_io.py
@@ -1,5 +1,11 @@
 import numpy as np
-from molSimplify.Scripts.io import lig_load
+from molSimplify.Scripts.io import (lig_load,
+                                    core_load,
+                                    printgeoms,
+                                    getsubstrates,
+                                    readdict_sub,
+                                    )
+from importlib_resources import files as resource_files
 
 
 def test_lig_load(resource_path_root):
@@ -18,3 +24,60 @@ def test_lig_load(resource_path_root):
     print(ref.coordsvect())
     np.testing.assert_allclose(mol.coordsvect(), ref.coordsvect())
     assert mol.charge == ref.charge
+
+
+def test_core_load():
+    file = str(resource_files("molSimplify").joinpath("Cores/ferrcore.xyz"))
+    core, emsg = core_load(file)
+    # Assert that the error message is empty
+    assert not emsg
+    core.convert2mol3D()
+    assert core.make_formula(latex=False) == "Fe1F1C10H9"
+
+    file = str(resource_files("molSimplify").joinpath("Cores/ferrocene.mol"))
+    core, emsg = core_load(file)
+    # Assert that the error message is empty
+    assert not emsg
+    core.convert2mol3D()
+    assert core.make_formula(latex=False) == "Fe1C10H10"
+
+
+def test_printgeoms(capsys):
+    printgeoms()
+    captured = capsys.readouterr()
+
+    ref = (
+        "Coordination: 1, geometry: none,\t short name: no \n"
+        "Coordination: 2, geometry: linear,\t short name: li \n"
+        "Coordination: 3, geometry: trigonal_planar,\t short name: tpl \n"
+        "Coordination: 4, geometry: square_planar,\t short name: sqp \n"
+        "Coordination: 4, geometry: tetrahedral,\t short name: thd \n"
+        "Coordination: 5, geometry: square_pyramidal,\t short name: spy \n"
+        "Coordination: 5, geometry: trigonal_bipyramidal,\t short name: tbp \n"
+        "Coordination: 6, geometry: octahedral,\t short name: oct \n"
+        "Coordination: 6, geometry: trigonal_prismatic,\t short name: tpr \n"
+        "Coordination: 7, geometry: pentagonal_bipyramidal,\t short name: pbp \n"
+        "Coordination: 8, geometry: square_antiprismatic,\t short name: sqap \n\n"
+    )
+    assert captured.out == ref
+
+
+def test_readdict_sub():
+    file = resource_files("molSimplify").joinpath("Substrates/substrates.dict")
+    sub_dict = readdict_sub(file)
+    assert sub_dict["methane"] == ['methane.xyz', 'ch4', '1', ['inter'],
+                                   ['N'], ['0', '#', 'BDH', '=', '104.9(0.1)']]
+    assert sub_dict["ethane"] == ['ethane.xyz', 'c2h6', '2', ['inter'],
+                                  ['B'], ['0', '#', 'BDH', '=', '101.1(0.4)']]
+
+
+def test_getsubstrates():
+    subs = getsubstrates()
+    ref = (
+        "acetaldehyde acetylene benzene biphenyl bromobenzene cumene "
+        "cyclohexene dha diphenylmethane estrogen ethanal ethane ethene "
+        "ethylene fluorene formaldehyde formicacid iodobenzene methanal "
+        "methane methanoicacid methanol methylazide n-quinolinylbutyramidate "
+        "n2 phenyl propane propene propylene propyne tert-butane toluene triazole xanthene"
+        )
+    assert subs == ref

From 613082ab532be730273319c0fe4a02e55ef8f9ef Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Fri, 10 Nov 2023 22:57:55 -0500
Subject: [PATCH 03/19] Add geometry tests

---
 tests/test_geometry.py | 44 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 tests/test_geometry.py

diff --git a/tests/test_geometry.py b/tests/test_geometry.py
new file mode 100644
index 00000000..fc3e7075
--- /dev/null
+++ b/tests/test_geometry.py
@@ -0,0 +1,44 @@
+import numpy as np
+from molSimplify.Scripts.geometry import (norm,
+                                          normalize,
+                                          checkplanar,
+                                          dihedral,
+                                          )
+from molSimplify.Classes.mol3D import mol3D
+from molSimplify.Classes.atom3D import atom3D
+
+
+def test_norm():
+    v = [1.2, -.2, 0.8]
+
+    assert abs(norm(v) - np.linalg.norm(v)) < 1e-6
+
+
+def test_normalize():
+    v = [1.8, 0.6, -1.8]
+    v_norm = normalize(v)
+
+    np.testing.assert_allclose(v_norm, np.array(v)/np.linalg.norm(v), atol=1e-6)
+
+
+def test_checkplanar():
+    a1 = [0.0, 0.0, 0.0]
+    a2 = [1.2, 0.6, 1.6]
+    a3 = [-1.1, 0.3, 0.8]
+    a4 = [0.4, -1.2, -0.3]
+
+    assert not checkplanar(a1, a2, a3, a4)
+    # Construct a set four point in plane with the first 3
+    a4 = [0.1, 0.9, 2.4]
+    assert checkplanar(a1, a2, a3, a4)
+
+
+def test_dihedral():
+    mol = mol3D()
+    mol.addAtom(atom3D(Sym='X', xyz=[0.5, 0.0, 1.2]))
+    mol.addAtom(atom3D(Sym='X', xyz=[0.0, 0.0, 0.0]))
+    mol.addAtom(atom3D(Sym='X', xyz=[0.0, 0.0, 1.0]))
+    mol.addAtom(atom3D(Sym='X', xyz=[0.5, 0.5, -0.2]))
+
+    d = dihedral(mol, 0, 1, 2, 3)
+    assert abs(d - 45.0) < 1e-6

From 252eb1b9b16d717722ded443fdb70a30d9d0bc6b Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Fri, 10 Nov 2023 22:58:37 -0500
Subject: [PATCH 04/19] Add test for deprecated ligand assign

---
 tests/test_ligand_assign.py | 58 +++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 tests/test_ligand_assign.py

diff --git a/tests/test_ligand_assign.py b/tests/test_ligand_assign.py
new file mode 100644
index 00000000..9ee199f4
--- /dev/null
+++ b/tests/test_ligand_assign.py
@@ -0,0 +1,58 @@
+from molSimplify.Classes.ligand import ligand_assign, ligand_breakdown
+from molSimplify.Classes.mol3D import mol3D
+
+
+def test_six_monodentate(resource_path_root):
+    xyz_file = (resource_path_root / "inputs" / "ligand_assign_consistent"
+                / "fe_water_ammonia_carbonyl_formaldehyde_hydrogensulfide_hydrocyanide.xyz")
+    mol = mol3D()
+    mol.readfromxyz(xyz_file)
+
+    liglist, ligdents, ligcons = ligand_breakdown(mol, BondedOct=True)
+    (ax_ligand_list, eq_ligand_list, ax_natoms_list, eq_natoms_list,
+     ax_con_int_list, eq_con_int_list, ax_con_list, eq_con_list,
+     built_ligand_list) = ligand_assign(mol, liglist, ligdents, ligcons)
+    # Expecting:
+    # ax_ligands: ['water', 'carbonyl']
+    # eq_ligands: ['hydrogensulfide', 'ammonia', 'hydrocyanide', 'formaldehyde']
+
+    ax_formulas = [lig.mol.make_formula(latex=False) for lig in ax_ligand_list]
+    assert ax_formulas == ['S1H2', 'N1C1H1']
+    eq_formulas = [lig.mol.make_formula(latex=False) for lig in eq_ligand_list]
+    assert eq_formulas == ['O1H2', 'N1H3', 'O1C1', 'O1C1H2']
+
+    assert ax_natoms_list == [3, 3]
+    assert eq_natoms_list == [3, 4, 2, 4]
+
+    assert ax_con_int_list == [[0], [1]]
+    assert eq_con_int_list == [[0], [0], [0], [1]]
+
+    assert ax_con_list == [[14], [18]]
+    assert eq_con_list == [[1], [4], [8], [11]]
+
+
+def test_triple_bidentate(resource_path_root):
+    xyz_file = (resource_path_root / "inputs" / "ligand_assign_consistent"
+                / "fe_acac_bipy_bipy.xyz")
+    mol = mol3D()
+    mol.readfromxyz(xyz_file)
+
+    liglist, ligdents, ligcons = ligand_breakdown(mol, BondedOct=True)
+    (ax_ligand_list, eq_ligand_list, ax_natoms_list, eq_natoms_list,
+     ax_con_int_list, eq_con_int_list, ax_con_list, eq_con_list,
+     built_ligand_list) = ligand_assign(mol, liglist, ligdents, ligcons)
+
+    print(ax_ligand_list, eq_ligand_list)
+    ax_formulas = [lig.mol.make_formula(latex=False) for lig in ax_ligand_list]
+    assert ax_formulas == ['O2C5H7']
+    eq_formulas = [lig.mol.make_formula(latex=False) for lig in eq_ligand_list]
+    assert eq_formulas == ['N2C10H8', 'N2C10H8']
+
+    assert ax_natoms_list == [14]
+    assert eq_natoms_list == [20, 20]
+
+    assert ax_con_int_list == [[0, 5]]
+    assert eq_con_int_list == [[0, 1], [0, 1]]
+
+    assert ax_con_list == [[1, 6]]
+    assert eq_con_list == [[15, 16], [35, 36]]

From 5cc7c875b7057ce48a8f406ad9256736ecb6bad5 Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Fri, 10 Nov 2023 23:03:52 -0500
Subject: [PATCH 05/19] Add tests for ligand class

---
 tests/test_ligand_class.py                    | 26 ++++++++++++
 .../inputs/ligand_class/acac_ref.mol2         | 42 +++++++++++++++++++
 .../inputs/ligand_class/fe_acac.mol2          | 38 +++++++++++++++++
 3 files changed, 106 insertions(+)
 create mode 100644 tests/test_ligand_class.py
 create mode 100644 tests/testresources/inputs/ligand_class/acac_ref.mol2
 create mode 100644 tests/testresources/inputs/ligand_class/fe_acac.mol2

diff --git a/tests/test_ligand_class.py b/tests/test_ligand_class.py
new file mode 100644
index 00000000..864eac54
--- /dev/null
+++ b/tests/test_ligand_class.py
@@ -0,0 +1,26 @@
+from molSimplify.Classes.ligand import ligand
+
+
+def test_ligand_class(resource_path_root):
+    mol2_file = str(
+        resource_path_root / "inputs" / "ligand_class" / "fe_acac.mol2"
+    )
+    lig = ligand(
+        master_mol=None,
+        index_list=None,
+        dent=None,
+        read_lig=mol2_file,
+    )
+    assert lig.dent == 2
+    assert lig.master_mol.make_formula(latex=False) == "Fe1O2C5H7"
+
+    lig_graph_det, mol2_str = lig.get_lig_mol2()
+    assert lig_graph_det == '-2.023585127e+17'
+
+    with open(resource_path_root / "inputs" / "ligand_class" / "acac_ref.mol2") as fin:
+        ref_str = fin.read()
+    # Remove last new line (because of our autoformatting)
+    assert mol2_str[:-1] == ref_str
+
+    buried_vol = lig.percent_buried_vol()
+    assert abs(buried_vol - 30.034) < 1e-3
diff --git a/tests/testresources/inputs/ligand_class/acac_ref.mol2 b/tests/testresources/inputs/ligand_class/acac_ref.mol2
new file mode 100644
index 00000000..d37d152c
--- /dev/null
+++ b/tests/testresources/inputs/ligand_class/acac_ref.mol2
@@ -0,0 +1,42 @@
+@<TRIPOS>MOLECULE
+ligand
+15	15	1
+SMALL
+PartialCharges
+****
+Generated from molSimplify
+
+@<TRIPOS>ATOM
+1 O1	3.1117  0.8158  -1.394 O.2	1 RES1 0.0
+2 C1	2.5035  0.2178  -0.5193 C.2	1 RES1 0.0
+3 C2	1.0119  0.1135  -0.5927 C.3	1 RES1 0.0
+4 C3	3.2352  -0.4172  0.6354 C.2	1 RES1 0.0
+5 C4	4.7377  -0.323  0.7389 C.2	1 RES1 0.0
+6 O2	5.3853  0.2682  -0.1114 O.2	1 RES1 0.0
+7 C5	5.4522  -0.9568  1.8929 C.3	1 RES1 0.0
+8 H1	0.6247  0.6297  -1.4972 H	1 RES1 0.0
+9 H2	0.5611  0.5821  0.307 H	1 RES1 0.0
+10 H3	0.7146  -0.9552  -0.636 H	1 RES1 0.0
+11 H4	4.7384  -1.4561  2.5816 H	1 RES1 0.0
+12 H5	6.007  -0.1796  2.459 H	1 RES1 0.0
+13 H6	6.1702  -1.7146  1.5151 H	1 RES1 0.0
+14 H7	2.7035  -0.9212  1.3622 H	1 RES1 0.0
+15 X1	0.0  0.0  0.0 X	1 RES1 0.0
+@<TRIPOS>BOND
+1 1 2 2
+1 1 15 1
+1 2 3 1
+1 2 4 1
+1 3 8 1
+1 3 9 1
+1 3 10 1
+1 4 5 2
+1 4 14 1
+1 5 6 1
+1 5 7 1
+1 6 15 1
+1 7 11 1
+1 7 12 1
+1 7 13 1
+@<TRIPOS>SUBSTRUCTURE
+1 RES1 15
diff --git a/tests/testresources/inputs/ligand_class/fe_acac.mol2 b/tests/testresources/inputs/ligand_class/fe_acac.mol2
new file mode 100644
index 00000000..117e1a50
--- /dev/null
+++ b/tests/testresources/inputs/ligand_class/fe_acac.mol2
@@ -0,0 +1,38 @@
+@<TRIPOS>MOLECULE
+*****
+ 15 15 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 O           3.1117    0.8158   -1.3940 O.2     1  UNL1       -0.2958
+      2 C           2.5035    0.2178   -0.5193 C.2     1  UNL1        0.1238
+      3 C           1.0119    0.1135   -0.5927 C.3     1  UNL1       -0.0046
+      4 C           3.2352   -0.4172    0.6354 C.2     1  UNL1       -0.1413
+      5 C           4.7377   -0.3230    0.7389 C.2     1  UNL1       -0.1413
+      6 O           5.3853    0.2682   -0.1114 O.2     1  UNL1       -0.5072
+      7 C           5.4522   -0.9568    1.8929 C.3     1  UNL1       -0.1389
+      8 H           0.6247    0.6297   -1.4972 H       1  UNL1        0.0308
+      9 H           0.5611    0.5821    0.3070 H       1  UNL1        0.0308
+     10 H           0.7146   -0.9552   -0.6360 H       1  UNL1        0.0308
+     11 H           4.7384   -1.4561    2.5816 H       1  UNL1       -0.0057
+     12 H           6.0070   -0.1796    2.4590 H       1  UNL1       -0.0057
+     13 H           6.1702   -1.7146    1.5151 H       1  UNL1       -0.0057
+     14 H           2.7035   -0.9212    1.3622 H       1  UNL1        0.0298
+     15 Fe          0.0000    0.0000    0.0000 Fe      1  UNL1        0.0000
+@<TRIPOS>BOND
+     1     1     2    2
+     2     2     3    1
+     3     2     4    1
+     4     3     8    1
+     5     3     9    1
+     6     3    10    1
+     7     4     5    2
+     8     4    14    1
+     9     5     6    1
+    10     5     7    1
+    11     7    11    1
+    12     7    12    1
+    13     7    13    1
+    14     1    15    1
+    15     6    15    1

From 8e0f9f47781b2d4b97b137326e368dc2a006b472 Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Fri, 10 Nov 2023 23:17:59 -0500
Subject: [PATCH 06/19] Switch report comparison to proper helper function

---
 tests/test_cli.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/tests/test_cli.py b/tests/test_cli.py
index 76e78b4a..18ae108a 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,17 +1,15 @@
 import pytest
+from helperFuncs import compare_report_new
 from molSimplify.__main__ import main
 
 
 def test_main_empty(tmpdir, resource_path_root):
     main(args=[f"-rundir {tmpdir}"])
-    with open(tmpdir / "fe_oct_2_water_6_s_5" /
-              "fe_oct_2_water_6_s_5_conf_1" /
-              "fe_oct_2_water_6_s_5_conf_1.report", "r") as fin:
-        lines = fin.readlines()
-    with open(resource_path_root / "refs" / "test_cli" /
-              "fe_oct_2_water_6_s_5_conf_1.report", "r") as fin:
-        lines_ref = fin.readlines()
-    assert lines == lines_ref
+    compare_report_new(
+        tmpdir / "fe_oct_2_water_6_s_5" / "fe_oct_2_water_6_s_5_conf_1" /
+        "fe_oct_2_water_6_s_5_conf_1.report",
+        resource_path_root / "refs" / "test_cli" /
+        "fe_oct_2_water_6_s_5_conf_1.report")
 
 
 @pytest.mark.skip("Test for help not working yet.")

From 0ecbea31bc10ff5c6808e896b66b0d765af707cb Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Fri, 15 Dec 2023 14:51:12 -0500
Subject: [PATCH 07/19] Removed duplicate file

---
 .../MOF_descriptors_alternate_functional_2.py | 586 ------------------
 1 file changed, 586 deletions(-)
 delete mode 100644 molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional_2.py

diff --git a/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional_2.py b/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional_2.py
deleted file mode 100644
index 13f58ec7..00000000
--- a/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional_2.py
+++ /dev/null
@@ -1,586 +0,0 @@
-from molSimplify.Scripts.cellbuilder_tools import *
-from molSimplify.Classes.mol3D import mol3D
-from molSimplify.Informatics.autocorrelation import *
-from molSimplify.Informatics.misc_descriptors import *
-from molSimplify.Informatics.graph_analyze import *
-from molSimplify.Informatics.RACassemble import *
-import os
-import numpy as np
-import pandas as pd
-from scipy import sparse
-import itertools
-from molSimplify.Informatics.MOF.PBC_functions import *
-
-#### NOTE: In addition to molSimplify's dependencies, this portion requires
-#### pymatgen to be installed. The RACs are intended to be computed
-#### on the primitive cell of the material. You can compute them
-#### using the commented out snippet of code if necessary.
-
-# Example usage is given at the bottom of the script.
-
-'''<<<< CODE TO COMPUTE PRIMITIVE UNIT CELLS >>>>'''
-#########################################################################################
-# This MOF RAC generator assumes that pymatgen is installed.                            #
-# Pymatgen is used to get the primitive cell.                                           #
-#########################################################################################
-from pymatgen.io.cif import CifParser
-def get_primitive(datapath, writepath):
-    s = CifParser(datapath, occupancy_tolerance=1).get_structures()[0]
-    sprim = s.get_primitive_structure()
-    sprim.to("cif",writepath)
-'''<<<< END OF CODE TO COMPUTE PRIMITIVE UNIT CELLS >>>>'''
-
-#########################################################################################
-# The RAC functions here average over the different SBUs or linkers present. This is    #
-# because one MOF could have multiple different linkers or multiple SBUs, and we need   #
-# the vector to be of constant dimension so we can correlate the output property.       #
-#########################################################################################
-
-def identify_main_chain(temp_mol, link_list):
-    G = nx.from_numpy_matrix(temp_mol.graph)
-    pairs = []
-    if len(link_list) == 1:
-        main = list(G.nodes)
-        return main
-    else:
-        for a,b in itertools.combinations(link_list, 2):
-            pair = (a,b)
-            pairs.append(pair)
-        shorts = []
-        for i in pairs:
-            short = list(nx.shortest_path(G, source=i[0], target=i[1]))
-            shorts.append(short)
-        paths = list(itertools.chain(*shorts))
-        min_cycles = (nx.minimum_cycle_basis(G))
-        min_cycles_copy = min_cycles.copy()
-        min_cycles_copy_2 = []
-        paths_copy = paths.copy()
-        while len(min_cycles_copy) != len(min_cycles_copy_2):
-            min_cycles_copy_2 = min_cycles_copy.copy()
-            for i in min_cycles:
-                paths = paths_copy.copy()
-                if set(paths) & set(i):
-                    if not set(i).issubset(set((paths))):
-                        #print('intersection')
-                        #print(set(i))
-                        paths_copy += set(i)
-                        #print(paths_copy)
-                        min_cycles_copy.remove(i)
-                        #print(min_cycles_copy)
-                        #print(len(min_cycles_copy))
-
-        main = paths
-        return main
-
-def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name,cell,anchoring_atoms, sbupath=False, connections_list=False, connections_subgraphlist=False):
-    descriptor_list = []
-    lc_descriptor_list = []
-    lc_names = []
-    names = []
-    n_sbu = len(SBUlist)
-    descriptor_names = []
-    descriptors = []
-    if sbupath:
-        sbu_descriptor_path = os.path.dirname(sbupath)
-        if os.path.getsize(sbu_descriptor_path+'/sbu_descriptors.csv')>0:
-            sbu_descriptors = pd.read_csv(sbu_descriptor_path+'/sbu_descriptors.csv')
-        else:
-            sbu_descriptors = pd.DataFrame()
-        if os.path.getsize(sbu_descriptor_path+'/lc_descriptors.csv')>0:
-            lc_descriptors = pd.read_csv(sbu_descriptor_path+'/lc_descriptors.csv')
-        else:
-            lc_descriptors = pd.DataFrame()
-
-    """""""""
-    Loop over all SBUs as identified by subgraphs. Then create the mol3Ds for each SBU.
-    """""""""
-    for i, SBU in enumerate(SBUlist):
-        descriptor_names = []
-        descriptors = []
-        SBU_mol = mol3D()
-        for val in SBU:
-            SBU_mol.addAtom(molcif.getAtom(val))
-        SBU_mol.graph = SBU_subgraph[i].todense()
-
-        """""""""
-        For each linker connected to the SBU, find the lc atoms for the lc-RACs.
-        """""""""
-        for j, linker in enumerate(connections_list):
-            descriptor_names = []
-            descriptors = []
-            if len(set(SBU).intersection(linker))>0:
-                #### This means that the SBU and linker are connected.
-                temp_mol = mol3D()
-                link_list = []
-                for jj, val2 in enumerate(linker):
-                    if val2 in anchoring_atoms:
-                        link_list.append(jj)
-                        #print(anchoring_atoms)
-                    # This builds a mol object for the linker --> even though it is in the SBU section.
-                    temp_mol.addAtom(molcif.getAtom(val2))
-
-                temp_mol.graph = connections_subgraphlist[j].todense()
-                """""""""
-                Generate all of the lc autocorrelations (from the connecting atoms)
-                """""""""
-                results_dictionary = generate_atomonly_autocorrelations(temp_mol, link_list, loud=False, depth=depth, oct=False, polarizability=False,Gval=True)
-                descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],results_dictionary['results'],'lc','all')
-                # print('1',len(descriptor_names),len(descriptors))
-                results_dictionary = generate_atomonly_deltametrics(temp_mol, link_list, loud=False, depth=depth, oct=False, polarizability=False,Gval=True)
-                descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],results_dictionary['results'],'D_lc','all')
-                # print('2',len(descriptor_names),len(descriptors))
-                """""""""
-                If heteroatom functional groups exist (anything that is not C or H, so methyl is missed, also excludes anything lc, so carboxylic metal-coordinating oxygens skipped),
-                compile the list of atoms
-                """""""""
-                functional_atoms = []
-                main = identify_main_chain(temp_mol, link_list)
-                for jj in range(len(temp_mol.graph)):
-                    #print(main)
-                    #print(link_list)
-                    if jj in main:
-                        if not jj in link_list:
-                            if not set({temp_mol.atoms[jj].sym}) & set({"C","H"}):
-                                functional_atoms.append(jj)
-                    else:
-                        if not set({temp_mol.atoms[jj].sym}) & set({"H"}):
-                            functional_atoms.append(jj)
-                #print(functional_atoms)
-
-                if len(functional_atoms) > 0:
-                    results_dictionary = generate_atomonly_autocorrelations(temp_mol, functional_atoms , loud=False, depth=depth, oct=False, polarizability=False,Gval=True)
-                    descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],results_dictionary['results'],'func','all')
-                    # print('3',len(descriptor_names),len(descriptors))
-                    results_dictionary = generate_atomonly_deltametrics(temp_mol, functional_atoms , loud=False, depth=depth, oct=False, polarizability=False,Gval=True)
-                    descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],results_dictionary['results'],'D_func','all')
-                    # print('4',len(descriptor_names),len(descriptors))
-                else:
-                    descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],list([numpy.zeros(int(6*(depth + 1)))]),'func','all')
-                    descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],list([numpy.zeros(int(6*(depth + 1)))]),'D_func','all')
-                    # print('5b',len(descriptor_names),len(descriptors))
-                for val in descriptors:
-                    if not (type(val) == float or isinstance(val, numpy.float64)):
-                        print('Mixed typing. Please convert to python float, and avoid np float')
-                        raise AssertionError('Mixed typing creates issues. Please convert your typing.')
-                descriptor_names += ['name']
-                descriptors += [name]
-                desc_dict = {key2: descriptors[kk] for kk, key2 in enumerate(descriptor_names)}
-                descriptors.remove(name)
-                descriptor_names.remove('name')
-                lc_descriptors = lc_descriptors.append(desc_dict, ignore_index=True)
-                lc_descriptor_list.append(descriptors)
-                if j == 0:
-                    lc_names = descriptor_names
-        averaged_lc_descriptors = np.mean(np.array(lc_descriptor_list), axis=0)
-        if sbupath:
-            lc_descriptors.to_csv(sbu_descriptor_path+'/lc_descriptors.csv', index=False)
-        descriptors = []
-        descriptor_names = []
-        SBU_mol_cart_coords = np.array([atom.coords() for atom in SBU_mol.atoms])
-        SBU_mol_atom_labels = [atom.sym for atom in SBU_mol.atoms]
-        SBU_mol_adj_mat = np.array(SBU_mol.graph)
-        ###### WRITE THE SBU MOL TO THE PLACE
-        if sbupath and not os.path.exists(sbupath+"/"+str(name)+str(i)+'.xyz'):
-            xyzname = sbupath+"/"+str(name)+"_sbu_"+str(i)+".xyz"
-            SBU_mol_fcoords_connected = XYZ_connected(cell , SBU_mol_cart_coords , SBU_mol_adj_mat )
-            writeXYZandGraph(xyzname , SBU_mol_atom_labels , cell , SBU_mol_fcoords_connected,SBU_mol_adj_mat)
-        """""""""
-        Generate all of the SBU based RACs (full scope, mc)
-        """""""""
-        results_dictionary = generate_full_complex_autocorrelations(SBU_mol,depth=depth,loud=False,flag_name=False,Gval=True)
-        descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],results_dictionary['results'],'f','all')
-        # print('6',len(descriptor_names),len(descriptors))
-        #### Now starts at every metal on the graph and autocorrelates
-        results_dictionary = generate_multimetal_autocorrelations(molcif,depth=depth,loud=False,Gval=True)
-        descriptor_names, descriptors =  append_descriptors(descriptor_names, descriptors, results_dictionary['colnames'],results_dictionary['results'],'mc','all')
-        # print('7',len(descriptor_names),len(descriptors))
-        results_dictionary = generate_multimetal_deltametrics(molcif,depth=depth,loud=False,Gval=True)
-        descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],results_dictionary['results'],'D_mc','all')
-        # print('8',len(descriptor_names),len(descriptors))
-        descriptor_names += ['name']
-        descriptors += [name]
-        descriptors == list(descriptors)
-        desc_dict = {key: descriptors[ii] for ii, key in enumerate(descriptor_names)}
-        descriptors.remove(name)
-        descriptor_names.remove('name')
-        sbu_descriptors = sbu_descriptors.append(desc_dict, ignore_index=True)
-        descriptor_list.append(descriptors)
-        if i == 0:
-            names = descriptor_names
-    if sbupath:
-        sbu_descriptors.to_csv(sbu_descriptor_path+'/sbu_descriptors.csv', index=False)
-    averaged_SBU_descriptors = np.mean(np.array(descriptor_list), axis=0)
-    return names, averaged_SBU_descriptors, lc_names, averaged_lc_descriptors
-
-def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, cell, linkerpath=False):
-    #### This function makes full scope linker RACs for MOFs ####
-    descriptor_list = []
-    nlink = len(linkerlist)
-    descriptor_names = []
-    descriptors = []
-    if linkerpath:
-        linker_descriptor_path = os.path.dirname(linkerpath)
-        if os.path.getsize(linker_descriptor_path+'/linker_descriptors.csv')>0:
-            linker_descriptors = pd.read_csv(linker_descriptor_path+'/linker_descriptors.csv')
-        else:
-            linker_descriptors = pd.DataFrame()
-    for i, linker in enumerate(linkerlist):
-        linker_mol = mol3D()
-        for val in linker:
-            linker_mol.addAtom(molcif.getAtom(val))
-        linker_mol.graph = linker_subgraphlist[i].todense()
-        linker_mol_cart_coords=np.array([atom.coords() for atom in  linker_mol.atoms])
-        linker_mol_atom_labels=[atom.sym for atom in  linker_mol.atoms]
-        linker_mol_adj_mat = np.array(linker_mol.graph)
-        ###### WRITE THE LINKER MOL TO THE PLACE
-        if linkerpath and not os.path.exists(linkerpath+"/"+str(name)+str(i)+".xyz"):
-            xyzname = linkerpath+"/"+str(name)+"_linker_"+str(i)+".xyz"
-            linker_mol_fcoords_connected = XYZ_connected(cell, linker_mol_cart_coords, linker_mol_adj_mat)
-            writeXYZandGraph(xyzname, linker_mol_atom_labels, cell, linker_mol_fcoords_connected, linker_mol_adj_mat)
-        allowed_strings = ['electronegativity', 'nuclear_charge', 'ident', 'topology', 'size','effective_nuclear_charge']
-        labels_strings = ['chi', 'Z', 'I', 'T', 'S','Gval']
-        colnames = []
-        lig_full = list()
-        for ii, properties in enumerate(allowed_strings):
-            if not list(descriptors):
-                ligand_ac_full = full_autocorrelation(linker_mol, properties, depth)
-            else:
-                ligand_ac_full += full_autocorrelation(linker_mol, properties, depth)
-            this_colnames = []
-            for j in range(0,depth+1):
-                this_colnames.append('f-lig-'+labels_strings[ii] + '-' + str(j))
-            colnames.append(this_colnames)
-            lig_full.append(ligand_ac_full)
-        lig_full = [item for sublist in lig_full for item in sublist] #flatten lists
-        colnames = [item for sublist in colnames for item in sublist]
-        colnames += ['name']
-        lig_full += [name]
-        desc_dict = {key: lig_full[i] for i, key in enumerate(colnames)}
-        linker_descriptors = linker_descriptors.append(desc_dict, ignore_index = True)
-        lig_full.remove(name)
-        colnames.remove('name')
-        descriptor_list.append(lig_full)
-    #### We dump the standard lc descriptors without averaging or summing so that the user
-    #### can make the modifications that they want. By default we take the average ones.
-    if linkerpath:
-        linker_descriptors.to_csv(linker_descriptor_path+'/linker_descriptors.csv', index=False)
-    averaged_ligand_descriptors = np.mean(np.array(descriptor_list), axis=0)
-    return colnames, averaged_ligand_descriptors
-
-
-def get_MOF_descriptors(data, depth, path=False, xyzpath = False):
-    if not path:
-        print('Need a directory to place all of the linker, SBU, and ligand objects. Exiting now.')
-        raise ValueError('Base path must be specified in order to write descriptors.')
-    else:
-        if path.endswith('/'):
-            path = path[:-1]
-        if not os.path.isdir(path+'/ligands'):
-            os.mkdir(path+'/ligands')
-        if not os.path.isdir(path+'/linkers'):
-            os.mkdir(path+'/linkers')
-        if not os.path.isdir(path+'/sbus'):
-            os.mkdir(path+'/sbus')
-        if not os.path.isdir(path+'/xyz'):
-            os.mkdir(path+'/xyz')
-        if not os.path.isdir(path+'/logs'):
-            os.mkdir(path+'/logs')
-        if not os.path.exists(path+'/sbu_descriptors.csv'):
-            with open(path+'/sbu_descriptors.csv','w') as f:
-                f.close()
-        if not os.path.exists(path+'/linker_descriptors.csv'):
-            with open(path+'/linker_descriptors.csv','w') as g:
-                g.close()
-        if not os.path.exists(path+'/lc_descriptors.csv'):
-            with open(path+'/lc_descriptors.csv','w') as h:
-                h.close()
-    ligandpath = path+'/ligands'
-    linkerpath = path+'/linkers'
-    sbupath = path+'/sbus'
-    logpath = path+"/logs"
-
-    """""""""
-    Input cif file and get the cell parameters and adjacency matrix. If overlap, do not featurize.
-    Simultaneously prepare mol3D class for MOF for future RAC featurization (molcif)
-    """""""""
-
-    cpar, allatomtypes, fcoords = readcif(data)
-    cell_v = mkcell(cpar)
-    cart_coords = fractional2cart(fcoords,cell_v)
-    name = os.path.basename(data).strip(".cif")
-    if len(cart_coords) > 2000:
-        print("Too large cif file, skipping it for now...")
-        full_names = [0]
-        full_descriptors = [0]
-        tmpstr = "Failed to featurize %s: large primitive cell\n"%(name)
-        write2file(path,"/FailedStructures.log",tmpstr)
-        return full_names, full_descriptors
-    distance_mat = compute_distance_matrix2(cell_v,cart_coords)
-    try:
-        adj_matrix, _ = compute_adj_matrix(distance_mat,allatomtypes)
-    except NotImplementedError:
-        full_names = [0]
-        full_descriptors = [0]
-        tmpstr = "Failed to featurize %s: atomic overlap\n"%(name)
-        write2file(path,"/FailedStructures.log",tmpstr)
-        return full_names, full_descriptors
-
-    writeXYZandGraph(xyzpath, allatomtypes, cell_v, fcoords, adj_matrix.todense())
-    molcif,_,_,_,_ = import_from_cif(data, True)
-    molcif.graph = adj_matrix.todense()
-
-    """""""""
-    check number of connected components.
-    if more than 1: it checks if the structure is interpenetrated. Fails if no metal in one of the connected components (identified by the graph).
-    This includes floating solvent molecules.
-    """""""""
-
-    n_components, labels_components = sparse.csgraph.connected_components(csgraph=adj_matrix, directed=False, return_labels=True)
-    metal_list = set([at for at in molcif.findMetal(transition_metals_only=False)])
-    # print('##### METAL LIST', metal_list, [molcif.getAtom(val).symbol() for val in list(metal_list)])
-    # print('##### METAL LIST', metal_list, [val.symbol() for val in molcif.atoms])
-    if not len(metal_list) > 0:
-        full_names = [0]
-        full_descriptors = [0]
-        tmpstr = "Failed to featurize %s: no metal found\n"%(name)
-        write2file(path,"/FailedStructures.log",tmpstr)
-        return full_names, full_descriptors
-
-    for comp in range(n_components):
-        inds_in_comp = [i for i in range(len(labels_components)) if labels_components[i]==comp]
-        if not set(inds_in_comp) & metal_list:
-            full_names = [0]
-            full_descriptors = [0]
-            tmpstr = "Failed to featurize %s: solvent molecules\n"%(name)
-            write2file(path,"/FailedStructures.log",tmpstr)
-            return full_names, full_descriptors
-
-    if n_components > 1 :
-        print("structure is interpenetrated")
-        tmpstr = "%s found to be an interpenetrated structure\n"%(name)
-        write2file(logpath,"/%s.log"%name,tmpstr)
-
-    """""""""
-    step 1: metallic part
-        removelist = metals (1) + atoms only connected to metals (2) + H connected to (1+2)
-        SBUlist = removelist + 1st coordination shell of the metals
-    removelist = set()
-    Logs the atom types of the connecting atoms to the metal in logpath.
-    """""""""
-    SBUlist = set()
-    metal_list = set([at for at in molcif.findMetal(transition_metals_only=False)])
-    # print('##### METAL LIST2', metal_list, [molcif.getAtom(val).symbol() for val in list(metal_list)])
-    # print('##### all LIST2', metal_list, [val.symbol() for val in molcif.atoms])
-    [SBUlist.update(set([metal])) for metal in molcif.findMetal(transition_metals_only=False)] #Remove all metals as part of the SBU
-    [SBUlist.update(set(molcif.getBondedAtomsSmart(metal))) for metal in molcif.findMetal(transition_metals_only=False)]
-    removelist = set()
-    [removelist.update(set([metal])) for metal in molcif.findMetal(transition_metals_only=False)] #Remove all metals as part of the SBU
-    for metal in removelist:
-        bonded_atoms = set(molcif.getBondedAtomsSmart(metal))
-        bonded_atoms_types = set([str(allatomtypes[at]) for at in set(molcif.getBondedAtomsSmart(metal))])
-        cn = len(bonded_atoms)
-        cn_atom = ",".join([at for at in bonded_atoms_types])
-        tmpstr = "atom %i with type of %s found to have %i coordinates with atom types of %s\n"%(metal,allatomtypes[metal],cn,cn_atom)
-        write2file(logpath,"/%s.log"%name,tmpstr)
-    [removelist.update(set([atom])) for atom in SBUlist if all((molcif.getAtom(val).ismetal() or molcif.getAtom(val).symbol().upper() == 'H') for val in molcif.getBondedAtomsSmart(atom))]
-    """""""""
-    adding hydrogens connected to atoms which are only connected to metals. In particular interstitial OH, like in UiO SBU.
-    """""""""
-    for atom in SBUlist:
-        for val in molcif.getBondedAtomsSmart(atom):
-            if molcif.getAtom(val).symbol().upper() == 'H':
-               removelist.update(set([val]))
-
-    """""""""
-    At this point:
-    The remove list only removes metals and things ONLY connected to metals or hydrogens.
-    Thus the coordinating atoms are double counted in the linker.
-
-    step 2: organic part
-        removelist = linkers are all atoms - the removelist (assuming no bond between
-        organiclinkers)
-    """""""""
-    allatoms = set(range(0, adj_matrix.shape[0]))
-    linkers = allatoms - removelist
-    linker_list, linker_subgraphlist = get_closed_subgraph(linkers.copy(), removelist.copy(), adj_matrix)
-    connections_list = copy.deepcopy(linker_list)
-    connections_subgraphlist = copy.deepcopy(linker_subgraphlist)
-    linker_length_list = [len(linker_val) for linker_val in linker_list]
-    adjmat = adj_matrix.todense()
-    """""""""
-    find all anchoring atoms on linkers and ligands (lc identification)
-    """""""""
-    anc_atoms = set()
-    for linker in linker_list:
-        for atom_linker in linker:
-            bonded2atom = np.nonzero(adj_matrix[atom_linker,:])[1]
-            if set(bonded2atom) & metal_list:
-                anc_atoms.add(atom_linker)
-    """""""""
-    step 3: linker or ligand ?
-    checking to find the anchors and #SBUs that are connected to an organic part
-    anchor <= 1 -> ligand
-    anchor > 1 and #SBU > 1 -> linker
-    else: walk over the linker graph and count #crossing PBC
-        if #crossing is odd -> linker
-        else -> ligand
-    """""""""
-    initial_SBU_list, initial_SBU_subgraphlist = get_closed_subgraph(removelist.copy(), linkers.copy(), adj_matrix)
-    templist = linker_list[:]
-    tempgraphlist = linker_subgraphlist[:]
-    long_ligands = False
-    max_min_linker_length , min_max_linker_length = (0,100)
-    for ii, atoms_list in reversed(list(enumerate(linker_list))): #Loop over all linker subgraphs
-        linkeranchors_list = set()
-        linkeranchors_atoms = set()
-        sbuanchors_list = set()
-        sbu_connect_list = set()
-        """""""""
-        Here, we are trying to identify what is actually a linker and what is a ligand.
-        To do this, we check if something is connected to more than one SBU. Set to
-        handle cases where primitive cell is small, ambiguous cases are recorded.
-        """""""""
-        for iii,atoms in enumerate(atoms_list): #loop over all atoms in a linker
-            connected_atoms = np.nonzero(adj_matrix[atoms,:])[1]
-            for kk, sbu_atoms_list in enumerate(initial_SBU_list): #loop over all SBU subgraphs
-                for sbu_atoms in sbu_atoms_list: #Loop over SBU
-                    if sbu_atoms in connected_atoms:
-                        linkeranchors_list.add(iii)
-                        linkeranchors_atoms.add(atoms)
-                        sbuanchors_list.add(sbu_atoms)
-                        sbu_connect_list.add(kk) #Add if unique SBUs
-        min_length,max_length = linker_length(linker_subgraphlist[ii].todense(),linkeranchors_list)
-
-        if len(linkeranchors_list) >=2 : # linker, and in one ambigous case, could be a ligand.
-            if len(sbu_connect_list) >= 2: #Something that connects two SBUs is certain to be a linker
-                max_min_linker_length = max(min_length,max_min_linker_length)
-                min_max_linker_length = min(max_length,min_max_linker_length)
-                continue
-            else:
-                # check number of times we cross PBC :
-                # TODO: we still can fail in multidentate ligands!
-                linker_cart_coords = np.array([
-                    at.coords() for at in [molcif.getAtom(val) for val in atoms_list]])
-                linker_adjmat = np.array(linker_subgraphlist[ii].todense())
-                pr_image_organic = ligand_detect(cell_v,linker_cart_coords,linker_adjmat,linkeranchors_list)
-                sbu_temp = linkeranchors_atoms.copy()
-                sbu_temp.update({val for val in initial_SBU_list[list(sbu_connect_list)[0]]})
-                sbu_temp = list(sbu_temp)
-                sbu_cart_coords = np.array([
-                    at.coords() for at in [molcif.getAtom(val) for val in sbu_temp]])
-                sbu_adjmat = slice_mat(adj_matrix.todense(),sbu_temp)
-                pr_image_sbu = ligand_detect(cell_v,sbu_cart_coords,sbu_adjmat,set(range(len(linkeranchors_list))))
-                if not (len(np.unique(pr_image_sbu, axis=0))==1 and len(np.unique(pr_image_organic, axis=0))==1): # linker
-                    max_min_linker_length = max(min_length,max_min_linker_length)
-                    min_max_linker_length = min(max_length,min_max_linker_length)
-                    tmpstr = str(name)+','+' Anchors list: '+str(sbuanchors_list) \
-                            +','+' SBU connectlist: '+str(sbu_connect_list)+' set to be linker\n'
-                    write2file(ligandpath,"/ambiguous.txt",tmpstr)
-                    continue
-                else: #  all anchoring atoms are in the same unitcell -> ligand
-                    removelist.update(set(templist[ii])) # we also want to remove these ligands
-                    SBUlist.update(set(templist[ii])) # we also want to remove these ligands
-                    linker_list.pop(ii)
-                    linker_subgraphlist.pop(ii)
-                    tmpstr = str(name)+','+' Anchors list: '+str(sbuanchors_list) \
-                            +','+' SBU connectlist: '+str(sbu_connect_list)+' set to be ligand\n'
-                    write2file(ligandpath,"/ambiguous.txt",tmpstr)
-                    tmpstr = str(name)+str(ii)+','+' Anchors list: '+ \
-                            str(sbuanchors_list)+','+' SBU connectlist: '+str(sbu_connect_list)+'\n'
-                    write2file(ligandpath,"/ligand.txt",tmpstr)
-        else: #definite ligand
-            write2file(logpath,"/%s.log"%name,"found ligand\n")
-            removelist.update(set(templist[ii])) # we also want to remove these ligands
-            SBUlist.update(set(templist[ii])) # we also want to remove these ligands
-            linker_list.pop(ii)
-            linker_subgraphlist.pop(ii)
-            tmpstr = str(name)+','+' Anchors list: '+str(sbuanchors_list) \
-         +','+' SBU connectlist: '+str(sbu_connect_list)+'\n'
-            write2file(ligandpath,"/ligand.txt",tmpstr)
-
-    tmpstr = str(name) + ", (min_max_linker_length,max_min_linker_length): " + \
-                str(min_max_linker_length) + " , " +str(max_min_linker_length) + "\n"
-    write2file(logpath,"/%s.log"%name,tmpstr)
-    if min_max_linker_length < 3:
-        write2file(linkerpath,"/short_ligands.txt",tmpstr)
-    if min_max_linker_length > 2:
-        # for N-C-C-N ligand ligand
-        if max_min_linker_length == min_max_linker_length:
-            long_ligands = True
-        elif min_max_linker_length > 3:
-            long_ligands = True
-
-    """""""""
-    In the case of long linkers, add second coordination shell without further checks. In the case of short linkers, start from metal
-    and grow outwards using the include_extra_shells function
-    """""""""
-    linker_length_list = [len(linker_val) for linker_val in linker_list]
-    if len(set(linker_length_list)) != 1:
-        write2file(linkerpath,"/uneven.txt",str(name)+'\n')
-    if not min_max_linker_length < 2: # treating the 2 atom ligands differently! Need caution
-        if long_ligands:
-            tmpstr = "\nStructure has LONG ligand\n\n"
-            write2file(logpath,"/%s.log"%name,tmpstr)
-            [[SBUlist.add(val) for val in  molcif.getBondedAtomsSmart(zero_first_shell)] for zero_first_shell in SBUlist.copy()] #First account for all of the carboxylic acid type linkers, add in the carbons.
-        truncated_linkers = allatoms - SBUlist
-        SBU_list, SBU_subgraphlist = get_closed_subgraph(SBUlist, truncated_linkers, adj_matrix)
-        if not long_ligands:
-            tmpstr = "\nStructure has SHORT ligand\n\n"
-            write2file(logpath,"/%s.log"%name,tmpstr)
-            SBU_list , SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
-    else:
-        tmpstr = "Structure %s has extreamly short ligands, check the outputs\n"%name
-        write2file(ligandpath,"/ambiguous.txt",tmpstr)
-        tmpstr = "Structure has extreamly short ligands\n"
-        write2file(logpath,"/%s.log"%name,tmpstr)
-        tmpstr = "Structure has extreamly short ligands\n"
-        write2file(logpath,"/%s.log"%name,tmpstr)
-        truncated_linkers = allatoms - removelist
-        SBU_list, SBU_subgraphlist = get_closed_subgraph(removelist, truncated_linkers, adj_matrix)
-        SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
-        SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
-
-    """""""""
-    For the cases that have a linker subgraph, do the featurization.
-    """""""""
-    if len(linker_subgraphlist)>=1: #Featurize cases that did not fail
-        try:
-        # if True:
-            descriptor_names, descriptors, lc_descriptor_names, lc_descriptors = make_MOF_SBU_RACs(SBU_list, SBU_subgraphlist, molcif, depth, name , cell_v,anc_atoms, sbupath, connections_list, connections_subgraphlist)
-            lig_descriptor_names, lig_descriptors = make_MOF_linker_RACs(linker_list, linker_subgraphlist, molcif, depth, name, cell_v, linkerpath)
-            full_names = descriptor_names+lig_descriptor_names+lc_descriptor_names #+ ECFP_names
-            full_descriptors = list(descriptors)+list(lig_descriptors)+list(lc_descriptors)
-            print(len(full_names),len(full_descriptors))
-        # else:
-        except:
-            full_names = [0]
-            full_descriptors = [0]
-    elif len(linker_subgraphlist) == 1: # this never happens, right?
-        print('Suspicious featurization')
-        full_names = [1]
-        full_descriptors = [1]
-    else:
-        print('Failed to featurize this MOF.')
-        full_names = [0]
-        full_descriptors = [0]
-    if (len(full_names) <= 1) and (len(full_descriptors) <= 1):
-        tmpstr = "Failed to featurize %s\n"%(name)
-        write2file(path,"/FailedStructures.log",tmpstr)
-    return full_names, full_descriptors
-
-
-##### Example of usage over a set of cif files.
-# featurization_list = []
-# import sys
-# featurization_directory = sys.argv[1]
-# for cif_file in os.listdir(featurization_directory+'/cif/'):
-#     #### This first part gets the primitive cells ####
-#     get_primitive(featurization_directory+'/cif/'+cif_file, featurization_directory+'/primitive/'+cif_file)
-#     full_names, full_descriptors = get_MOF_descriptors(featurization_directory+'/primitive/'+cif_file,3,path=featurization_directory+'/',
-#         xyzpath=featurization_directory+'/xyz/'+cif_file.replace('cif','xyz'))
-#     full_names.append('filename')
-#     full_descriptors.append(cif_file)
-#     featurization = dict(zip(full_names, full_descriptors))
-#     featurization_list.append(featurization)
-# df = pd.DataFrame(featurization_list)
-# df.to_csv('./full_featurization_frame.csv',index=False)

From 06040bfba1134b42a8011560dbef428daf8c7b7f Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Sat, 16 Dec 2023 14:50:12 -0500
Subject: [PATCH 08/19] Add test cases for MOF_descriptors

---
 .../Informatics/MOF/MOF_descriptors.py        | 392 ++++++++--------
 tests/informatics/test_MOF_descriptors.py     |  57 +++
 .../inputs/cif_files/odac-21383.cif           | 261 +++++++++++
 .../inputs/cif_files/odac-21433.cif           | 169 +++++++
 .../inputs/cif_files/odac-21478.cif           | 209 +++++++++
 .../inputs/cif_files/odac-21735.cif           | 139 ++++++
 .../inputs/cif_files/odac-21816.cif           | 417 ++++++++++++++++++
 .../refs/MOF_descriptors/odac-21383.json      |   1 +
 .../refs/MOF_descriptors/odac-21433.json      |   1 +
 .../refs/MOF_descriptors/odac-21478.json      |   1 +
 .../refs/MOF_descriptors/odac-21735.json      |   1 +
 .../refs/MOF_descriptors/odac-21816.json      |   1 +
 12 files changed, 1473 insertions(+), 176 deletions(-)
 create mode 100644 tests/informatics/test_MOF_descriptors.py
 create mode 100644 tests/testresources/inputs/cif_files/odac-21383.cif
 create mode 100644 tests/testresources/inputs/cif_files/odac-21433.cif
 create mode 100644 tests/testresources/inputs/cif_files/odac-21478.cif
 create mode 100644 tests/testresources/inputs/cif_files/odac-21735.cif
 create mode 100644 tests/testresources/inputs/cif_files/odac-21816.cif
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21383.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21433.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21478.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21735.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21816.json

diff --git a/molSimplify/Informatics/MOF/MOF_descriptors.py b/molSimplify/Informatics/MOF/MOF_descriptors.py
index e0967e19..6224276b 100644
--- a/molSimplify/Informatics/MOF/MOF_descriptors.py
+++ b/molSimplify/Informatics/MOF/MOF_descriptors.py
@@ -56,6 +56,7 @@
 # This function is commented out and should be uncommented if used.
 from pymatgen.io.cif import CifParser
 
+
 def get_primitive(datapath, writepath, occupancy_tolerance=1):
     """
     Calculates and writes the primitive cell of the provided structure.
@@ -77,10 +78,12 @@ def get_primitive(datapath, writepath, occupancy_tolerance=1):
 
     s = CifParser(datapath, occupancy_tolerance=occupancy_tolerance).get_structures()[0]
     sprim = s.get_primitive_structure()
-    sprim.to("cif", writepath) # Output structure to a file.
+    sprim.to("cif", writepath)  # Output structure to a file.
+
 
 '''<<<< END OF CODE TO COMPUTE PRIMITIVE UNIT CELLS >>>>'''
 
+
 def load_sbu_lc_descriptors(sbupath):
     """
     Loads the sbu and lc descriptors.
@@ -99,17 +102,18 @@ def load_sbu_lc_descriptors(sbupath):
 
     """
     sbu_descriptor_path = os.path.dirname(sbupath)
-    if os.path.getsize(sbu_descriptor_path+'/sbu_descriptors.csv')>0: # Checking if there is a file there.
+    if os.path.getsize(sbu_descriptor_path+'/sbu_descriptors.csv') > 0:  # Checking if there is a file there.
         sbu_descriptors = pd.read_csv(sbu_descriptor_path+'/sbu_descriptors.csv')
     else:
         sbu_descriptors = pd.DataFrame()
-    if os.path.getsize(sbu_descriptor_path+'/lc_descriptors.csv')>0: # Checking if there is a file there.
+    if os.path.getsize(sbu_descriptor_path+'/lc_descriptors.csv') > 0:  # Checking if there is a file there.
         lc_descriptors = pd.read_csv(sbu_descriptor_path+'/lc_descriptors.csv')
     else:
         lc_descriptors = pd.DataFrame()
 
     return sbu_descriptor_path, sbu_descriptors, lc_descriptors
 
+
 def gen_and_append_desc(temp_mol, target_list, depth, descriptor_names, descriptors, Gval, feature_type):
     """
     Generate and append descriptors, both standard and delta.
@@ -141,11 +145,23 @@ def gen_and_append_desc(temp_mol, target_list, depth, descriptor_names, descript
         The updated RAC descriptor values.
     """
 
-    results_dictionary = generate_atomonly_autocorrelations(temp_mol, target_list, depth=depth, loud=False, oct=False, polarizability=True, Gval=Gval)
-    descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors, results_dictionary['colnames'], results_dictionary['results'], feature_type, 'all')
+    results_dictionary = generate_atomonly_autocorrelations(
+        temp_mol, target_list, depth=depth, loud=False, oct=False,
+        polarizability=True, Gval=Gval
+    )
+    descriptor_names, descriptors = append_descriptors(
+        descriptor_names, descriptors, results_dictionary['colnames'],
+        results_dictionary['results'], feature_type, 'all'
+    )
 
-    results_dictionary = generate_atomonly_deltametrics(temp_mol, target_list, depth=depth, loud=False, oct=False, polarizability=True, Gval=Gval)
-    descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors, results_dictionary['colnames'], results_dictionary['results'], f'D_{feature_type}', 'all')
+    results_dictionary = generate_atomonly_deltametrics(
+        temp_mol, target_list, depth=depth, loud=False, oct=False,
+        polarizability=True, Gval=Gval
+    )
+    descriptor_names, descriptors = append_descriptors(
+        descriptor_names, descriptors, results_dictionary['colnames'],
+        results_dictionary['results'], f'D_{feature_type}', 'all'
+    )
 
     return results_dictionary, descriptor_names, descriptors
 
@@ -155,8 +171,10 @@ def gen_and_append_desc(temp_mol, target_list, depth, descriptor_names, descript
 # the vector to be of constant dimension so we can correlate the output property.       #
 #########################################################################################
 
-def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name, cell_v, anchoring_atoms, sbupath, linkeranchors_superlist,
-    Gval, connections_list=False, connections_subgraphlist=False):
+
+def make_MOF_SBU_RACs(
+        SBUlist, SBU_subgraph, molcif, depth, name, cell_v, anchoring_atoms, sbupath,
+        linkeranchors_superlist, Gval, connections_list=False, connections_subgraphlist=False):
     """
     Generated RACs on the SBUs of the MOF, as well as on the lc atoms (SBU-connected atoms of linkers).
 
@@ -227,14 +245,14 @@ def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name, cell_v, anchor
         For each linker connected to the SBU, find the lc atoms for the lc-RACs.
         lc atoms are those bonded to a metal.
         """""""""
-        for j, linker in enumerate(connections_list): # Iterating over the different linkers
+        for j, linker in enumerate(connections_list):  # Iterating over the different linkers
             descriptor_names = []
             descriptors = []
-            if len(set(SBU).intersection(linker))>0:
-                #### This means that the SBU and the current linker are connected.
+            if len(set(SBU).intersection(linker)) > 0:
+                # This means that the SBU and the current linker are connected.
                 temp_mol = mol3D()
-                link_list = [] # Will hold the lc atoms for the current linker.
-                for jj, val2 in enumerate(linker): # linker is a list of global atom indices for the atoms in that linker
+                link_list = []  # Will hold the lc atoms for the current linker.
+                for jj, val2 in enumerate(linker):  # linker is a list of global atom indices for the atoms in that linker
                     if val2 in anchoring_atoms:
                         link_list.append(jj)
                     # This builds a mol object for the linker --> even though it is in the SBU section.
@@ -244,32 +262,40 @@ def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name, cell_v, anchor
                 """""""""
                 Generate all of the lc autocorrelations (from the connecting atoms)
                 """""""""
-                results_dictionary, descriptor_names, descriptors = gen_and_append_desc(temp_mol, link_list, depth, descriptor_names, descriptors, Gval, 'lc')
+                results_dictionary, descriptor_names, descriptors = gen_and_append_desc(
+                    temp_mol, link_list, depth, descriptor_names, descriptors, Gval, 'lc')
                 """""""""
                 If heteroatom functional groups exist (anything that is not C or H, so methyl is missed, also excludes anything lc, so carboxylic metal-coordinating oxygens skipped),
                 compile the list of atoms
                 """""""""
                 functional_atoms = []
                 for jj in range(len(temp_mol.graph)):
-                    if not jj in link_list: # linker atom is not bonded to a metal
-                        if not set({temp_mol.atoms[jj].sym}) & set({"C","H"}): # not a carbon nor a hydrogen. syms get symbols.
+                    if jj not in link_list:  # linker atom is not bonded to a metal
+                        if not set({temp_mol.atoms[jj].sym}) & set({"C", "H"}):  # not a carbon nor a hydrogen. syms get symbols.
                             functional_atoms.append(jj)
                 """""""""
                 Generate all of the functional group autocorrelations
                 """""""""
                 if len(functional_atoms) > 0:
-                    results_dictionary, descriptor_names, descriptors = gen_and_append_desc(temp_mol, functional_atoms, depth, descriptor_names, descriptors, Gval, 'func')
-                else: # There are no functional atoms.
+                    results_dictionary, descriptor_names, descriptors = gen_and_append_desc(
+                        temp_mol, functional_atoms, depth, descriptor_names, descriptors, Gval, 'func')
+                else:  # There are no functional atoms.
                     if Gval:
                         num_atomic_properties = 7
                     else:
                         num_atomic_properties = 6
 
-                    descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],list([np.zeros(int(num_atomic_properties*(depth + 1)))]),'func','all')
-                    descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],list([np.zeros(int(num_atomic_properties*(depth + 1)))]),'D_func','all')
+                    descriptor_names, descriptors = append_descriptors(
+                        descriptor_names, descriptors, results_dictionary['colnames'],
+                        list([np.zeros(int(num_atomic_properties*(depth + 1)))]), 'func', 'all'
+                    )
+                    descriptor_names, descriptors = append_descriptors(
+                        descriptor_names, descriptors, results_dictionary['colnames'],
+                        list([np.zeros(int(num_atomic_properties*(depth + 1)))]), 'D_func', 'all'
+                    )
 
                 for val in descriptors:
-                    if not (type(val) == float or isinstance(val, np.float64)):
+                    if not (type(val) is float or isinstance(val, np.float64)):
                         print('Mixed typing. Please convert to python float, and avoid np float')
                         raise AssertionError('Mixed typing creates issues. Please convert your typing.')
 
@@ -284,27 +310,27 @@ def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name, cell_v, anchor
                 if j == 0:
                     lc_names = descriptor_names
 
-        averaged_lc_descriptors = np.mean(np.array(lc_descriptor_list), axis=0) # Average the lc RACs over all of the linkers in the MOF.
+        averaged_lc_descriptors = np.mean(np.array(lc_descriptor_list), axis=0)  # Average the lc RACs over all of the linkers in the MOF.
         # This CSV will be overwritten until the last SBU, but information on all linkers is being kept thanks to the append function
-        lc_descriptors.to_csv(sbu_descriptor_path+'/lc_descriptors.csv',index=False)
+        lc_descriptors.to_csv(sbu_descriptor_path+'/lc_descriptors.csv', index=False)
         descriptors = []
         descriptor_names = []
-        SBU_mol_cart_coords=np.array([atom.coords() for atom in SBU_mol.atoms])
-        SBU_mol_atom_labels=[atom.sym for atom in SBU_mol.atoms]
+        SBU_mol_cart_coords = np.array([atom.coords() for atom in SBU_mol.atoms])
+        SBU_mol_atom_labels = [atom.sym for atom in SBU_mol.atoms]
         SBU_mol_adj_mat = np.array(SBU_mol.graph)
 
-        ###### WRITE THE SBU MOL TO THE PLACE
+        # WRITE THE SBU MOL TO THE PLACE
         xyz_path = f'{sbupath}/{name}_sbu_{i}.xyz'
         if not os.path.exists(xyz_path):
             SBU_mol_fcoords_connected = XYZ_connected(cell_v, SBU_mol_cart_coords, SBU_mol_adj_mat)
-            writeXYZandGraph(xyz_path, SBU_mol_atom_labels, cell_v, SBU_mol_fcoords_connected,SBU_mol_adj_mat)
+            writeXYZandGraph(xyz_path, SBU_mol_atom_labels, cell_v, SBU_mol_fcoords_connected, SBU_mol_adj_mat)
 
         # Write TXT file indicating the connecting atoms
         sbu_index_connection_indices = []
         for item in global_connection_indices:
             if item in SBU:
                 sbu_index_connection_indices.append(SBU.index(item))
-        sbu_index_connection_indices = list(np.sort(sbu_index_connection_indices)) # Sort in ascending order
+        sbu_index_connection_indices = list(np.sort(sbu_index_connection_indices))  # Sort in ascending order
         sbu_index_connection_indices = [str(item) for item in sbu_index_connection_indices]
         with open(f'{sbupath}/{name}_connection_indices_sbu_{i}.txt', 'w') as f:
             f.write(' '.join(sbu_index_connection_indices))
@@ -312,13 +338,17 @@ def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name, cell_v, anchor
         """""""""
         Generate all of the SBU based RACs (full scope, mc)
         """""""""
-        results_dictionary = generate_full_complex_autocorrelations(SBU_mol,depth=depth,loud=False,flag_name=False,Gval=Gval)
-        descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],results_dictionary['results'],'f','all')
+        results_dictionary = generate_full_complex_autocorrelations(
+            SBU_mol, depth=depth, loud=False, flag_name=False, Gval=Gval)
+        descriptor_names, descriptors = append_descriptors(
+            descriptor_names, descriptors, results_dictionary['colnames'], results_dictionary['results'], 'f', 'all')
         #### Now starts at every metal on the graph and autocorrelates
-        results_dictionary = generate_multimetal_autocorrelations(molcif,depth=depth,loud=False,Gval=Gval)
-        descriptor_names, descriptors =  append_descriptors(descriptor_names, descriptors, results_dictionary['colnames'],results_dictionary['results'],'mc','all')
-        results_dictionary = generate_multimetal_deltametrics(molcif,depth=depth,loud=False,Gval=Gval)
-        descriptor_names, descriptors = append_descriptors(descriptor_names, descriptors,results_dictionary['colnames'],results_dictionary['results'],'D_mc','all')
+        results_dictionary = generate_multimetal_autocorrelations(molcif, depth=depth, loud=False, Gval=Gval)
+        descriptor_names, descriptors = append_descriptors(
+            descriptor_names, descriptors, results_dictionary['colnames'], results_dictionary['results'], 'mc', 'all')
+        results_dictionary = generate_multimetal_deltametrics(molcif, depth=depth, loud=False, Gval=Gval)
+        descriptor_names, descriptors = append_descriptors(
+            descriptor_names, descriptors, results_dictionary['colnames'], results_dictionary['results'], 'D_mc', 'all')
 
         # Some formatting
         descriptor_names += ['name']
@@ -332,11 +362,14 @@ def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name, cell_v, anchor
         if i == 0:
             names = descriptor_names
 
-    sbu_descriptors.to_csv(sbu_descriptor_path+'/sbu_descriptors.csv',index=False)
-    averaged_SBU_descriptors = np.mean(np.array(descriptor_list), axis=0) # Average the SBU RACs over all of the SBUs in the MOF.
+    sbu_descriptors.to_csv(sbu_descriptor_path+'/sbu_descriptors.csv', index=False)
+    averaged_SBU_descriptors = np.mean(np.array(descriptor_list), axis=0)  # Average the SBU RACs over all of the SBUs in the MOF.
     return names, averaged_SBU_descriptors, lc_names, averaged_lc_descriptors
 
-def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, cell_v, linkerpath, linkeranchors_superlist, Gval):
+
+def make_MOF_linker_RACs(
+        linkerlist, linker_subgraphlist, molcif, depth, name, cell_v,
+        linkerpath, linkeranchors_superlist, Gval):
     """
     Generate RACs on the linkers of the MOF.
 
@@ -375,7 +408,7 @@ def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, c
     descriptors = []
     if linkerpath:
         linker_descriptor_path = os.path.dirname(linkerpath)
-        if os.path.getsize(linker_descriptor_path+'/linker_descriptors.csv')>0: # Checking if there is a file there.
+        if os.path.getsize(linker_descriptor_path+'/linker_descriptors.csv') > 0:  # Checking if there is a file there.
             linker_descriptors = pd.read_csv(linker_descriptor_path+'/linker_descriptors.csv')
         else:
             linker_descriptors = pd.DataFrame()
@@ -384,15 +417,15 @@ def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, c
     for item in linkeranchors_superlist:
         global_connection_indices.extend(list(item))
 
-    for i, linker in enumerate(linkerlist): # Iterating through the linkers.
+    for i, linker in enumerate(linkerlist):  # Iterating through the linkers.
         # Preparing a mol3D object for the current linker.
         linker_mol = mol3D()
         for val in linker:
             linker_mol.addAtom(molcif.getAtom(val))
         linker_mol.graph = linker_subgraphlist[i].todense()
 
-        linker_mol_cart_coords=np.array([atom.coords() for atom in linker_mol.atoms])
-        linker_mol_atom_labels=[atom.sym for atom in linker_mol.atoms]
+        linker_mol_cart_coords = np.array([atom.coords() for atom in linker_mol.atoms])
+        linker_mol_atom_labels = [atom.sym for atom in linker_mol.atoms]
         linker_mol_adj_mat = np.array(linker_mol.graph)
 
         ###### WRITE THE LINKER MOL TO THE PLACE
@@ -406,7 +439,7 @@ def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, c
         for item in global_connection_indices:
             if item in linker:
                 linker_index_connection_indices.append(linker.index(item))
-        linker_index_connection_indices = list(np.sort(linker_index_connection_indices)) # Sort in ascending order
+        linker_index_connection_indices = list(np.sort(linker_index_connection_indices))  # Sort in ascending order
         linker_index_connection_indices = [str(item) for item in linker_index_connection_indices]
         with open(f'{linkerpath}/{name}_connection_indices_linker_{i}.txt', 'w') as f:
             f.write(' '.join(linker_index_connection_indices))
@@ -423,18 +456,18 @@ def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, c
         Generate all of the linker based RACs
         """""""""
         for ii, properties in enumerate(allowed_strings):
-            if not list(descriptors): # This is the case when just starting and the list is empty.
-                ligand_ac_full = full_autocorrelation(linker_mol, properties, depth) # RACs
+            if not list(descriptors):  # This is the case when just starting and the list is empty.
+                ligand_ac_full = full_autocorrelation(linker_mol, properties, depth)  # RACs
             else:
                 ligand_ac_full += full_autocorrelation(linker_mol, properties, depth)
             this_colnames = []
-            for j in range(0,depth+1):
+            for j in range(0, depth+1):
                 this_colnames.append('f-lig-'+labels_strings[ii] + '-' + str(j))
             colnames.append(this_colnames)
             lig_full.append(ligand_ac_full)
 
         # Some formatting
-        lig_full = [item for sublist in lig_full for item in sublist] # flatten lists
+        lig_full = [item for sublist in lig_full for item in sublist]  # flatten lists
         colnames = [item for sublist in colnames for item in sublist]
         colnames += ['name']
         lig_full += [name]
@@ -444,12 +477,13 @@ def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, c
         colnames.remove('name')
         descriptor_list.append(lig_full)
 
-    #### We dump the standard lc descriptors without averaging or summing so that the user
-    #### can make the modifications that they want. By default we take the average ones.
+    # We dump the standard lc descriptors without averaging or summing so that the user
+    # can make the modifications that they want. By default we take the average ones.
     linker_descriptors.to_csv(linker_descriptor_path+'/linker_descriptors.csv', index=False)
     averaged_ligand_descriptors = np.mean(np.array(descriptor_list), axis=0)
     return colnames, averaged_ligand_descriptors
 
+
 def mkdir_if_absent(folder_paths):
     """
     Makes a folder at each path in folder_path if it does not yet exist.
@@ -469,6 +503,7 @@ def mkdir_if_absent(folder_paths):
         if not os.path.exists(folder_path):
             os.mkdir(folder_path)
 
+
 def make_file_if_absent(path, filenames):
     """
     Makes the specified files if they do not yet exist.
@@ -488,9 +523,10 @@ def make_file_if_absent(path, filenames):
 
     for filename in filenames:
         if not os.path.exists(f'{path}/{filename}'):
-            with open(f'{path}/{filename}','w') as f:
+            with open(f'{path}/{filename}', 'w') as f:
                 f.close()
 
+
 def path_maker(path):
     """
     Makes the required folders and files.
@@ -513,6 +549,7 @@ def path_maker(path):
     required_files = ['sbu_descriptors.csv', 'linker_descriptors.csv', 'lc_descriptors.csv']
     make_file_if_absent(path, required_files)
 
+
 def failure_response(path, failure_str):
     """
     Writes to the log file about the encountered failure.
@@ -529,9 +566,10 @@ def failure_response(path, failure_str):
     """
     full_names = [0]
     full_descriptors = [0]
-    write2file(path,"/FailedStructures.log",failure_str)
+    write2file(path, "/FailedStructures.log", failure_str)
     return full_names, full_descriptors
 
+
 def bond_information_write(linker_list, linkeranchors_superlist, adj_matrix, molcif, cell_v, path):
     """
     Attains and writes bond information about the bonds between SBUs and linkers.
@@ -559,30 +597,30 @@ def bond_information_write(linker_list, linkeranchors_superlist, adj_matrix, mol
 
     bond_length_list = []
     scaled_bond_length_list = []
-    for linker_idx, linker_atoms_list in enumerate(linker_list): # Iterate over all linkers
+    for linker_idx, linker_atoms_list in enumerate(linker_list):  # Iterate over all linkers
         # Getting the connection points of the linker
         for anchor_super_idx in range(len(linkeranchors_superlist)):
-            if list(linkeranchors_superlist[anchor_super_idx])[0] in linker_atoms_list: # Any anchor index in the current entry of linkeranchors_superlist is in the current linker's indices
-                linker_connection_points = list(linkeranchors_superlist[anchor_super_idx]) # Indices of the connection points in the linker
+            if list(linkeranchors_superlist[anchor_super_idx])[0] in linker_atoms_list:  # Any anchor index in the current entry of linkeranchors_superlist is in the current linker's indices
+                linker_connection_points = list(linkeranchors_superlist[anchor_super_idx])  # Indices of the connection points in the linker
         for con_point in linker_connection_points:
-            connected_atoms = adj_matrix.todense()[con_point,:]
+            connected_atoms = adj_matrix.todense()[con_point, :]
             connected_atoms = np.ravel(connected_atoms)
 
-            connected_atoms = np.nonzero(connected_atoms)[0] # The indices of atoms connected to atom with index con_point.
+            connected_atoms = np.nonzero(connected_atoms)[0]  # The indices of atoms connected to atom with index con_point.
 
             for con_atom in connected_atoms:
-                con_atom3D = molcif.getAtom(con_atom) # atom3D of an atom connected to the connection point
-                con_point3D = molcif.getAtom(con_point) # atom3D of the connection point on the linker
+                con_atom3D = molcif.getAtom(con_atom)  # atom3D of an atom connected to the connection point
+                con_point3D = molcif.getAtom(con_point)  # atom3D of the connection point on the linker
                 # Check if the atom is a metal
                 if con_atom3D.ismetal(transition_metals_only=False):
                     # Finding the optimal unit cell shift
                     molcif_cart_coords = np.array([atom.coords() for atom in molcif.atoms])
-                    fcoords=frac_coord(molcif_cart_coords,cell_v) # fractional coordinates
-                    fcoords[con_atom]+=compute_image_flag(cell_v,fcoords[con_point],fcoords[con_atom]) # Shifting the connected metal to get it close to the connection point
+                    fcoords = frac_coord(molcif_cart_coords, cell_v)  # fractional coordinates
+                    fcoords[con_atom] += compute_image_flag(cell_v, fcoords[con_point], fcoords[con_atom])  # Shifting the connected metal to get it close to the connection point
                     ccoords = fractional2cart(fcoords, cell_v)
-                    shifted_con_atom3D = atom3D(Sym=con_atom3D.symbol(), xyz=list(ccoords[con_atom,:]))
+                    shifted_con_atom3D = atom3D(Sym=con_atom3D.symbol(), xyz=list(ccoords[con_atom, :]))
 
-                    bond_len = shifted_con_atom3D.distance(con_point3D) # Bond length between the connected metal and the connection point.
+                    bond_len = shifted_con_atom3D.distance(con_point3D)  # Bond length between the connected metal and the connection point.
                     con_atom_radius = COVALENT_RADII[shifted_con_atom3D.symbol()]
                     con_point_radius = COVALENT_RADII[con_point3D.symbol()]
                     relative_bond_len = bond_len / (con_atom_radius + con_point_radius)
@@ -590,8 +628,8 @@ def bond_information_write(linker_list, linkeranchors_superlist, adj_matrix, mol
                     bond_length_list.append(bond_len)
                     scaled_bond_length_list.append(relative_bond_len)
 
-    mean_bond_len = np.mean(bond_length_list) # Average over all SBU-linker atom to atom connections
-    mean_scaled_bond_len = np.mean(scaled_bond_length_list) # Average over all SBU-linker atom to atom connections
+    mean_bond_len = np.mean(bond_length_list)  # Average over all SBU-linker atom to atom connections
+    mean_scaled_bond_len = np.mean(scaled_bond_length_list)  # Average over all SBU-linker atom to atom connections
     std_bond_len = np.std(bond_length_list)
     std_scaled_bond_len = np.std(scaled_bond_length_list)
 
@@ -601,6 +639,7 @@ def bond_information_write(linker_list, linkeranchors_superlist, adj_matrix, mol
         f.write(f'Stdev bond length: {std_bond_len}\n')
         f.write(f'Stdev scaled bond length: {std_scaled_bond_len}')
 
+
 def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_v, allatomtypes, name):
     """
     Writes XYZ files for all SBUs provided, with each SBU surrounded by all linkers coordinated to it.
@@ -633,8 +672,8 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
     for SBU_idx, atoms_sbu in enumerate(SBU_list):
         # atoms_sbu are the indices of atoms in the SBU with index SBU_idx
 
-        connection_atoms = [] # List of lists of the coordinating atoms of each of the connected linkers. Length is # of connected linkers.
-        atoms_connected_linkers = [] # List of lists of the atoms of each of the connected linkers. Length is # of connected linkers.
+        connection_atoms = []  # List of lists of the coordinating atoms of each of the connected linkers. Length is # of connected linkers.
+        atoms_connected_linkers = []  # List of lists of the atoms of each of the connected linkers. Length is # of connected linkers.
         for atoms_linker in linker_list:
             atoms_in_common = list(set(atoms_sbu).intersection(set(atoms_linker)))
             if len(atoms_in_common) != 0:
@@ -646,13 +685,13 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
         # For each atom index in an inner list in connection_atoms, build out the corresponding linker (inner list) in atoms_connected_linkers.
 
         ### Start with the atoms of the SBU
-        surrounded_sbu = mol3D() # SBU surrounded by linkers
+        surrounded_sbu = mol3D()  # SBU surrounded by linkers
         starting_atom_idx = atoms_sbu[0]
-        added_idx = [starting_atom_idx] # This list will contain the SBU indices that no longer need to be considered for branching.
+        added_idx = [starting_atom_idx]  # This list will contain the SBU indices that no longer need to be considered for branching.
         starting_atom3D = molcif.getAtom(starting_atom_idx)
         # The mol3D object starts out with a single atom. Atoms will be added branching out from this initial atom.
         surrounded_sbu.addAtom(starting_atom3D)
-        atom3D_dict = {starting_atom_idx: starting_atom3D} # atom3D objects of the SBU
+        atom3D_dict = {starting_atom_idx: starting_atom3D}  # atom3D objects of the SBU
 
         dense_adj_mat = np.array(adj_matrix.todense())
 
@@ -663,23 +702,21 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
         sbu_atoms_to_branch_from = {starting_atom_idx: atoms_connected_to_start}
         sbu_atoms_to_branch_from_keys = [starting_atom_idx]
 
-
         while len(sbu_atoms_to_branch_from_keys) != 0:
-
             # Take from the first key, i.e. [0], of the dictionary
             my_key = sbu_atoms_to_branch_from_keys[0]
-            neighbor_idx = sbu_atoms_to_branch_from[my_key][0] # Grabbing a neighbor to calculate its position.
+            neighbor_idx = sbu_atoms_to_branch_from[my_key][0]  # Grabbing a neighbor to calculate its position.
 
             # Remove that index from further consideration
             sbu_atoms_to_branch_from[my_key].remove(neighbor_idx)
 
             # If the list associated with a key is now empty, remove the key.
             if len(sbu_atoms_to_branch_from[my_key]) == 0:
-                sbu_atoms_to_branch_from_keys.remove(my_key) # sbu_atoms_to_branch_from_keys = [i for i in sbu_atoms_to_branch_from_keys if i != my_key]
+                sbu_atoms_to_branch_from_keys.remove(my_key)  # sbu_atoms_to_branch_from_keys = [i for i in sbu_atoms_to_branch_from_keys if i != my_key]
                 sbu_atoms_to_branch_from.pop(my_key)
 
             if neighbor_idx in added_idx:
-                continue # Skip this index if it has already been added
+                continue  # Skip this index if it has already been added
 
             # Getting the optimal position of the neighbor, relative to my_key
             fcoords_my_key = frac_coord(atom3D_dict[my_key].coords(), cell_v)
@@ -687,7 +724,7 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
             fcoords_neighbor_initial = frac_coord(molcif.getAtom(neighbor_idx).coords(), cell_v)
             fcoords_neighbor = fcoords_neighbor_initial + compute_image_flag(cell_v, fcoords_my_key, fcoords_neighbor_initial)
             coords_neighbor = fractional2cart(fcoords_neighbor, cell_v)
-            symbol_neighbor = allatomtypes[neighbor_idx] # Element
+            symbol_neighbor = allatomtypes[neighbor_idx]  # Element
             new_atom3D = atom3D(Sym=symbol_neighbor, xyz=coords_neighbor)
             surrounded_sbu.addAtom(new_atom3D)
 
@@ -711,7 +748,7 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
             for starting_atom_idx in connection_atoms[linker_idx]:
                 atom3D_dict_copy = atom3D_dict.copy()
                 added_idx = [starting_atom_idx]
-                starting_atom3D = atom3D_dict_copy[starting_atom_idx] # Position of the starting atom in the SBU, which has been built by this point in the code.
+                starting_atom3D = atom3D_dict_copy[starting_atom_idx]  # Position of the starting atom in the SBU, which has been built by this point in the code.
 
                 atoms_connected_to_start = list(np.nonzero(dense_adj_mat[starting_atom_idx])[0])
                 atoms_connected_to_start = [i for i in atoms_connected_to_start if i in linker_indices]
@@ -722,7 +759,7 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
 
                     # Take from the first key, i.e. [0], of the dictionary
                     my_key = linker_atoms_to_branch_from_keys[0]
-                    neighbor_idx = linker_atoms_to_branch_from[my_key][0] # Grabbing a neighbor to calculate its position.
+                    neighbor_idx = linker_atoms_to_branch_from[my_key][0]  # Grabbing a neighbor to calculate its position.
 
                     # Remove that index from further consideration
                     linker_atoms_to_branch_from[my_key].remove(neighbor_idx)
@@ -733,7 +770,7 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
                         linker_atoms_to_branch_from.pop(my_key)
 
                     if neighbor_idx in added_idx:
-                        continue # Skip this index if it has already been added
+                        continue  # Skip this index if it has already been added
 
                     # Getting the optimal position of the neighbor, relative to my_key
                     fcoords_my_key = frac_coord(atom3D_dict_copy[my_key].coords(), cell_v)
@@ -741,12 +778,12 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
                     fcoords_neighbor_initial = frac_coord(molcif.getAtom(neighbor_idx).coords(), cell_v)
                     fcoords_neighbor = fcoords_neighbor_initial + compute_image_flag(cell_v, fcoords_my_key, fcoords_neighbor_initial)
                     coords_neighbor = fractional2cart(fcoords_neighbor, cell_v)
-                    symbol_neighbor = allatomtypes[neighbor_idx] # Element
+                    symbol_neighbor = allatomtypes[neighbor_idx]  # Element
                     new_atom3D = atom3D(Sym=symbol_neighbor, xyz=coords_neighbor)
 
                     # Only add the new atom if it does not overlap with an atom that is already in surrounded sbu.
                     # If there is overlap, then the atom was already added in the SBU.
-                    min_dist = 100 # Starting from a big number that will be replaced in the subsequent lines.
+                    min_dist = 100  # Starting from a big number that will be replaced in the subsequent lines.
                     num_atoms = surrounded_sbu.getNumAtoms()
                     for i in range(num_atoms):
                         pair_dist = new_atom3D.distance(surrounded_sbu.getAtom(i))
@@ -763,9 +800,9 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
                         linker_atoms_to_branch_from[neighbor_idx] = atoms_connected_to_neighbor_to_check
                         linker_atoms_to_branch_from_keys.append(neighbor_idx)
 
-
         surrounded_sbu.writexyz(xyz_path)
 
+
 def dist_mat_comp(X):
     """
     Computes the pairwise distances between the rows of the coordinate information X.
@@ -788,9 +825,10 @@ def dist_mat_comp(X):
     X1 = np.expand_dims(X, axis=1)
     X2 = np.expand_dims(X, axis=0)
     Z = X1 - X2
-    dist_mat = np.sqrt(np.sum(np.square(Z), axis=-1)) # The pairwise distance matrix. Distances between all atoms.
+    dist_mat = np.sqrt(np.sum(np.square(Z), axis=-1))  # The pairwise distance matrix. Distances between all atoms.
     return dist_mat
 
+
 def detect_1D_rod(SBU_list, molcif, allatomtypes, cell_v, logpath, name):
     """
     Writes to the log file if the MOF is likely to contain a 1D rod.
@@ -824,29 +862,29 @@ def detect_1D_rod(SBU_list, molcif, allatomtypes, cell_v, logpath, name):
 
     # allatomtypes_sbus_initial = [i for idx, i in enumerate(allatomtypes) if idx in sbu_atom_indices]
     cart_coords_sbus_initial = [molcif.getAtom(i).coords() for i in sbu_atom_indices]
-    allatomtypes_sbus_with_shifts = [] # Will contain the symbols of all SBU atoms, across the 8 unit cell shifts
-    cart_coords_sbus_with_shifts = [] # Will contain the cartesian coordinates of all SBU atoms, across the 8 unit cell shifts
+    allatomtypes_sbus_with_shifts = []  # Will contain the symbols of all SBU atoms, across the 8 unit cell shifts
+    cart_coords_sbus_with_shifts = []  # Will contain the cartesian coordinates of all SBU atoms, across the 8 unit cell shifts
 
     # Applying all possible unit cell shifts in 0, 1, for all SBU atoms
     for idx, i in enumerate(sbu_atom_indices):
         supercells = np.array(list(itertools.product((0, 1), repeat=3)))
         fractional_coords = frac_coord(cart_coords_sbus_initial[idx], cell_v)
-        fractional_coords_shifts = fractional_coords + supercells # 8 versions of fractional_coords, shifted some cells over in different directions
+        fractional_coords_shifts = fractional_coords + supercells  # 8 versions of fractional_coords, shifted some cells over in different directions
         for j in fractional_coords_shifts:
             allatomtypes_sbus_with_shifts.append(allatomtypes[i])
             cart_coords_sbus_with_shifts.append(fractional2cart(j, cell_v))
 
-    cart_coords_sbus_with_shifts = np.array(cart_coords_sbus_with_shifts) # Converting nested list to a numpy array
+    cart_coords_sbus_with_shifts = np.array(cart_coords_sbus_with_shifts)  # Converting nested list to a numpy array
 
     distance_mat = dist_mat_comp(cart_coords_sbus_with_shifts)
-    adj_matrix, _ = compute_adj_matrix(distance_mat, allatomtypes_sbus_with_shifts, handle_overlap=True) # Ignoring overlap
+    adj_matrix, _ = compute_adj_matrix(distance_mat, allatomtypes_sbus_with_shifts, handle_overlap=True)  # Ignoring overlap
 
     # For each connected component, see how long it is
     adj_matrix = sparse.csr_matrix(adj_matrix)
     n_components, labels_components = sparse.csgraph.connected_components(csgraph=adj_matrix, directed=False, return_labels=True)
 
     # What is the shortest cell vector?
-    min_vec_len = np.min(np.linalg.norm(cell_v, axis=1)) # Equivalent to min(cpar[:3])
+    min_vec_len = np.min(np.linalg.norm(cell_v, axis=1))  # Equivalent to min(cpar[:3])
 
     is_1d_rod = False
     for i in range(n_components):
@@ -860,13 +898,15 @@ def detect_1D_rod(SBU_list, molcif, allatomtypes, cell_v, logpath, name):
             break
 
     if is_1d_rod:
-        print(f'Likely 1D rod')
+        print('Likely 1D rod')
         tmpstr = "MOF SBU is likely a 1D rod"
-        write2file(logpath,"/%s.log"%name,tmpstr)
+        write2file(logpath, "/%s.log" % name, tmpstr)
 
-def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=False, wiggle_room=1,
-    max_num_atoms=2000, get_sbu_linker_bond_info=False, surrounded_sbu_file_generation=False, detect_1D_rod_sbu=False,
-    Gval=False):
+
+def get_MOF_descriptors(
+        data, depth, path=False, xyzpath=False, graph_provided=False, wiggle_room=1,
+        max_num_atoms=2000, get_sbu_linker_bond_info=False, surrounded_sbu_file_generation=False,
+        detect_1D_rod_sbu=False, Gval=False):
     """
     Generates RAC descriptors on a MOF, assuming it has P1 symmetry.
     Writes three files: sbu_descriptors.csv, linker_descriptors.csv, and lc_descriptors.csv
@@ -912,7 +952,7 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
 
     """
 
-    if not path: # Throw an error if the user did not supply a path to which to write the output.
+    if not path:  # Throw an error if the user did not supply a path to which to write the output.
         print('Need a directory to place all of the linker, SBU, and ligand objects. Exiting now.')
         raise ValueError('Base path must be specified in order to write descriptors.')
     else:
@@ -935,7 +975,7 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
     cell_v = mkcell(cpar)
     cart_coords = fractional2cart(fcoords, cell_v)
     name = os.path.basename(data).replace(".cif", "")
-    if len(cart_coords) > max_num_atoms: # Don't deal with large cifs because of computational resources required for their treatment.
+    if len(cart_coords) > max_num_atoms:  # Don't deal with large cifs because of computational resources required for their treatment.
         print("cif file is too large, skipping it for now...")
         failure_str = f"Failed to featurize {name}: large primitive cell\n {len(cart_coords)} atoms"
         full_names, full_descriptors = failure_response(path, failure_str)
@@ -944,7 +984,7 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
     """""""""
     Getting the adjacency matrix.
     """""""""
-    if not graph_provided: # Make the adjacency matrix.
+    if not graph_provided:  # Make the adjacency matrix.
         distance_mat = compute_distance_matrix3(cell_v, cart_coords)
         try:
             adj_matrix, _ = compute_adj_matrix(distance_mat, allatomtypes, wiggle_room)
@@ -952,10 +992,10 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
             failure_str = f"Failed to featurize {name}: atomic overlap\n"
             full_names, full_descriptors = failure_response(path, failure_str)
             return full_names, full_descriptors
-    else: # Grab the adjacency matrix from the cif file.
+    else:  # Grab the adjacency matrix from the cif file.
         adj_matrix_list = []
         max_sofar = 0
-        with open(data.replace('primitive','cif'),'r') as f:
+        with open(data.replace('primitive', 'cif'), 'r') as f:
             readdata = f.readlines()
             flag = False
             for i, row in enumerate(readdata):
@@ -964,19 +1004,19 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
                     continue
                 if flag:
                     splitrow = row.split()
-                    atom1 = int(re.findall(r'\d+',splitrow[0])[0])
-                    atom2 = int(re.findall(r'\d+',splitrow[1])[0])
+                    atom1 = int(re.findall(r'\d+', splitrow[0])[0])
+                    atom2 = int(re.findall(r'\d+', splitrow[1])[0])
                     max_sofar = max(atom1, max_sofar)
                     max_sofar = max(atom2, max_sofar)
-                    adj_matrix_list.append((atom1,atom2))
-        adj_matrix = np.zeros((max_sofar+1,max_sofar+1)) # 0 indicates the absence of a bond.
+                    adj_matrix_list.append((atom1, atom2))
+        adj_matrix = np.zeros((max_sofar + 1, max_sofar + 1))  # 0 indicates the absence of a bond.
         for i, row in enumerate(adj_matrix_list):
-            adj_matrix[row[0],row[1]] = 1 # 1 is indicative of a bond.
-            adj_matrix[row[1],row[0]] = 1
+            adj_matrix[row[0], row[1]] = 1  # 1 is indicative of a bond.
+            adj_matrix[row[1], row[0]] = 1
     adj_matrix = sparse.csr_matrix(adj_matrix)
 
     writeXYZandGraph(xyzpath, allatomtypes, cell_v, fcoords, adj_matrix.todense())
-    molcif,_,_,_,_ = import_from_cif(data, True) # molcif is a mol3D class of a single unit cell (or the cell of the cif file)
+    molcif, _, _, _, _ = import_from_cif(data, True)  # molcif is a mol3D class of a single unit cell (or the cell of the cif file)
     molcif.graph = adj_matrix.todense()
 
     """""""""
@@ -986,7 +1026,7 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
     """""""""
 
     n_components, labels_components = sparse.csgraph.connected_components(csgraph=adj_matrix, directed=False, return_labels=True)
-    metal_list = set([at for at in molcif.findMetal(transition_metals_only=False)]) # the atom indices of the metals
+    metal_list = set([at for at in molcif.findMetal(transition_metals_only=False)])  # the atom indices of the metals
     # print('##### METAL LIST', metal_list, [molcif.getAtom(val).symbol() for val in list(metal_list)])
     # print('##### METAL LIST', metal_list, [val.symbol() for val in molcif.atoms])
     if not len(metal_list) > 0:
@@ -994,17 +1034,17 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
         full_names, full_descriptors = failure_response(path, failure_str)
         return full_names, full_descriptors
     for comp in range(n_components):
-        inds_in_comp = [i for i in range(len(labels_components)) if labels_components[i]==comp]
-        if not set(inds_in_comp) & metal_list: # In the context of sets, & is the intersection. If the intersection is null, the (&) expression is False; the `not` would then make it True.
+        inds_in_comp = [i for i in range(len(labels_components)) if labels_components[i] == comp]
+        if not set(inds_in_comp) & metal_list:  # In the context of sets, & is the intersection. If the intersection is null, the (&) expression is False; the `not` would then make it True.
             # If this if statement is entered, there is an entire connected component that has no metals in it. No connections to any metal.
             failure_str = f"Failed to featurize {name}: solvent molecules\n"
             full_names, full_descriptors = failure_response(path, failure_str)
             return full_names, full_descriptors
 
-    if n_components > 1 : # There are multiple connected components that have a metal in them in this case.
+    if n_components > 1:  # There are multiple connected components that have a metal in them in this case.
         print("structure is interpenetrated")
-        tmpstr = "%s found to be an interpenetrated structure\n"%(name)
-        write2file(logpath,"/%s.log"%name,tmpstr)
+        tmpstr = "%s found to be an interpenetrated structure\n" % (name)
+        write2file(logpath, "/%s.log" % name, tmpstr)
 
     """""""""
     step 1: metallic part
@@ -1028,7 +1068,7 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
         cn = len(bonded_atoms)
         cn_atom = ",".join([at for at in bonded_atoms_types])
         tmpstr = "atom %i with type of %s found to have %i coordinates with atom types of %s\n"%(metal,allatomtypes[metal],cn,cn_atom)
-        write2file(logpath,"/%s.log"%name,tmpstr)
+        write2file(logpath, "/%s.log" % name, tmpstr)
     [removelist.update(set([atom])) for atom in SBUlist if all((molcif.getAtom(val).ismetal() or molcif.getAtom(val).symbol().upper() == 'H') for val in molcif.getBondedAtomsSmart(atom))]
     """""""""
     adding hydrogens connected to atoms which are only connected to metals. In particular interstitial OH, like in UiO SBU.
@@ -1036,7 +1076,7 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
     for atom in SBUlist:
         for val in molcif.getBondedAtomsSmart(atom):
             if molcif.getAtom(val).symbol().upper() == 'H':
-               removelist.update(set([val]))
+                removelist.update(set([val]))
 
     """""""""
     At this point:
@@ -1047,21 +1087,21 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
         removelist = linkers are all atoms - the removelist (assuming no bond between
         organiclinkers)
     """""""""
-    allatoms = set(range(0, adj_matrix.shape[0])) # The indices of all the atoms.
+    allatoms = set(range(0, adj_matrix.shape[0]))  # The indices of all the atoms.
     linkers = allatoms - removelist
     linker_list, linker_subgraphlist = get_closed_subgraph(linkers.copy(), removelist.copy(), adj_matrix)
     connections_list = copy.deepcopy(linker_list)
     connections_subgraphlist = copy.deepcopy(linker_subgraphlist)
-    linker_length_list = [len(linker_val) for linker_val in linker_list] # The number of atoms in each linker.
+    linker_length_list = [len(linker_val) for linker_val in linker_list]  # The number of atoms in each linker.
     """""""""
     find all anchoring atoms on linkers and ligands (lc identification)
         The atoms that are bonded to a metal.
     """""""""
     anc_atoms = set()
-    for linker in linker_list: # Checking all of the linkers one by one.
-        for atom_linker in linker: # Checking each atom in the current linker.
-            bonded2atom = np.nonzero(adj_matrix[atom_linker,:])[1] # indices of atoms with bonds to the atom with the index atom_linker
-            if set(bonded2atom) & metal_list: # This means one of the atoms bonded to the atom with the index atom_linker is a metal.
+    for linker in linker_list:  # Checking all of the linkers one by one.
+        for atom_linker in linker:  # Checking each atom in the current linker.
+            bonded2atom = np.nonzero(adj_matrix[atom_linker, :])[1]  # indices of atoms with bonds to the atom with the index atom_linker
+            if set(bonded2atom) & metal_list:  # This means one of the atoms bonded to the atom with the index atom_linker is a metal.
                 anc_atoms.add(atom_linker)
     """""""""
     step 3: determine whether linker or ligand
@@ -1075,9 +1115,9 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
     initial_SBU_list, initial_SBU_subgraphlist = get_closed_subgraph(removelist.copy(), linkers.copy(), adj_matrix)
     templist = linker_list.copy()
     long_ligands = False
-    max_min_linker_length , min_max_linker_length = (0,100) # The maximum value of the minimum linker length, and the minimum value of the maximum linker length. Updated later.
-    linkeranchors_superlist = [] # Will contain the indices of the linker atoms that coordinate to metals
-    for ii, atoms_list in reversed(list(enumerate(linker_list))): # Loop over all linker subgraphs
+    max_min_linker_length, min_max_linker_length = (0, 100)  # The maximum value of the minimum linker length, and the minimum value of the maximum linker length. Updated later.
+    linkeranchors_superlist = []  # Will contain the indices of the linker atoms that coordinate to metals
+    for ii, atoms_list in reversed(list(enumerate(linker_list))):  # Loop over all linker subgraphs
         linkeranchors_list = set()
         linkeranchors_atoms = set()
         sbuanchors_list = set()
@@ -1087,70 +1127,70 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
         To do this, we check if something is connected to more than one SBU. Set to
         handle cases where primitive cell is small, ambiguous cases are recorded.
         """""""""
-        for iii,atoms in enumerate(atoms_list): # loop over all atom indices in a linker
-            connected_atoms = np.nonzero(adj_matrix[atoms,:])[1] # indices of atoms with bonds to the atom with the index atoms
-            for kk, sbu_atoms_list in enumerate(initial_SBU_list): # loop over all SBU subgraphs
-                for sbu_atoms in sbu_atoms_list: # Loop over SBU
-                    if sbu_atoms in connected_atoms: # found an SBU atom bonded to an atom in the linker defined by atoms_list
+        for iii, atoms in enumerate(atoms_list):  # loop over all atom indices in a linker
+            connected_atoms = np.nonzero(adj_matrix[atoms, :])[1]  # indices of atoms with bonds to the atom with the index atoms
+            for kk, sbu_atoms_list in enumerate(initial_SBU_list):  # loop over all SBU subgraphs
+                for sbu_atoms in sbu_atoms_list:  # Loop over SBU
+                    if sbu_atoms in connected_atoms:  # found an SBU atom bonded to an atom in the linker defined by atoms_list
                         linkeranchors_list.add(iii)
                         linkeranchors_atoms.add(atoms)
                         sbuanchors_list.add(sbu_atoms)
-                        sbu_connect_list.add(kk) #Add if unique SBUs
-        min_length,max_length = linker_length(linker_subgraphlist[ii].todense(), linkeranchors_list)
+                        sbu_connect_list.add(kk)  # Add if unique SBUs
+        min_length, max_length = linker_length(linker_subgraphlist[ii].todense(), linkeranchors_list)
         linkeranchors_superlist.append(linkeranchors_atoms)
 
-        if len(linkeranchors_list) >= 2 : # linker, and in one ambiguous case, could be a ligand.
-            if len(sbu_connect_list) >= 2: # Something that connects two SBUs is certain to be a linker
-                max_min_linker_length = max(min_length,max_min_linker_length)
-                min_max_linker_length = min(max_length,min_max_linker_length)
+        if len(linkeranchors_list) >= 2:  # linker, and in one ambiguous case, could be a ligand.
+            if len(sbu_connect_list) >= 2:  # Something that connects two SBUs is certain to be a linker
+                max_min_linker_length = max(min_length, max_min_linker_length)
+                min_max_linker_length = min(max_length, min_max_linker_length)
                 continue
             else:
                 # check number of times we cross PBC :
                 # TODO: we still can fail in multidentate ligands!
                 linker_cart_coords = np.array([
-                    at.coords() for at in [molcif.getAtom(val) for val in atoms_list]]) # Cartesian coordinates of the atoms in the linker
+                    at.coords() for at in [molcif.getAtom(val) for val in atoms_list]])  # Cartesian coordinates of the atoms in the linker
                 linker_adjmat = np.array(linker_subgraphlist[ii].todense())
-                pr_image_organic = ligand_detect(cell_v,linker_cart_coords,linker_adjmat,linkeranchors_list) # Periodic images for the organic component
+                pr_image_organic = ligand_detect(cell_v, linker_cart_coords, linker_adjmat, linkeranchors_list)  # Periodic images for the organic component
                 sbu_temp = linkeranchors_atoms.copy()
-                sbu_temp.update({val for val in initial_SBU_list[list(sbu_connect_list)[0]]}) # Adding atoms. Not sure why the [0] is there? TODO
+                sbu_temp.update({val for val in initial_SBU_list[list(sbu_connect_list)[0]]})  # Adding atoms. Not sure why the [0] is there? TODO
                 sbu_temp = list(sbu_temp)
                 sbu_cart_coords = np.array([
                     at.coords() for at in [molcif.getAtom(val) for val in sbu_temp]])
-                sbu_adjmat = slice_mat(adj_matrix.todense(),sbu_temp)
-                pr_image_sbu = ligand_detect(cell_v,sbu_cart_coords,sbu_adjmat,set(range(len(linkeranchors_list)))) # Periodic images for the SBU
-                if not (len(np.unique(pr_image_sbu, axis=0))==1 and len(np.unique(pr_image_organic, axis=0))==1): # linker. More than one periodic image for sbu or organic component
-                    max_min_linker_length = max(min_length,max_min_linker_length)
-                    min_max_linker_length = min(max_length,min_max_linker_length)
+                sbu_adjmat = slice_mat(adj_matrix.todense(), sbu_temp)
+                pr_image_sbu = ligand_detect(cell_v, sbu_cart_coords, sbu_adjmat, set(range(len(linkeranchors_list))))  # Periodic images for the SBU
+                if not (len(np.unique(pr_image_sbu, axis=0)) == 1 and len(np.unique(pr_image_organic, axis=0)) == 1):  # linker. More than one periodic image for sbu or organic component
+                    max_min_linker_length = max(min_length, max_min_linker_length)
+                    min_max_linker_length = min(max_length, min_max_linker_length)
                     tmpstr = str(name)+','+' Anchors list: '+str(sbuanchors_list) \
-                            +','+' SBU connectlist: '+str(sbu_connect_list)+' set to be linker\n'
-                    write2file(ligandpath,"/ambiguous.txt",tmpstr)
+                        + ',' + ' SBU connectlist: ' + str(sbu_connect_list) + ' set to be linker\n'
+                    write2file(ligandpath, "/ambiguous.txt", tmpstr)
                     continue
-                else: #  all anchoring atoms are in the same unitcell -> ligand
-                    removelist.update(set(templist[ii])) # we also want to remove these ligands
-                    SBUlist.update(set(templist[ii])) # we also want to remove these SBUs
+                else:  # all anchoring atoms are in the same unitcell -> ligand
+                    removelist.update(set(templist[ii]))  # we also want to remove these ligands
+                    SBUlist.update(set(templist[ii]))  # we also want to remove these SBUs
                     linker_list.pop(ii)
                     linker_subgraphlist.pop(ii)
                     tmpstr = str(name)+','+' Anchors list: '+str(sbuanchors_list) \
-                            +','+' SBU connectlist: '+str(sbu_connect_list)+' set to be ligand\n'
-                    write2file(ligandpath,"/ambiguous.txt",tmpstr)
-                    tmpstr = str(name)+str(ii)+','+' Anchors list: '+ \
-                            str(sbuanchors_list)+','+' SBU connectlist: '+str(sbu_connect_list)+'\n'
-                    write2file(ligandpath,"/ligand.txt",tmpstr)
-        else: # definite ligand
-            write2file(logpath,"/%s.log"%name,"found ligand\n")
-            removelist.update(set(templist[ii])) # we also want to remove these ligands
-            SBUlist.update(set(templist[ii])) # we also want to remove these ligands
+                        + ',' + ' SBU connectlist: ' + str(sbu_connect_list) + ' set to be ligand\n'
+                    write2file(ligandpath, "/ambiguous.txt", tmpstr)
+                    tmpstr = str(name)+str(ii)+','+' Anchors list: '\
+                        + str(sbuanchors_list) + ',' + ' SBU connectlist: ' + str(sbu_connect_list) + '\n'
+                    write2file(ligandpath, "/ligand.txt", tmpstr)
+        else:  # definite ligand
+            write2file(logpath, "/%s.log" % name, "found ligand\n")
+            removelist.update(set(templist[ii]))  # we also want to remove these ligands
+            SBUlist.update(set(templist[ii]))  # we also want to remove these ligands
             linker_list.pop(ii)
             linker_subgraphlist.pop(ii)
             tmpstr = str(name)+','+' Anchors list: '+str(sbuanchors_list) \
-         +','+' SBU connectlist: '+str(sbu_connect_list)+'\n'
-            write2file(ligandpath,"/ligand.txt",tmpstr)
+                + ','+' SBU connectlist: '+str(sbu_connect_list)+'\n'
+            write2file(ligandpath, "/ligand.txt", tmpstr)
 
-    tmpstr = str(name) + ", (min_max_linker_length,max_min_linker_length): " + \
-                str(min_max_linker_length) + " , " +str(max_min_linker_length) + "\n"
-    write2file(logpath,"/%s.log"%name,tmpstr)
+    tmpstr = str(name) + ", (min_max_linker_length,max_min_linker_length): " \
+        + str(min_max_linker_length) + " , " + str(max_min_linker_length) + "\n"
+    write2file(logpath, "/%s.log" % name, tmpstr)
     if min_max_linker_length < 3:
-        write2file(linkerpath,"/short_ligands.txt",tmpstr)
+        write2file(linkerpath, "/short_ligands.txt", tmpstr)
     if min_max_linker_length > 2:
         # for N-C-C-N ligand ligand
         if max_min_linker_length == min_max_linker_length:
@@ -1164,26 +1204,26 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
     """""""""
     linker_length_list = [len(linker_val) for linker_val in linker_list]
     if len(set(linker_length_list)) != 1:
-        write2file(linkerpath,"/uneven.txt",str(name)+'\n') # Linkers are different lengths.
-    if not min_max_linker_length < 2: # treating the 2 atom ligands differently! Need caution
+        write2file(linkerpath, "/uneven.txt", str(name)+'\n')  # Linkers are different lengths.
+    if not min_max_linker_length < 2:  # treating the 2 atom ligands differently! Need caution
         if long_ligands:
             tmpstr = "\nStructure has LONG ligand\n\n"
-            write2file(logpath,"/%s.log"%name,tmpstr)
+            write2file(logpath, "/%s.log" % name, tmpstr)
             # Expanding the number of atoms considered to be part of the SBU
-            [[SBUlist.add(val) for val in  molcif.getBondedAtomsSmart(zero_first_shell)] for zero_first_shell in SBUlist.copy()] #First account for all of the carboxylic acid type linkers, add in the carbons.
-        truncated_linkers = allatoms - SBUlist # Taking the difference of sets
+            [[SBUlist.add(val) for val in molcif.getBondedAtomsSmart(zero_first_shell)] for zero_first_shell in SBUlist.copy()]  # First account for all of the carboxylic acid type linkers, add in the carbons.
+        truncated_linkers = allatoms - SBUlist  # Taking the difference of sets
         SBU_list, SBU_subgraphlist = get_closed_subgraph(SBUlist, truncated_linkers, adj_matrix)
         if not long_ligands:
             tmpstr = "\nStructure has SHORT ligand\n\n"
-            write2file(logpath,"/%s.log"%name,tmpstr)
-            SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif,adj_matrix)
+            write2file(logpath, "/%s.log" % name, tmpstr)
+            SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list, SBU_subgraphlist, molcif, adj_matrix)
     else:
-        tmpstr = "Structure %s has extremely short ligands, check the outputs\n"%name
-        write2file(ligandpath,"/ambiguous.txt",tmpstr)
+        tmpstr = "Structure %s has extremely short ligands, check the outputs\n" % name
+        write2file(ligandpath, "/ambiguous.txt", tmpstr)
         tmpstr = "Structure has extremely short ligands\n"
-        write2file(logpath,"/%s.log"%name,tmpstr)
+        write2file(logpath, "/%s.log" % name, tmpstr)
         tmpstr = "Structure has extremely short ligands\n"
-        write2file(logpath,"/%s.log"%name,tmpstr)
+        write2file(logpath, "/%s.log" % name, tmpstr)
         truncated_linkers = allatoms - removelist
         SBU_list, SBU_subgraphlist = get_closed_subgraph(removelist, truncated_linkers, adj_matrix)
         SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list, SBU_subgraphlist, molcif, adj_matrix)
@@ -1192,17 +1232,17 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
     """""""""
     For the cases that have a linker subgraph, do the featurization.
     """""""""
-    if len(linker_subgraphlist)>=1: # Featurize cases that did not fail.
+    if len(linker_subgraphlist) >= 1:  # Featurize cases that did not fail.
         # try:
             descriptor_names, descriptors, lc_descriptor_names, lc_descriptors = make_MOF_SBU_RACs(SBU_list, SBU_subgraphlist, molcif, depth, name, cell_v, anc_atoms, sbupath, linkeranchors_superlist, Gval, connections_list, connections_subgraphlist)
             lig_descriptor_names, lig_descriptors = make_MOF_linker_RACs(linker_list, linker_subgraphlist, molcif, depth, name, cell_v, linkerpath, linkeranchors_superlist, Gval)
             full_names = descriptor_names+lig_descriptor_names+lc_descriptor_names #+ ECFP_names
             full_descriptors = list(descriptors)+list(lig_descriptors)+list(lc_descriptors)
-            print(len(full_names),len(full_descriptors))
+            print(len(full_names), len(full_descriptors))
         # except:
         #     full_names = [0]
         #     full_descriptors = [0]
-    elif len(linker_subgraphlist) == 1: # Only one linker identified.
+    elif len(linker_subgraphlist) == 1:  # Only one linker identified.
         print(f'Suspicious featurization for {name}: Only one linker identified.')
         full_names = [1]
         full_descriptors = [1]
@@ -1226,7 +1266,7 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
             surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_v, allatomtypes, name)
         except:
             tmpstr = "Failed to generate surrounded SBU"
-            write2file(logpath,"/%s.log"%name,tmpstr)
+            write2file(logpath, "/%s.log" % name, tmpstr)
 
     if detect_1D_rod_sbu:
         detect_1D_rod(SBU_list, molcif, allatomtypes, cell_v, logpath, name)
diff --git a/tests/informatics/test_MOF_descriptors.py b/tests/informatics/test_MOF_descriptors.py
new file mode 100644
index 00000000..22bc518a
--- /dev/null
+++ b/tests/informatics/test_MOF_descriptors.py
@@ -0,0 +1,57 @@
+import pytest
+import json
+import numpy as np
+from molSimplify.Informatics.MOF.MOF_descriptors import get_MOF_descriptors
+from molSimplify.utils.timer import DebugTimer
+
+
+@pytest.fixture
+def ref_names(depth=3):
+
+    def RACs_names(starts, properties, depth, scope="all"):
+        names = []
+        for start in starts:
+            for prop in properties:
+                for d in range(depth + 1):
+                    if scope is None:
+                        names.append(f"{start}-{prop}-{d}")
+                    else:
+                        names.append(f"{start}-{prop}-{d}-{scope}")
+        return names
+
+    properties = ["chi", "Z", "I", "T", "S", "Gval"]
+
+    names = RACs_names(["f", "mc", "D_mc"], properties, depth)
+    # f-lig does not include the "scope"
+    names.extend(RACs_names(["f-lig"], properties, depth, scope=None))
+
+    # Same for the starts that include the additional property alpha
+    properties.append("alpha")
+    names.extend(
+        RACs_names(["lc", "D_lc", "func", "D_func"], properties, depth))
+    return names
+
+
+@pytest.mark.parametrize(
+    "name",
+    ["odac-21383.cif",
+     "odac-21433.cif",
+     "odac-21478.cif",
+     "odac-21735.cif",
+     "odac-21816.cif"])
+def test_get_MOF_descriptors(resource_path_root, tmpdir, name, ref_names):
+    with DebugTimer("get_MOF_descriptors()"):
+        full_names, full_descriptors = get_MOF_descriptors(
+            str(resource_path_root / "inputs" / "cif_files" / name),
+            depth=3,
+            path=str(tmpdir),
+            xyzpath=str(tmpdir / "test.xyz"),
+            Gval=True,
+        )
+
+    with open(resource_path_root / "refs" / "MOF_descriptors"
+              / name.replace("cif", "json"), "r") as fin:
+        ref = json.load(fin)
+
+    assert full_names == ref_names
+    np.testing.assert_allclose(full_descriptors, ref["descriptors"], atol=1e-6)
diff --git a/tests/testresources/inputs/cif_files/odac-21383.cif b/tests/testresources/inputs/cif_files/odac-21383.cif
new file mode 100644
index 00000000..1d3ed003
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/odac-21383.cif
@@ -0,0 +1,261 @@
+data_image0
+_chemical_formula_structural       Ga36P36O148F16
+_chemical_formula_sum              "Ga36 P36 O148 F16"
+_cell_length_a       17.7002
+_cell_length_b       32.7061
+_cell_length_c       10.1684
+_cell_angle_alpha    90
+_cell_angle_beta     90
+_cell_angle_gamma    90
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Ga  Ga1       1.0  0.43059  0.92287  0.05643  1.0000
+  Ga  Ga2       1.0  0.48410  0.02595  0.02197  1.0000
+  Ga  Ga3       1.0  0.15815  0.98867  0.88183  1.0000
+  Ga  Ga4       1.0  0.34659  0.50676  0.58670  1.0000
+  Ga  Ga5       1.0  0.08393  0.57961  0.42319  1.0000
+  Ga  Ga6       1.0  0.02252  0.47611  0.45525  1.0000
+  Ga  Ga7       1.0  0.34114  0.66620  0.58927  1.0000
+  Ga  Ga8       1.0  0.17185  0.82627  0.88792  1.0000
+  Ga  Ga9       1.0  0.30408  0.75647  0.92147  1.0000
+  Ga  Ga10      1.0  0.57037  0.07744  0.55502  1.0000
+  Ga  Ga11      1.0  0.51611  0.97446  0.52138  1.0000
+  Ga  Ga12      1.0  0.84196  0.01129  0.38288  1.0000
+  Ga  Ga13      1.0  0.65341  0.49313  0.08664  1.0000
+  Ga  Ga14      1.0  0.91594  0.42029  0.92329  1.0000
+  Ga  Ga15      1.0  0.97747  0.52383  0.95523  1.0000
+  Ga  Ga16      1.0  0.65877  0.33342  0.08974  1.0000
+  Ga  Ga17      1.0  0.82830  0.17378  0.38821  1.0000
+  Ga  Ga18      1.0  0.69648  0.24360  0.42307  1.0000
+  Ga  Ga19      1.0  0.92996  0.07736  0.05544  1.0000
+  Ga  Ga20      1.0  0.98407  0.97427  0.02212  1.0000
+  Ga  Ga21      1.0  0.65807  0.01135  0.88314  1.0000
+  Ga  Ga22      1.0  0.84658  0.49311  0.58664  1.0000
+  Ga  Ga23      1.0  0.58408  0.42027  0.42331  1.0000
+  Ga  Ga24      1.0  0.52254  0.52381  0.45523  1.0000
+  Ga  Ga25      1.0  0.84123  0.33342  0.58976  1.0000
+  Ga  Ga26      1.0  0.67187  0.17378  0.88815  1.0000
+  Ga  Ga27      1.0  0.80356  0.24360  0.92309  1.0000
+  Ga  Ga28      1.0  0.07041  0.92272  0.55490  1.0000
+  Ga  Ga29      1.0  0.01582  0.02574  0.52223  1.0000
+  Ga  Ga30      1.0  0.34172  0.98885  0.38206  1.0000
+  Ga  Ga31      1.0  0.15340  0.50686  0.08665  1.0000
+  Ga  Ga32      1.0  0.41599  0.57969  0.92325  1.0000
+  Ga  Ga33      1.0  0.47749  0.47615  0.95522  1.0000
+  Ga  Ga34      1.0  0.15876  0.66660  0.08951  1.0000
+  Ga  Ga35      1.0  0.32817  0.82575  0.38620  1.0000
+  Ga  Ga36      1.0  0.19617  0.75627  0.42252  1.0000
+  P   P1        1.0  0.31337  0.99434  0.05803  1.0000
+  P   P2        1.0  0.52467  0.95466  0.82822  1.0000
+  P   P3        1.0  0.06651  0.90510  0.84888  1.0000
+  P   P4        1.0  0.98376  0.54782  0.64882  1.0000
+  P   P5        1.0  0.19351  0.50343  0.40645  1.0000
+  P   P6        1.0  0.43845  0.59028  0.62901  1.0000
+  P   P7        1.0  0.34400  0.75646  0.60991  1.0000
+  P   P8        1.0  0.32414  0.83918  0.05928  1.0000
+  P   P9        1.0  0.30802  0.66116  0.89815  1.0000
+  P   P10       1.0  0.68688  0.00560  0.55914  1.0000
+  P   P11       1.0  0.47548  0.04576  0.32815  1.0000
+  P   P12       1.0  0.93349  0.09497  0.34958  1.0000
+  P   P13       1.0  0.01619  0.45214  0.14882  1.0000
+  P   P14       1.0  0.80646  0.49652  0.90645  1.0000
+  P   P15       1.0  0.56162  0.40957  0.12895  1.0000
+  P   P16       1.0  0.65635  0.24318  0.11197  1.0000
+  P   P17       1.0  0.67615  0.16085  0.56051  1.0000
+  P   P18       1.0  0.69209  0.33884  0.39813  1.0000
+  P   P19       1.0  0.81321  0.00562  0.05928  1.0000
+  P   P20       1.0  0.02477  0.04560  0.82869  1.0000
+  P   P21       1.0  0.56658  0.09505  0.84935  1.0000
+  P   P22       1.0  0.48383  0.45210  0.64886  1.0000
+  P   P23       1.0  0.69355  0.49651  0.40640  1.0000
+  P   P24       1.0  0.93839  0.40956  0.62898  1.0000
+  P   P25       1.0  0.84372  0.24318  0.61195  1.0000
+  P   P26       1.0  0.82395  0.16081  0.06056  1.0000
+  P   P27       1.0  0.80794  0.33884  0.89816  1.0000
+  P   P28       1.0  0.18650  0.99472  0.55712  1.0000
+  P   P29       1.0  0.97498  0.95435  0.32876  1.0000
+  P   P30       1.0  0.43347  0.90507  0.34924  1.0000
+  P   P31       1.0  0.51619  0.54784  0.14887  1.0000
+  P   P32       1.0  0.30646  0.50345  0.90646  1.0000
+  P   P33       1.0  0.06160  0.59043  0.12887  1.0000
+  P   P34       1.0  0.15658  0.75695  0.11105  1.0000
+  P   P35       1.0  0.17591  0.83898  0.55953  1.0000
+  P   P36       1.0  0.19176  0.66107  0.39794  1.0000
+  O   O1        1.0  0.36930  0.56124  0.63882  1.0000
+  O   O2        1.0  0.13538  0.93385  0.83366  1.0000
+  O   O3        1.0  0.13323  0.47188  0.45118  1.0000
+  O   O4        1.0  0.35030  0.77223  0.75240  1.0000
+  O   O5        1.0  0.02578  0.50758  0.62007  1.0000
+  O   O6        1.0  0.20934  0.77214  0.83963  1.0000
+  O   O7        1.0  0.37244  0.02727  0.02004  1.0000
+  O   O8        1.0  0.48241  0.99468  0.85946  1.0000
+  O   O9        1.0  0.26051  0.74525  0.58022  1.0000
+  O   O10       1.0  0.25240  0.85096  0.98186  1.0000
+  O   O11       1.0  0.26725  0.49188  0.47540  1.0000
+  O   O12       1.0  0.34503  0.70353  0.92025  1.0000
+  O   O13       1.0  0.24142  0.00420  0.98193  1.0000
+  O   O14       1.0  0.00114  0.92187  0.93177  1.0000
+  O   O15       1.0  0.35517  0.79645  0.02209  1.0000
+  O   O16       1.0  0.50873  0.57242  0.56275  1.0000
+  O   O17       1.0  0.49419  0.91819  0.90872  1.0000
+  O   O18       1.0  0.02066  0.58375  0.57395  1.0000
+  O   O19       1.0  0.61031  0.95927  0.85926  1.0000
+  O   O20       1.0  0.33849  0.95034  0.02262  1.0000
+  O   O21       1.0  0.17320  0.54790  0.44401  1.0000
+  O   O22       1.0  0.89885  0.54430  0.60927  1.0000
+  O   O23       1.0  0.29692  0.65271  0.74928  1.0000
+  O   O24       1.0  0.51714  0.94311  0.68271  1.0000
+  O   O25       1.0  0.29712  0.99885  0.20677  1.0000
+  O   O26       1.0  0.20409  0.49766  0.25662  1.0000
+  O   O27       1.0  0.30596  0.84210  0.20712  1.0000
+  O   O28       1.0  0.45944  0.60410  0.77088  1.0000
+  O   O29       1.0  0.98309  0.55794  0.79664  1.0000
+  O   O30       1.0  0.41696  0.62880  0.54922  1.0000
+  O   O31       1.0  0.03144  0.89719  0.71005  1.0000
+  O   O32       1.0  0.09016  0.86348  0.90607  1.0000
+  O   O33       1.0  0.38689  0.86952  0.02345  1.0000
+  O   O34       1.0  0.35971  0.62936  0.96217  1.0000
+  O   O35       1.0  0.37646  0.78989  0.51811  1.0000
+  O   O36       1.0  0.22762  0.65917  0.95502  1.0000
+  O   O37       1.0  0.39109  0.71673  0.59096  1.0000
+  O   O38       1.0  0.63080  0.43859  0.13845  1.0000
+  O   O39       1.0  0.86463  0.06617  0.33478  1.0000
+  O   O40       1.0  0.86677  0.52806  0.95121  1.0000
+  O   O41       1.0  0.65035  0.22706  0.25425  1.0000
+  O   O42       1.0  0.97419  0.49239  0.12012  1.0000
+  O   O43       1.0  0.79109  0.22794  0.34040  1.0000
+  O   O44       1.0  0.62792  0.97264  0.52061  1.0000
+  O   O45       1.0  0.51828  0.00588  0.35879  1.0000
+  O   O46       1.0  0.73962  0.25472  0.08150  1.0000
+  O   O47       1.0  0.74868  0.14943  0.48499  1.0000
+  O   O48       1.0  0.73273  0.50809  0.97540  1.0000
+  O   O49       1.0  0.65515  0.29645  0.42014  1.0000
+  O   O50       1.0  0.75906  0.99570  0.48383  1.0000
+  O   O51       1.0  0.99891  0.07817  0.43222  1.0000
+  O   O52       1.0  0.64543  0.20379  0.52464  1.0000
+  O   O53       1.0  0.49140  0.42745  0.06253  1.0000
+  O   O54       1.0  0.50551  0.08228  0.40883  1.0000
+  O   O55       1.0  0.97927  0.41620  0.07401  1.0000
+  O   O56       1.0  0.38972  0.04098  0.35840  1.0000
+  O   O57       1.0  0.66225  0.04962  0.52348  1.0000
+  O   O58       1.0  0.82674  0.45206  0.94402  1.0000
+  O   O59       1.0  0.10110  0.45567  0.10921  1.0000
+  O   O60       1.0  0.70310  0.34730  0.24929  1.0000
+  O   O61       1.0  0.48190  0.05759  0.18258  1.0000
+  O   O62       1.0  0.70271  0.00112  0.70804  1.0000
+  O   O63       1.0  0.79589  0.50230  0.75663  1.0000
+  O   O64       1.0  0.69299  0.15733  0.70856  1.0000
+  O   O65       1.0  0.54054  0.39589  0.27094  1.0000
+  O   O66       1.0  0.01692  0.44200  0.29663  1.0000
+  O   O67       1.0  0.58300  0.37090  0.04979  1.0000
+  O   O68       1.0  0.96869  0.10281  0.21083  1.0000
+  O   O69       1.0  0.90998  0.13662  0.40655  1.0000
+  O   O70       1.0  0.61388  0.13072  0.52021  1.0000
+  O   O71       1.0  0.64035  0.37061  0.46216  1.0000
+  O   O72       1.0  0.62400  0.20954  0.02083  1.0000
+  O   O73       1.0  0.77248  0.34088  0.45509  1.0000
+  O   O74       1.0  0.60895  0.28284  0.09347  1.0000
+  O   O75       1.0  0.86921  0.43858  0.63850  1.0000
+  O   O76       1.0  0.63547  0.06626  0.83488  1.0000
+  O   O77       1.0  0.63325  0.52804  0.45116  1.0000
+  O   O78       1.0  0.84968  0.22707  0.75423  1.0000
+  O   O79       1.0  0.52585  0.49234  0.62010  1.0000
+  O   O80       1.0  0.70899  0.22793  0.84042  1.0000
+  O   O81       1.0  0.87235  0.97278  0.02073  1.0000
+  O   O82       1.0  0.98231  0.00562  0.85957  1.0000
+  O   O83       1.0  0.76046  0.25473  0.58146  1.0000
+  O   O84       1.0  0.75143  0.14937  0.98501  1.0000
+  O   O85       1.0  0.76727  0.50808  0.47539  1.0000
+  O   O86       1.0  0.84486  0.29644  0.92017  1.0000
+  O   O87       1.0  0.74119  0.99564  0.98348  1.0000
+  O   O88       1.0  0.50101  0.07834  0.93188  1.0000
+  O   O89       1.0  0.85465  0.20374  0.02451  1.0000
+  O   O90       1.0  0.00861  0.42743  0.56256  1.0000
+  O   O91       1.0  0.99443  0.08214  0.90892  1.0000
+  O   O92       1.0  0.52079  0.41616  0.57408  1.0000
+  O   O93       1.0  0.11043  0.04089  0.85990  1.0000
+  O   O94       1.0  0.83796  0.04964  0.02387  1.0000
+  O   O95       1.0  0.67328  0.45204  0.44394  1.0000
+  O   O96       1.0  0.39893  0.45560  0.60918  1.0000
+  O   O97       1.0  0.79690  0.34730  0.74932  1.0000
+  O   O98       1.0  0.01811  0.05723  0.68309  1.0000
+  O   O99       1.0  0.79723  0.00104  0.20807  1.0000
+  O   O100      1.0  0.70412  0.50230  0.25658  1.0000
+  O   O101      1.0  0.80705  0.15737  0.20863  1.0000
+  O   O102      1.0  0.95948  0.39588  0.77098  1.0000
+  O   O103      1.0  0.48312  0.44200  0.79669  1.0000
+  O   O104      1.0  0.91700  0.37090  0.54982  1.0000
+  O   O105      1.0  0.53158  0.10289  0.71045  1.0000
+  O   O106      1.0  0.59001  0.13674  0.90626  1.0000
+  O   O107      1.0  0.88625  0.13064  0.02064  1.0000
+  O   O108      1.0  0.85968  0.37061  0.96216  1.0000
+  O   O109      1.0  0.87609  0.20956  0.52077  1.0000
+  O   O110      1.0  0.72755  0.34089  0.95513  1.0000
+  O   O111      1.0  0.89111  0.28285  0.59352  1.0000
+  O   O112      1.0  0.13077  0.56141  0.13839  1.0000
+  O   O113      1.0  0.36486  0.93401  0.33335  1.0000
+  O   O114      1.0  0.36679  0.47193  0.95124  1.0000
+  O   O115      1.0  0.15043  0.77288  0.25355  1.0000
+  O   O116      1.0  0.47419  0.50759  0.12012  1.0000
+  O   O117      1.0  0.29075  0.77159  0.33906  1.0000
+  O   O118      1.0  0.12760  0.02776  0.51858  1.0000
+  O   O119      1.0  0.01726  0.99438  0.35953  1.0000
+  O   O120      1.0  0.23993  0.74567  0.08037  1.0000
+  O   O121      1.0  0.24902  0.85001  0.48481  1.0000
+  O   O122      1.0  0.23275  0.49191  0.97548  1.0000
+  O   O123      1.0  0.15479  0.70345  0.41987  1.0000
+  O   O124      1.0  0.25878  0.00476  0.48239  1.0000
+  O   O125      1.0  0.49850  0.92183  0.43293  1.0000
+  O   O126      1.0  0.14485  0.79620  0.52319  1.0000
+  O   O127      1.0  0.99139  0.57256  0.06240  1.0000
+  O   O128      1.0  0.00537  0.91783  0.40898  1.0000
+  O   O129      1.0  0.47925  0.58378  0.07409  1.0000
+  O   O130      1.0  0.88932  0.95902  0.35999  1.0000
+  O   O131      1.0  0.16143  0.95090  0.52064  1.0000
+  O   O132      1.0  0.32676  0.54793  0.94387  1.0000
+  O   O133      1.0  0.60110  0.54432  0.10925  1.0000
+  O   O134      1.0  0.20291  0.65263  0.24910  1.0000
+  O   O135      1.0  0.98165  0.94277  0.18305  1.0000
+  O   O136      1.0  0.20119  0.99946  0.70616  1.0000
+  O   O137      1.0  0.29586  0.49760  0.75667  1.0000
+  O   O138      1.0  0.19274  0.84238  0.70777  1.0000
+  O   O139      1.0  0.04040  0.60406  0.27087  1.0000
+  O   O140      1.0  0.51691  0.55794  0.29670  1.0000
+  O   O141      1.0  0.08297  0.62912  0.04986  1.0000
+  O   O142      1.0  0.46941  0.89718  0.21113  1.0000
+  O   O143      1.0  0.40903  0.86353  0.40577  1.0000
+  O   O144      1.0  0.11446  0.86961  0.51959  1.0000
+  O   O145      1.0  0.13998  0.62932  0.46198  1.0000
+  O   O146      1.0  0.12400  0.79067  0.02045  1.0000
+  O   O147      1.0  0.27211  0.65893  0.45496  1.0000
+  O   O148      1.0  0.10925  0.71727  0.09222  1.0000
+  F   F1        1.0  0.59454  0.01931  0.03888  1.0000
+  F   F2        1.0  0.03282  0.52842  0.36063  1.0000
+  F   F3        1.0  0.47617  0.97356  0.12043  1.0000
+  F   F4        1.0  0.41305  0.51613  0.43540  1.0000
+  F   F5        1.0  0.40605  0.98157  0.53697  1.0000
+  F   F6        1.0  0.96715  0.47151  0.86070  1.0000
+  F   F7        1.0  0.52466  0.02671  0.61962  1.0000
+  F   F8        1.0  0.58697  0.48383  0.93532  1.0000
+  F   F9        1.0  0.09449  0.98073  0.03817  1.0000
+  F   F10       1.0  0.53286  0.47150  0.36075  1.0000
+  F   F11       1.0  0.97607  0.02672  0.11986  1.0000
+  F   F12       1.0  0.91305  0.48380  0.43533  1.0000
+  F   F13       1.0  0.90545  0.01913  0.53909  1.0000
+  F   F14       1.0  0.46722  0.52847  0.86074  1.0000
+  F   F15       1.0  0.02440  0.97339  0.61988  1.0000
+  F   F16       1.0  0.08695  0.51615  0.93532  1.0000
diff --git a/tests/testresources/inputs/cif_files/odac-21433.cif b/tests/testresources/inputs/cif_files/odac-21433.cif
new file mode 100644
index 00000000..b3554cbd
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/odac-21433.cif
@@ -0,0 +1,169 @@
+data_image0
+_chemical_formula_structural       Al24P24O96
+_chemical_formula_sum              "Al24 P24 O96"
+_cell_length_a       18.7247
+_cell_length_b       18.7247
+_cell_length_c       9.4862
+_cell_angle_alpha    90
+_cell_angle_beta     90
+_cell_angle_gamma    90.0001
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Al  Al1       1.0  0.95507  0.83477  0.84024  1.0000
+  Al  Al2       1.0  0.16576  0.93612  0.91662  1.0000
+  Al  Al3       1.0  0.06583  0.94694  0.33735  1.0000
+  Al  Al4       1.0  0.54508  0.66527  0.83989  1.0000
+  Al  Al5       1.0  0.33427  0.56385  0.91669  1.0000
+  Al  Al6       1.0  0.43405  0.55299  0.33746  1.0000
+  Al  Al7       1.0  0.66518  0.95501  0.84012  1.0000
+  Al  Al8       1.0  0.56381  0.16567  0.91648  1.0000
+  Al  Al9       1.0  0.55294  0.06572  0.33734  1.0000
+  Al  Al10      1.0  0.83478  0.54492  0.84010  1.0000
+  Al  Al11      1.0  0.93619  0.33432  0.91650  1.0000
+  Al  Al12      1.0  0.94709  0.43432  0.33731  1.0000
+  Al  Al13      1.0  0.04498  0.16528  0.15993  1.0000
+  Al  Al14      1.0  0.83431  0.06384  0.08358  1.0000
+  Al  Al15      1.0  0.93429  0.05297  0.66264  1.0000
+  Al  Al16      1.0  0.45505  0.33472  0.15992  1.0000
+  Al  Al17      1.0  0.66567  0.43615  0.08362  1.0000
+  Al  Al18      1.0  0.56571  0.44701  0.66262  1.0000
+  Al  Al19      1.0  0.33476  0.04486  0.15998  1.0000
+  Al  Al20      1.0  0.43584  0.83431  0.08383  1.0000
+  Al  Al21      1.0  0.44704  0.93429  0.66265  1.0000
+  Al  Al22      1.0  0.16529  0.45519  0.16007  1.0000
+  Al  Al23      1.0  0.06367  0.66554  0.08351  1.0000
+  Al  Al24      1.0  0.05303  0.56570  0.66263  1.0000
+  P   P1        1.0  0.06553  0.83448  0.09144  1.0000
+  P   P2        1.0  0.83432  0.95131  0.84001  1.0000
+  P   P3        1.0  0.05645  0.93368  0.66221  1.0000
+  P   P4        1.0  0.43486  0.66519  0.09112  1.0000
+  P   P5        1.0  0.66569  0.54866  0.84000  1.0000
+  P   P6        1.0  0.44356  0.56634  0.66222  1.0000
+  P   P7        1.0  0.66531  0.06534  0.09135  1.0000
+  P   P8        1.0  0.54855  0.83433  0.84023  1.0000
+  P   P9        1.0  0.56631  0.05640  0.66210  1.0000
+  P   P10       1.0  0.83470  0.43466  0.09137  1.0000
+  P   P11       1.0  0.95127  0.66568  0.83986  1.0000
+  P   P12       1.0  0.93370  0.44359  0.66209  1.0000
+  P   P13       1.0  0.93466  0.16531  0.90868  1.0000
+  P   P14       1.0  0.16567  0.04871  0.16002  1.0000
+  P   P15       1.0  0.94364  0.06626  0.33786  1.0000
+  P   P16       1.0  0.56534  0.33468  0.90868  1.0000
+  P   P17       1.0  0.33435  0.45122  0.16004  1.0000
+  P   P18       1.0  0.55633  0.43378  0.33784  1.0000
+  P   P19       1.0  0.33470  0.93462  0.90842  1.0000
+  P   P20       1.0  0.45128  0.16564  0.16000  1.0000
+  P   P21       1.0  0.43369  0.94351  0.33798  1.0000
+  P   P22       1.0  0.16534  0.56554  0.90885  1.0000
+  P   P23       1.0  0.04874  0.33439  0.15998  1.0000
+  P   P24       1.0  0.06634  0.55647  0.33801  1.0000
+  O   O1        1.0  0.99702  0.84563  0.00411  1.0000
+  O   O2        1.0  0.05535  0.87068  0.23465  1.0000
+  O   O3        1.0  0.13060  0.86521  0.01367  1.0000
+  O   O4        1.0  0.07989  0.75515  0.11712  1.0000
+  O   O5        1.0  0.87340  0.87943  0.83702  1.0000
+  O   O6        1.0  0.84495  0.98470  0.98711  1.0000
+  O   O7        1.0  0.75516  0.93785  0.80993  1.0000
+  O   O8        1.0  0.86300  0.00156  0.72489  1.0000
+  O   O9        1.0  0.12251  0.94211  0.75543  1.0000
+  O   O10       1.0  0.01277  0.00297  0.67165  1.0000
+  O   O11       1.0  0.01125  0.86919  0.70897  1.0000
+  O   O12       1.0  0.08168  0.92068  0.51068  1.0000
+  O   O13       1.0  0.50322  0.65370  0.00367  1.0000
+  O   O14       1.0  0.44472  0.62910  0.23447  1.0000
+  O   O15       1.0  0.36937  0.63492  0.01375  1.0000
+  O   O16       1.0  0.42073  0.74448  0.11697  1.0000
+  O   O17       1.0  0.62670  0.62057  0.83690  1.0000
+  O   O18       1.0  0.65506  0.51529  0.98711  1.0000
+  O   O19       1.0  0.74485  0.56212  0.80992  1.0000
+  O   O20       1.0  0.63699  0.49842  0.72487  1.0000
+  O   O21       1.0  0.37751  0.55793  0.75554  1.0000
+  O   O22       1.0  0.48722  0.49704  0.67163  1.0000
+  O   O23       1.0  0.48875  0.63084  0.70887  1.0000
+  O   O24       1.0  0.41833  0.57942  0.51073  1.0000
+  O   O25       1.0  0.65376  0.99697  0.00380  1.0000
+  O   O26       1.0  0.62912  0.05522  0.23457  1.0000
+  O   O27       1.0  0.63467  0.13070  0.01418  1.0000
+  O   O28       1.0  0.74466  0.07909  0.11661  1.0000
+  O   O29       1.0  0.62043  0.87340  0.83724  1.0000
+  O   O30       1.0  0.51506  0.84467  0.98726  1.0000
+  O   O31       1.0  0.56211  0.75521  0.80990  1.0000
+  O   O32       1.0  0.49836  0.86302  0.72501  1.0000
+  O   O33       1.0  0.55786  0.12249  0.75529  1.0000
+  O   O34       1.0  0.49701  0.01275  0.67166  1.0000
+  O   O35       1.0  0.63079  0.01121  0.70882  1.0000
+  O   O36       1.0  0.57921  0.08165  0.51058  1.0000
+  O   O37       1.0  0.84625  0.50303  0.00382  1.0000
+  O   O38       1.0  0.87089  0.44479  0.23457  1.0000
+  O   O39       1.0  0.86532  0.36931  0.01417  1.0000
+  O   O40       1.0  0.75534  0.42093  0.11661  1.0000
+  O   O41       1.0  0.87941  0.62662  0.83681  1.0000
+  O   O42       1.0  0.98460  0.65513  0.98710  1.0000
+  O   O43       1.0  0.93786  0.74483  0.80977  1.0000
+  O   O44       1.0  0.00161  0.63701  0.72491  1.0000
+  O   O45       1.0  0.94215  0.37751  0.75530  1.0000
+  O   O46       1.0  0.00301  0.48726  0.67169  1.0000
+  O   O47       1.0  0.86922  0.48878  0.70879  1.0000
+  O   O48       1.0  0.92081  0.41837  0.51056  1.0000
+  O   O49       1.0  0.00302  0.15376  0.99624  1.0000
+  O   O50       1.0  0.94479  0.12914  0.76544  1.0000
+  O   O51       1.0  0.86929  0.13466  0.98579  1.0000
+  O   O52       1.0  0.92090  0.24467  0.88341  1.0000
+  O   O53       1.0  0.12664  0.12060  0.16298  1.0000
+  O   O54       1.0  0.15504  0.01528  0.01294  1.0000
+  O   O55       1.0  0.24482  0.06220  0.19004  1.0000
+  O   O56       1.0  0.13697  0.99848  0.27516  1.0000
+  O   O57       1.0  0.87754  0.05780  0.24468  1.0000
+  O   O58       1.0  0.98731  0.99695  0.32837  1.0000
+  O   O59       1.0  0.98881  0.13075  0.29113  1.0000
+  O   O60       1.0  0.91837  0.07919  0.48937  1.0000
+  O   O61       1.0  0.49699  0.34625  0.99624  1.0000
+  O   O62       1.0  0.55521  0.37086  0.76545  1.0000
+  O   O63       1.0  0.63071  0.36534  0.98578  1.0000
+  O   O64       1.0  0.57910  0.25533  0.88342  1.0000
+  O   O65       1.0  0.37333  0.37931  0.16283  1.0000
+  O   O66       1.0  0.34499  0.48472  0.01298  1.0000
+  O   O67       1.0  0.25521  0.43770  0.18996  1.0000
+  O   O68       1.0  0.36311  0.50131  0.27525  1.0000
+  O   O69       1.0  0.62242  0.44224  0.24467  1.0000
+  O   O70       1.0  0.51266  0.50308  0.32841  1.0000
+  O   O71       1.0  0.51117  0.36929  0.29111  1.0000
+  O   O72       1.0  0.58161  0.42085  0.48934  1.0000
+  O   O73       1.0  0.34621  0.00291  0.99621  1.0000
+  O   O74       1.0  0.37077  0.94496  0.76512  1.0000
+  O   O75       1.0  0.36555  0.86918  0.98486  1.0000
+  O   O76       1.0  0.25535  0.92083  0.88312  1.0000
+  O   O77       1.0  0.37943  0.12657  0.16302  1.0000
+  O   O78       1.0  0.48467  0.15505  0.01289  1.0000
+  O   O79       1.0  0.43784  0.24479  0.19007  1.0000
+  O   O80       1.0  0.50156  0.13699  0.27509  1.0000
+  O   O81       1.0  0.44233  0.87742  0.24484  1.0000
+  O   O82       1.0  0.50298  0.98720  0.32856  1.0000
+  O   O83       1.0  0.36929  0.98878  0.29125  1.0000
+  O   O84       1.0  0.42075  0.91821  0.48946  1.0000
+  O   O85       1.0  0.15379  0.49721  0.99639  1.0000
+  O   O86       1.0  0.12914  0.55535  0.76567  1.0000
+  O   O87       1.0  0.13471  0.63101  0.98572  1.0000
+  O   O88       1.0  0.24469  0.57939  0.88358  1.0000
+  O   O89       1.0  0.12058  0.37347  0.16295  1.0000
+  O   O90       1.0  0.01533  0.34497  0.01288  1.0000
+  O   O91       1.0  0.06218  0.25523  0.19006  1.0000
+  O   O92       1.0  0.99846  0.36305  0.27509  1.0000
+  O   O93       1.0  0.05782  0.62258  0.24482  1.0000
+  O   O94       1.0  0.99694  0.51294  0.32853  1.0000
+  O   O95       1.0  0.13056  0.51102  0.29139  1.0000
+  O   O96       1.0  0.07926  0.58184  0.48946  1.0000
diff --git a/tests/testresources/inputs/cif_files/odac-21478.cif b/tests/testresources/inputs/cif_files/odac-21478.cif
new file mode 100644
index 00000000..81afed13
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/odac-21478.cif
@@ -0,0 +1,209 @@
+data_image0
+_chemical_formula_structural       Zn24P32H32O96
+_chemical_formula_sum              "Zn24 P32 H32 O96"
+_cell_length_a       17.0323
+_cell_length_b       9.06338
+_cell_length_c       24.5579
+_cell_angle_alpha    89.9998
+_cell_angle_beta     107.472
+_cell_angle_gamma    90
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Zn  Zn1       1.0  0.10629  0.75801  0.27142  1.0000
+  Zn  Zn2       1.0  0.75579  0.72476  0.16434  1.0000
+  Zn  Zn3       1.0  0.22745  0.48941  0.49468  1.0000
+  Zn  Zn4       1.0  0.29113  0.98105  0.49893  1.0000
+  Zn  Zn5       1.0  0.29105  0.29821  0.17638  1.0000
+  Zn  Zn6       1.0  0.38342  0.74294  0.72159  1.0000
+  Zn  Zn7       1.0  0.89323  0.25726  0.22752  1.0000
+  Zn  Zn8       1.0  0.24335  0.22443  0.33461  1.0000
+  Zn  Zn9       1.0  0.77121  0.99023  0.00498  1.0000
+  Zn  Zn10      1.0  0.70923  0.48529  0.00071  1.0000
+  Zn  Zn11      1.0  0.70883  0.79879  0.32336  1.0000
+  Zn  Zn12      1.0  0.61671  0.24284  0.77848  1.0000
+  Zn  Zn13      1.0  0.89319  0.24283  0.72816  1.0000
+  Zn  Zn14      1.0  0.24398  0.27586  0.83543  1.0000
+  Zn  Zn15      1.0  0.77180  0.51106  0.50487  1.0000
+  Zn  Zn16      1.0  0.70859  0.01894  0.50086  1.0000
+  Zn  Zn17      1.0  0.70910  0.70244  0.82375  1.0000
+  Zn  Zn18      1.0  0.61649  0.25672  0.27818  1.0000
+  Zn  Zn19      1.0  0.10662  0.74250  0.77230  1.0000
+  Zn  Zn20      1.0  0.75602  0.77523  0.66485  1.0000
+  Zn  Zn21      1.0  0.22688  0.00881  0.99562  1.0000
+  Zn  Zn22      1.0  0.28961  0.51504  0.99903  1.0000
+  Zn  Zn23      1.0  0.29135  0.20090  0.67666  1.0000
+  Zn  Zn24      1.0  0.38393  0.75667  0.22232  1.0000
+  P   P1        1.0  0.92717  0.59618  0.25294  1.0000
+  P   P2        1.0  0.19101  0.48165  0.24440  1.0000
+  P   P3        1.0  0.16720  0.76977  0.41317  1.0000
+  P   P4        1.0  0.65055  0.77972  0.03503  1.0000
+  P   P5        1.0  0.18043  0.19978  0.54651  1.0000
+  P   P6        1.0  0.32245  0.71635  0.58862  1.0000
+  P   P7        1.0  0.44264  0.43047  0.27043  1.0000
+  P   P8        1.0  0.65617  0.55040  0.23040  1.0000
+  P   P9        1.0  0.07236  0.09565  0.24466  1.0000
+  P   P10       1.0  0.80897  0.98124  0.25521  1.0000
+  P   P11       1.0  0.83042  0.26858  0.08595  1.0000
+  P   P12       1.0  0.34804  0.27848  0.46396  1.0000
+  P   P13       1.0  0.82114  0.70454  0.95396  1.0000
+  P   P14       1.0  0.67750  0.21864  0.91144  1.0000
+  P   P15       1.0  0.55717  0.93151  0.22952  1.0000
+  P   P16       1.0  0.34375  0.05029  0.26952  1.0000
+  P   P17       1.0  0.07262  0.40365  0.74671  1.0000
+  P   P18       1.0  0.80872  0.51879  0.75566  1.0000
+  P   P19       1.0  0.83232  0.23083  0.58642  1.0000
+  P   P20       1.0  0.34816  0.22023  0.96495  1.0000
+  P   P21       1.0  0.81940  0.80028  0.45346  1.0000
+  P   P22       1.0  0.67725  0.28350  0.41108  1.0000
+  P   P23       1.0  0.55765  0.56922  0.72990  1.0000
+  P   P24       1.0  0.34380  0.44946  0.76954  1.0000
+  P   P25       1.0  0.92716  0.90369  0.75364  1.0000
+  P   P26       1.0  0.19144  0.01856  0.74513  1.0000
+  P   P27       1.0  0.16737  0.73021  0.91405  1.0000
+  P   P28       1.0  0.65097  0.72130  0.53531  1.0000
+  P   P29       1.0  0.17863  0.29685  0.04666  1.0000
+  P   P30       1.0  0.32343  0.78009  0.08921  1.0000
+  P   P31       1.0  0.44311  0.06806  0.77053  1.0000
+  P   P32       1.0  0.65611  0.94990  0.73026  1.0000
+  H   H1        1.0  0.91814  0.68659  0.29737  1.0000
+  H   H2        1.0  0.11086  0.43129  0.23912  1.0000
+  H   H3        1.0  0.11732  0.81275  0.44689  1.0000
+  H   H4        1.0  0.58512  0.81258  0.05681  1.0000
+  H   H5        1.0  0.11417  0.17164  0.56811  1.0000
+  H   H6        1.0  0.38491  0.60883  0.60176  1.0000
+  H   H7        1.0  0.39656  0.38397  0.30626  1.0000
+  H   H8        1.0  0.57656  0.58850  0.23169  1.0000
+  H   H9        1.0  0.08112  0.18536  0.20001  1.0000
+  H   H10       1.0  0.88900  0.93080  0.26015  1.0000
+  H   H11       1.0  0.88015  0.30503  0.05139  1.0000
+  H   H12       1.0  0.41332  0.31127  0.44192  1.0000
+  H   H13       1.0  0.88813  0.67700  0.93311  1.0000
+  H   H14       1.0  0.61444  0.11233  0.89899  1.0000
+  H   H15       1.0  0.60284  0.88444  0.19350  1.0000
+  H   H16       1.0  0.42330  0.08855  0.26816  1.0000
+  H   H17       1.0  0.08155  0.31322  0.70226  1.0000
+  H   H18       1.0  0.88882  0.56944  0.76099  1.0000
+  H   H19       1.0  0.88216  0.18808  0.55265  1.0000
+  H   H20       1.0  0.41368  0.18674  0.94326  1.0000
+  H   H21       1.0  0.88564  0.82831  0.43184  1.0000
+  H   H22       1.0  0.61467  0.39077  0.39781  1.0000
+  H   H23       1.0  0.60353  0.61539  0.69389  1.0000
+  H   H24       1.0  0.42343  0.41118  0.76835  1.0000
+  H   H25       1.0  0.91810  0.81351  0.79810  1.0000
+  H   H26       1.0  0.11139  0.06904  0.74008  1.0000
+  H   H27       1.0  0.11754  0.68984  0.94803  1.0000
+  H   H28       1.0  0.58538  0.68863  0.55705  1.0000
+  H   H29       1.0  0.11286  0.32684  0.06855  1.0000
+  H   H30       1.0  0.38724  0.88498  0.10185  1.0000
+  H   H31       1.0  0.39703  0.11382  0.80645  1.0000
+  H   H32       1.0  0.57652  0.91145  0.73152  1.0000
+  O   O1        1.0  0.01335  0.61855  0.24681  1.0000
+  O   O2        1.0  0.86336  0.64019  0.19667  1.0000
+  O   O3        1.0  0.91534  0.43790  0.27098  1.0000
+  O   O4        1.0  0.19214  0.65029  0.25078  1.0000
+  O   O5        1.0  0.21076  0.43647  0.18976  1.0000
+  O   O6        1.0  0.25070  0.41342  0.29840  1.0000
+  O   O7        1.0  0.11465  0.79078  0.35109  1.0000
+  O   O8        1.0  0.24367  0.86997  0.42780  1.0000
+  O   O9        1.0  0.18990  0.60571  0.42487  1.0000
+  O   O10       1.0  0.66054  0.91036  0.99769  1.0000
+  O   O11       1.0  0.73155  0.76041  0.08387  1.0000
+  O   O12       1.0  0.62757  0.63454  0.00182  1.0000
+  O   O13       1.0  0.19243  0.05928  0.51505  1.0000
+  O   O14       1.0  0.15591  0.33516  0.50732  1.0000
+  O   O15       1.0  0.25879  0.23394  0.59585  1.0000
+  O   O16       1.0  0.24142  0.64382  0.55333  1.0000
+  O   O17       1.0  0.31223  0.77937  0.64439  1.0000
+  O   O18       1.0  0.35100  0.83788  0.55517  1.0000
+  O   O19       1.0  0.53016  0.37313  0.29720  1.0000
+  O   O20       1.0  0.44091  0.59928  0.26977  1.0000
+  O   O21       1.0  0.40355  0.36564  0.21024  1.0000
+  O   O22       1.0  0.66408  0.61081  0.17376  1.0000
+  O   O23       1.0  0.66489  0.38199  0.23275  1.0000
+  O   O24       1.0  0.71977  0.61876  0.28276  1.0000
+  O   O25       1.0  0.98644  0.11820  0.25123  1.0000
+  O   O26       1.0  0.13634  0.13961  0.30087  1.0000
+  O   O27       1.0  0.08419  0.93709  0.22683  1.0000
+  O   O28       1.0  0.80799  0.14986  0.24886  1.0000
+  O   O29       1.0  0.78957  0.93604  0.30998  1.0000
+  O   O30       1.0  0.74894  0.91289  0.20139  1.0000
+  O   O31       1.0  0.88413  0.28965  0.14767  1.0000
+  O   O32       1.0  0.75605  0.37384  0.07170  1.0000
+  O   O33       1.0  0.80363  0.10596  0.07517  1.0000
+  O   O34       1.0  0.33789  0.41069  0.50054  1.0000
+  O   O35       1.0  0.26703  0.25786  0.41517  1.0000
+  O   O36       1.0  0.37091  0.13391  0.49758  1.0000
+  O   O37       1.0  0.80811  0.56446  0.98524  1.0000
+  O   O38       1.0  0.84558  0.83980  0.99340  1.0000
+  O   O39       1.0  0.74343  0.73967  0.90431  1.0000
+  O   O40       1.0  0.75825  0.14536  0.94677  1.0000
+  O   O41       1.0  0.68793  0.27953  0.85543  1.0000
+  O   O42       1.0  0.64961  0.34218  0.94432  1.0000
+  O   O43       1.0  0.46946  0.87476  0.20305  1.0000
+  O   O44       1.0  0.55955  0.10028  0.23014  1.0000
+  O   O45       1.0  0.59634  0.86662  0.28968  1.0000
+  O   O46       1.0  0.33578  0.11124  0.32608  1.0000
+  O   O47       1.0  0.33524  0.88183  0.26752  1.0000
+  O   O48       1.0  0.28006  0.11816  0.21710  1.0000
+  O   O49       1.0  0.98641  0.38179  0.75283  1.0000
+  O   O50       1.0  0.13630  0.35934  0.80298  1.0000
+  O   O51       1.0  0.08492  0.56183  0.72876  1.0000
+  O   O52       1.0  0.80769  0.35016  0.74923  1.0000
+  O   O53       1.0  0.78892  0.56336  0.81033  1.0000
+  O   O54       1.0  0.74903  0.58708  0.70167  1.0000
+  O   O55       1.0  0.88501  0.21036  0.64847  1.0000
+  O   O56       1.0  0.75606  0.13014  0.57194  1.0000
+  O   O57       1.0  0.80925  0.39471  0.57466  1.0000
+  O   O58       1.0  0.33718  0.08882  0.00159  1.0000
+  O   O59       1.0  0.26751  0.24164  0.91595  1.0000
+  O   O60       1.0  0.37129  0.36487  0.99851  1.0000
+  O   O61       1.0  0.80739  0.94087  0.48485  1.0000
+  O   O62       1.0  0.84387  0.66501  0.49270  1.0000
+  O   O63       1.0  0.74105  0.76582  0.40415  1.0000
+  O   O64       1.0  0.75819  0.35643  0.44633  1.0000
+  O   O65       1.0  0.68766  0.22018  0.35541  1.0000
+  O   O66       1.0  0.64878  0.16206  0.44460  1.0000
+  O   O67       1.0  0.46992  0.62555  0.70302  1.0000
+  O   O68       1.0  0.55993  0.40043  0.73083  1.0000
+  O   O69       1.0  0.59670  0.63473  0.78998  1.0000
+  O   O70       1.0  0.33586  0.38935  0.82623  1.0000
+  O   O71       1.0  0.33506  0.61787  0.76711  1.0000
+  O   O72       1.0  0.28021  0.38096  0.71722  1.0000
+  O   O73       1.0  0.01339  0.88148  0.74759  1.0000
+  O   O74       1.0  0.86349  0.85962  0.69733  1.0000
+  O   O75       1.0  0.91499  0.06190  0.77161  1.0000
+  O   O76       1.0  0.19251  0.84997  0.75164  1.0000
+  O   O77       1.0  0.21094  0.06341  0.69037  1.0000
+  O   O78       1.0  0.25135  0.08713  0.79897  1.0000
+  O   O79       1.0  0.11457  0.70986  0.85199  1.0000
+  O   O80       1.0  0.24314  0.62817  0.92837  1.0000
+  O   O81       1.0  0.19182  0.89376  0.92543  1.0000
+  O   O82       1.0  0.66115  0.58929  0.49862  1.0000
+  O   O83       1.0  0.73180  0.74103  0.58430  1.0000
+  O   O84       1.0  0.62860  0.86623  0.50186  1.0000
+  O   O85       1.0  0.19053  0.43491  0.01387  1.0000
+  O   O86       1.0  0.15317  0.15896  0.00882  1.0000
+  O   O87       1.0  0.25755  0.26405  0.09570  1.0000
+  O   O88       1.0  0.24289  0.85511  0.05461  1.0000
+  O   O89       1.0  0.31319  0.71857  0.14520  1.0000
+  O   O90       1.0  0.35011  0.65656  0.05572  1.0000
+  O   O91       1.0  0.53062  0.12536  0.79736  1.0000
+  O   O92       1.0  0.44111  0.89927  0.76938  1.0000
+  O   O93       1.0  0.40400  0.13366  0.71047  1.0000
+  O   O94       1.0  0.66418  0.88980  0.67362  1.0000
+  O   O95       1.0  0.66475  0.11832  0.73271  1.0000
+  O   O96       1.0  0.71986  0.88156  0.78252  1.0000
diff --git a/tests/testresources/inputs/cif_files/odac-21735.cif b/tests/testresources/inputs/cif_files/odac-21735.cif
new file mode 100644
index 00000000..04257992
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/odac-21735.cif
@@ -0,0 +1,139 @@
+data_image0
+_chemical_formula_structural       Zr6H28C48O32
+_chemical_formula_sum              "Zr6 H28 C48 O32"
+_cell_length_a       14.7589
+_cell_length_b       14.7589
+_cell_length_c       14.7589
+_cell_angle_alpha    60
+_cell_angle_beta     60
+_cell_angle_gamma    60
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Zr  Zr1       1.0  0.88062  0.11969  0.11996  1.0000
+  Zr  Zr2       1.0  0.12013  0.88017  0.88056  1.0000
+  Zr  Zr3       1.0  0.12016  0.88015  0.12009  1.0000
+  Zr  Zr4       1.0  0.88064  0.11977  0.88045  1.0000
+  Zr  Zr5       1.0  0.12023  0.11965  0.88039  1.0000
+  Zr  Zr6       1.0  0.88068  0.88010  0.12005  1.0000
+  H   H1        1.0  0.84757  0.13815  0.42213  1.0000
+  H   H2        1.0  0.13788  0.84700  0.59344  1.0000
+  H   H3        1.0  0.42387  0.59399  0.84593  1.0000
+  H   H4        1.0  0.59268  0.42201  0.13852  1.0000
+  H   H5        1.0  0.42413  0.84540  0.13697  1.0000
+  H   H6        1.0  0.59269  0.13826  0.84776  1.0000
+  H   H7        1.0  0.84752  0.42194  0.59324  1.0000
+  H   H8        1.0  0.13673  0.59430  0.42380  1.0000
+  H   H9        1.0  0.14064  0.41983  0.84925  1.0000
+  H   H10       1.0  0.84564  0.59468  0.13590  1.0000
+  H   H11       1.0  0.59265  0.84762  0.42169  1.0000
+  H   H12       1.0  0.42175  0.13851  0.59242  1.0000
+  H   H13       1.0  0.13802  0.84688  0.42275  1.0000
+  H   H14       1.0  0.84746  0.13835  0.59276  1.0000
+  H   H15       1.0  0.59471  0.42348  0.84588  1.0000
+  H   H16       1.0  0.42215  0.59267  0.13829  1.0000
+  H   H17       1.0  0.84496  0.42476  0.13513  1.0000
+  H   H18       1.0  0.14171  0.58942  0.85040  1.0000
+  H   H19       1.0  0.42195  0.84756  0.59238  1.0000
+  H   H20       1.0  0.59241  0.13860  0.42173  1.0000
+  H   H21       1.0  0.42207  0.13802  0.84789  1.0000
+  H   H22       1.0  0.59467  0.84563  0.13689  1.0000
+  H   H23       1.0  0.84721  0.59266  0.42270  1.0000
+  H   H24       1.0  0.13680  0.42375  0.59451  1.0000
+  H   H25       1.0  0.09476  0.09447  0.09434  1.0000
+  H   H26       1.0  0.09454  0.09444  0.71734  1.0000
+  H   H27       1.0  0.09490  0.71699  0.09501  1.0000
+  H   H28       1.0  0.71748  0.09426  0.09440  1.0000
+  C   C1        1.0  0.91052  0.07496  0.46055  1.0000
+  C   C2        1.0  0.07483  0.91013  0.55508  1.0000
+  C   C3        1.0  0.46183  0.55557  0.90931  1.0000
+  C   C4        1.0  0.55488  0.46050  0.07501  1.0000
+  C   C5        1.0  0.46184  0.90899  0.07423  1.0000
+  C   C6        1.0  0.55491  0.07469  0.91050  1.0000
+  C   C7        1.0  0.91027  0.46057  0.55527  1.0000
+  C   C8        1.0  0.07397  0.55569  0.46178  1.0000
+  C   C9        1.0  0.07685  0.45886  0.91155  1.0000
+  C   C10       1.0  0.90968  0.55553  0.07373  1.0000
+  C   C11       1.0  0.55441  0.91066  0.46003  1.0000
+  C   C12       1.0  0.46012  0.07531  0.55423  1.0000
+  C   C13       1.0  0.07491  0.91008  0.46089  1.0000
+  C   C14       1.0  0.91045  0.07504  0.55473  1.0000
+  C   C15       1.0  0.55607  0.46147  0.90927  1.0000
+  C   C16       1.0  0.46073  0.55467  0.07493  1.0000
+  C   C17       1.0  0.90937  0.46169  0.07332  1.0000
+  C   C18       1.0  0.07726  0.55255  0.91208  1.0000
+  C   C19       1.0  0.46024  0.91062  0.55422  1.0000
+  C   C20       1.0  0.55429  0.07537  0.46005  1.0000
+  C   C21       1.0  0.46076  0.07458  0.91058  1.0000
+  C   C22       1.0  0.55602  0.90907  0.07416  1.0000
+  C   C23       1.0  0.91009  0.55482  0.46116  1.0000
+  C   C24       1.0  0.07408  0.46148  0.55590  1.0000
+  C   C25       1.0  0.99579  0.99553  0.30909  1.0000
+  C   C26       1.0  0.99328  0.99303  0.41269  1.0000
+  C   C27       1.0  0.99550  0.99547  0.70064  1.0000
+  C   C28       1.0  0.99311  0.99310  0.60190  1.0000
+  C   C29       1.0  0.30945  0.70036  0.99542  1.0000
+  C   C30       1.0  0.41319  0.60197  0.99274  1.0000
+  C   C31       1.0  0.70062  0.30903  0.99560  1.0000
+  C   C32       1.0  0.60239  0.41290  0.99278  1.0000
+  C   C33       1.0  0.30949  0.99499  0.99571  1.0000
+  C   C34       1.0  0.41320  0.99233  0.99304  1.0000
+  C   C35       1.0  0.70091  0.99512  0.99539  1.0000
+  C   C36       1.0  0.60241  0.99248  0.99287  1.0000
+  C   C37       1.0  0.99564  0.30917  0.70075  1.0000
+  C   C38       1.0  0.99292  0.41288  0.60240  1.0000
+  C   C39       1.0  0.99535  0.70049  0.30958  1.0000
+  C   C40       1.0  0.99258  0.60217  0.41335  1.0000
+  C   C41       1.0  0.99575  0.30905  0.99515  1.0000
+  C   C42       1.0  -0.00651  0.41240  -0.00717  1.0000
+  C   C43       1.0  0.99649  0.69948  0.99615  1.0000
+  C   C44       1.0  0.99412  0.60084  0.99363  1.0000
+  C   C45       1.0  0.70029  0.99568  0.30883  1.0000
+  C   C46       1.0  0.60139  0.99347  0.41211  1.0000
+  C   C47       1.0  0.30899  0.99550  0.70017  1.0000
+  C   C48       1.0  0.41226  0.99339  0.60127  1.0000
+  O   O1        1.0  0.92048  0.07421  0.26786  1.0000
+  O   O2        1.0  0.07371  0.91969  0.73896  1.0000
+  O   O3        1.0  0.26847  0.73847  0.91985  1.0000
+  O   O4        1.0  0.73838  0.26782  0.07437  1.0000
+  O   O5        1.0  0.26822  0.91968  0.07433  1.0000
+  O   O6        1.0  0.73859  0.07398  0.92022  1.0000
+  O   O7        1.0  0.92019  0.26801  0.73887  1.0000
+  O   O8        1.0  0.07413  0.73827  0.26823  1.0000
+  O   O9        1.0  0.07461  0.26766  0.92002  1.0000
+  O   O10       1.0  0.92091  0.73751  0.07465  1.0000
+  O   O11       1.0  0.73820  0.92028  0.26768  1.0000
+  O   O12       1.0  0.26821  0.07374  0.73851  1.0000
+  O   O13       1.0  0.07427  0.91999  0.26813  1.0000
+  O   O14       1.0  0.92029  0.07429  0.73835  1.0000
+  O   O15       1.0  0.73846  0.26782  0.92029  1.0000
+  O   O16       1.0  0.26811  0.73802  0.07429  1.0000
+  O   O17       1.0  0.91983  0.26845  0.07332  1.0000
+  O   O18       1.0  0.07508  0.73744  0.92073  1.0000
+  O   O19       1.0  0.26784  0.92014  0.73805  1.0000
+  O   O20       1.0  0.73860  0.07392  0.26804  1.0000
+  O   O21       1.0  0.26825  0.07370  0.92034  1.0000
+  O   O22       1.0  0.73917  0.91951  0.07378  1.0000
+  O   O23       1.0  0.91995  0.73852  0.26835  1.0000
+  O   O24       1.0  0.07459  0.26762  0.73840  1.0000
+  O   O25       1.0  0.95066  0.14914  0.95049  1.0000
+  O   O26       1.0  0.06794  0.79746  0.06791  1.0000
+  O   O27       1.0  0.14956  0.95018  0.95055  1.0000
+  O   O28       1.0  0.79796  0.06743  0.06766  1.0000
+  O   O29       1.0  0.95067  0.95010  0.95055  1.0000
+  O   O30       1.0  0.06782  0.06759  0.06769  1.0000
+  O   O31       1.0  0.95058  0.95027  0.14950  1.0000
+  O   O32       1.0  0.06780  0.06740  0.79781  1.0000
diff --git a/tests/testresources/inputs/cif_files/odac-21816.cif b/tests/testresources/inputs/cif_files/odac-21816.cif
new file mode 100644
index 00000000..0fd41b5d
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/odac-21816.cif
@@ -0,0 +1,417 @@
+data_image0
+_chemical_formula_structural       Cu16H88C192N16O80
+_chemical_formula_sum              "Cu16 H88 C192 N16 O80"
+_cell_length_a       18.9609
+_cell_length_b       18.9609
+_cell_length_c       34.7406
+_cell_angle_alpha    90
+_cell_angle_beta     90
+_cell_angle_gamma    90.0002
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Cu  Cu1       1.0  0.73250  0.29250  0.22324  1.0000
+  Cu  Cu2       1.0  0.26750  0.70750  0.22324  1.0000
+  Cu  Cu3       1.0  0.70750  0.73250  0.22324  1.0000
+  Cu  Cu4       1.0  0.29250  0.26750  0.22324  1.0000
+  Cu  Cu5       1.0  0.76750  0.79250  0.27676  1.0000
+  Cu  Cu6       1.0  0.23250  0.20750  0.27676  1.0000
+  Cu  Cu7       1.0  0.79250  0.23250  0.27676  1.0000
+  Cu  Cu8       1.0  0.20750  0.76750  0.27676  1.0000
+  Cu  Cu9       1.0  0.26750  0.70750  0.77676  1.0000
+  Cu  Cu10      1.0  0.73249  0.29251  0.77678  1.0000
+  Cu  Cu11      1.0  0.29251  0.26749  0.77678  1.0000
+  Cu  Cu12      1.0  0.70750  0.73249  0.77676  1.0000
+  Cu  Cu13      1.0  0.23249  0.20750  0.72324  1.0000
+  Cu  Cu14      1.0  0.76749  0.79252  0.72322  1.0000
+  Cu  Cu15      1.0  0.20750  0.76750  0.72324  1.0000
+  Cu  Cu16      1.0  0.79252  0.23249  0.72322  1.0000
+  H   H1        1.0  0.01520  0.45173  0.06202  1.0000
+  H   H2        1.0  0.96906  0.35933  0.09267  1.0000
+  H   H3        1.0  0.90202  0.32039  0.14556  1.0000
+  H   H4        1.0  0.01255  0.24349  0.24520  1.0000
+  H   H5        1.0  0.12878  0.29649  0.14259  1.0000
+  H   H6        1.0  0.98480  0.54827  0.06202  1.0000
+  H   H7        1.0  0.03094  0.64067  0.09267  1.0000
+  H   H8        1.0  0.09798  0.67961  0.14556  1.0000
+  H   H9        1.0  0.98745  0.75651  0.24520  1.0000
+  H   H10       1.0  0.87122  0.70351  0.14259  1.0000
+  H   H11       1.0  0.54827  0.01520  0.06202  1.0000
+  H   H12       1.0  0.64067  0.96906  0.09267  1.0000
+  H   H13       1.0  0.67961  0.90202  0.14556  1.0000
+  H   H14       1.0  0.75651  0.01255  0.24520  1.0000
+  H   H15       1.0  0.70351  0.12879  0.14259  1.0000
+  H   H16       1.0  0.45173  0.98480  0.06202  1.0000
+  H   H17       1.0  0.35933  0.03094  0.09267  1.0000
+  H   H18       1.0  0.32039  0.09798  0.14556  1.0000
+  H   H19       1.0  0.24349  0.98745  0.24520  1.0000
+  H   H20       1.0  0.29649  0.87121  0.14259  1.0000
+  H   H21       1.0  0.48480  0.95173  0.43798  1.0000
+  H   H22       1.0  0.53094  0.85933  0.40733  1.0000
+  H   H23       1.0  0.59798  0.82039  0.35444  1.0000
+  H   H24       1.0  0.48745  0.74349  0.25479  1.0000
+  H   H25       1.0  0.37121  0.79649  0.35741  1.0000
+  H   H26       1.0  0.51520  0.04827  0.43798  1.0000
+  H   H27       1.0  0.46906  0.14067  0.40733  1.0000
+  H   H28       1.0  0.40202  0.17961  0.35444  1.0000
+  H   H29       1.0  0.51255  0.25651  0.25480  1.0000
+  H   H30       1.0  0.62879  0.20351  0.35741  1.0000
+  H   H31       1.0  0.95173  0.51520  0.43798  1.0000
+  H   H32       1.0  0.85933  0.46906  0.40733  1.0000
+  H   H33       1.0  0.82039  0.40202  0.35444  1.0000
+  H   H34       1.0  0.74349  0.51255  0.25480  1.0000
+  H   H35       1.0  0.79649  0.62878  0.35741  1.0000
+  H   H36       1.0  0.04827  0.48480  0.43798  1.0000
+  H   H37       1.0  0.14067  0.53094  0.40733  1.0000
+  H   H38       1.0  0.17961  0.59798  0.35444  1.0000
+  H   H39       1.0  0.25651  0.48745  0.25480  1.0000
+  H   H40       1.0  0.20351  0.37122  0.35741  1.0000
+  H   H41       1.0  0.98480  0.54827  0.93795  1.0000
+  H   H42       1.0  0.03095  0.64067  0.90731  1.0000
+  H   H43       1.0  0.09799  0.67961  0.85442  1.0000
+  H   H44       1.0  0.98745  0.75652  0.75478  1.0000
+  H   H45       1.0  0.87122  0.70351  0.85739  1.0000
+  H   H46       1.0  0.01520  0.45173  0.93795  1.0000
+  H   H47       1.0  0.96905  0.35933  0.90731  1.0000
+  H   H48       1.0  0.90201  0.32039  0.85442  1.0000
+  H   H49       1.0  0.01255  0.24348  0.75478  1.0000
+  H   H50       1.0  0.12878  0.29649  0.85739  1.0000
+  H   H51       1.0  0.45173  0.98480  0.93795  1.0000
+  H   H52       1.0  0.35935  0.03095  0.90731  1.0000
+  H   H53       1.0  0.32041  0.09798  0.85442  1.0000
+  H   H54       1.0  0.24348  0.98745  0.75478  1.0000
+  H   H55       1.0  0.29649  0.87122  0.85739  1.0000
+  H   H56       1.0  0.54826  0.01521  0.93795  1.0000
+  H   H57       1.0  0.64066  0.96906  0.90730  1.0000
+  H   H58       1.0  0.67961  0.90203  0.85441  1.0000
+  H   H59       1.0  0.75653  0.01253  0.75476  1.0000
+  H   H60       1.0  0.70345  0.12880  0.85738  1.0000
+  H   H61       1.0  0.51521  0.04826  0.56205  1.0000
+  H   H62       1.0  0.46906  0.14066  0.59269  1.0000
+  H   H63       1.0  0.40203  0.17961  0.64559  1.0000
+  H   H64       1.0  0.51255  0.25648  0.74525  1.0000
+  H   H65       1.0  0.62880  0.20345  0.64262  1.0000
+  H   H66       1.0  0.48480  0.95173  0.56205  1.0000
+  H   H67       1.0  0.53095  0.85935  0.59269  1.0000
+  H   H68       1.0  0.59798  0.82041  0.64558  1.0000
+  H   H69       1.0  0.48745  0.74347  0.74522  1.0000
+  H   H70       1.0  0.37122  0.79649  0.64261  1.0000
+  H   H71       1.0  0.04827  0.48480  0.56205  1.0000
+  H   H72       1.0  0.14067  0.53095  0.59269  1.0000
+  H   H73       1.0  0.17961  0.59799  0.64558  1.0000
+  H   H74       1.0  0.25652  0.48745  0.74522  1.0000
+  H   H75       1.0  0.20351  0.37122  0.64261  1.0000
+  H   H76       1.0  0.95173  0.51520  0.56205  1.0000
+  H   H77       1.0  0.85933  0.46905  0.59269  1.0000
+  H   H78       1.0  0.82039  0.40201  0.64558  1.0000
+  H   H79       1.0  0.74348  0.51255  0.74522  1.0000
+  H   H80       1.0  0.79649  0.62878  0.64261  1.0000
+  H   H81       1.0  0.08231  0.26766  0.99999  1.0000
+  H   H82       1.0  0.91769  0.73234  0.99999  1.0000
+  H   H83       1.0  0.73234  0.08231  0.99999  1.0000
+  H   H84       1.0  0.26766  0.91769  0.99999  1.0000
+  H   H85       1.0  0.41769  0.76766  0.50001  1.0000
+  H   H86       1.0  0.58231  0.23234  0.50001  1.0000
+  H   H87       1.0  0.76766  0.58231  0.50001  1.0000
+  H   H88       1.0  0.23234  0.41769  0.50001  1.0000
+  C   C1        1.0  0.02268  0.42546  0.03444  1.0000
+  C   C2        1.0  0.04692  0.35574  0.03464  1.0000
+  C   C3        1.0  0.06127  0.31811  0.07185  1.0000
+  C   C4        1.0  0.01555  0.31019  0.13907  1.0000
+  C   C5        1.0  0.95177  0.30591  0.15919  1.0000
+  C   C6        1.0  0.95068  0.28183  0.19722  1.0000
+  C   C7        1.0  0.01337  0.26264  0.21569  1.0000
+  C   C8        1.0  0.07714  0.26950  0.19585  1.0000
+  C   C9        1.0  0.07871  0.29250  0.15757  1.0000
+  C   C10       1.0  0.88158  0.27570  0.21757  1.0000
+  C   C11       1.0  0.14553  0.25531  0.21584  1.0000
+  C   C12       1.0  0.97732  0.57454  0.03444  1.0000
+  C   C13       1.0  0.95308  0.64426  0.03464  1.0000
+  C   C14       1.0  0.93873  0.68189  0.07185  1.0000
+  C   C15       1.0  0.98445  0.68981  0.13907  1.0000
+  C   C16       1.0  0.04823  0.69409  0.15919  1.0000
+  C   C17       1.0  0.04932  0.71817  0.19722  1.0000
+  C   C18       1.0  0.98663  0.73736  0.21569  1.0000
+  C   C19       1.0  0.92286  0.73050  0.19585  1.0000
+  C   C20       1.0  0.92129  0.70750  0.15757  1.0000
+  C   C21       1.0  0.11842  0.72430  0.21757  1.0000
+  C   C22       1.0  0.85447  0.74469  0.21584  1.0000
+  C   C23       1.0  0.57454  0.02268  0.03444  1.0000
+  C   C24       1.0  0.64426  0.04693  0.03464  1.0000
+  C   C25       1.0  0.68189  0.06127  0.07185  1.0000
+  C   C26       1.0  0.68981  0.01555  0.13907  1.0000
+  C   C27       1.0  0.69409  0.95177  0.15919  1.0000
+  C   C28       1.0  0.71817  0.95069  0.19722  1.0000
+  C   C29       1.0  0.73736  0.01337  0.21569  1.0000
+  C   C30       1.0  0.73050  0.07715  0.19585  1.0000
+  C   C31       1.0  0.70750  0.07871  0.15757  1.0000
+  C   C32       1.0  0.72430  0.88158  0.21757  1.0000
+  C   C33       1.0  0.74469  0.14553  0.21584  1.0000
+  C   C34       1.0  0.42546  0.97732  0.03444  1.0000
+  C   C35       1.0  0.35574  0.95307  0.03464  1.0000
+  C   C36       1.0  0.31811  0.93873  0.07185  1.0000
+  C   C37       1.0  0.31019  0.98445  0.13907  1.0000
+  C   C38       1.0  0.30591  0.04823  0.15919  1.0000
+  C   C39       1.0  0.28183  0.04931  0.19722  1.0000
+  C   C40       1.0  0.26264  0.98663  0.21569  1.0000
+  C   C41       1.0  0.26950  0.92285  0.19585  1.0000
+  C   C42       1.0  0.29250  0.92129  0.15757  1.0000
+  C   C43       1.0  0.27570  0.11842  0.21757  1.0000
+  C   C44       1.0  0.25531  0.85447  0.21584  1.0000
+  C   C45       1.0  0.47732  0.92546  0.46556  1.0000
+  C   C46       1.0  0.45307  0.85574  0.46536  1.0000
+  C   C47       1.0  0.43873  0.81811  0.42815  1.0000
+  C   C48       1.0  0.48445  0.81019  0.36093  1.0000
+  C   C49       1.0  0.54823  0.80591  0.34081  1.0000
+  C   C50       1.0  0.54931  0.78183  0.30278  1.0000
+  C   C51       1.0  0.48663  0.76264  0.28431  1.0000
+  C   C52       1.0  0.42286  0.76950  0.30415  1.0000
+  C   C53       1.0  0.42129  0.79250  0.34243  1.0000
+  C   C54       1.0  0.61842  0.77570  0.28243  1.0000
+  C   C55       1.0  0.35447  0.75531  0.28416  1.0000
+  C   C56       1.0  0.52268  0.07454  0.46556  1.0000
+  C   C57       1.0  0.54693  0.14426  0.46536  1.0000
+  C   C58       1.0  0.56127  0.18189  0.42815  1.0000
+  C   C59       1.0  0.51555  0.18981  0.36093  1.0000
+  C   C60       1.0  0.45177  0.19409  0.34081  1.0000
+  C   C61       1.0  0.45069  0.21817  0.30278  1.0000
+  C   C62       1.0  0.51337  0.23736  0.28431  1.0000
+  C   C63       1.0  0.57715  0.23050  0.30415  1.0000
+  C   C64       1.0  0.57871  0.20750  0.34243  1.0000
+  C   C65       1.0  0.38158  0.22430  0.28243  1.0000
+  C   C66       1.0  0.64553  0.24469  0.28416  1.0000
+  C   C67       1.0  0.92546  0.52268  0.46556  1.0000
+  C   C68       1.0  0.85574  0.54692  0.46536  1.0000
+  C   C69       1.0  0.81811  0.56127  0.42815  1.0000
+  C   C70       1.0  0.81019  0.51555  0.36093  1.0000
+  C   C71       1.0  0.80591  0.45177  0.34081  1.0000
+  C   C72       1.0  0.78183  0.45068  0.30278  1.0000
+  C   C73       1.0  0.76264  0.51337  0.28431  1.0000
+  C   C74       1.0  0.76950  0.57714  0.30415  1.0000
+  C   C75       1.0  0.79250  0.57871  0.34243  1.0000
+  C   C76       1.0  0.77570  0.38158  0.28243  1.0000
+  C   C77       1.0  0.75531  0.64553  0.28416  1.0000
+  C   C78       1.0  0.07454  0.47732  0.46556  1.0000
+  C   C79       1.0  0.14426  0.45308  0.46536  1.0000
+  C   C80       1.0  0.18189  0.43873  0.42815  1.0000
+  C   C81       1.0  0.18981  0.48445  0.36093  1.0000
+  C   C82       1.0  0.19409  0.54823  0.34081  1.0000
+  C   C83       1.0  0.21817  0.54932  0.30278  1.0000
+  C   C84       1.0  0.23736  0.48663  0.28431  1.0000
+  C   C85       1.0  0.23050  0.42286  0.30415  1.0000
+  C   C86       1.0  0.20750  0.42129  0.34243  1.0000
+  C   C87       1.0  0.22430  0.61842  0.28243  1.0000
+  C   C88       1.0  0.24469  0.35447  0.28416  1.0000
+  C   C89       1.0  0.97731  0.57453  0.96554  1.0000
+  C   C90       1.0  0.95307  0.64426  0.96533  1.0000
+  C   C91       1.0  0.93873  0.68188  0.92812  1.0000
+  C   C92       1.0  0.98445  0.68981  0.86091  1.0000
+  C   C93       1.0  0.04823  0.69409  0.84079  1.0000
+  C   C94       1.0  0.04932  0.71817  0.80276  1.0000
+  C   C95       1.0  0.98663  0.73736  0.78429  1.0000
+  C   C96       1.0  0.92286  0.73050  0.80414  1.0000
+  C   C97       1.0  0.92129  0.70750  0.84241  1.0000
+  C   C98       1.0  0.11842  0.72431  0.78241  1.0000
+  C   C99       1.0  0.85448  0.74470  0.78415  1.0000
+  C   C100      1.0  0.02268  0.42547  0.96554  1.0000
+  C   C101      1.0  0.04693  0.35574  0.96533  1.0000
+  C   C102      1.0  0.06127  0.31812  0.92812  1.0000
+  C   C103      1.0  0.01555  0.31020  0.86091  1.0000
+  C   C104      1.0  0.95177  0.30591  0.84079  1.0000
+  C   C105      1.0  0.95068  0.28182  0.80276  1.0000
+  C   C106      1.0  0.01337  0.26263  0.78429  1.0000
+  C   C107      1.0  0.07714  0.26950  0.80414  1.0000
+  C   C108      1.0  0.07870  0.29250  0.84241  1.0000
+  C   C109      1.0  0.88158  0.27569  0.78241  1.0000
+  C   C110      1.0  0.14552  0.25530  0.78415  1.0000
+  C   C111      1.0  0.42547  0.97731  0.96554  1.0000
+  C   C112      1.0  0.35574  0.95307  0.96533  1.0000
+  C   C113      1.0  0.31812  0.93873  0.92812  1.0000
+  C   C114      1.0  0.31019  0.98445  0.86091  1.0000
+  C   C115      1.0  0.30591  0.04823  0.84079  1.0000
+  C   C116      1.0  0.28184  0.04932  0.80276  1.0000
+  C   C117      1.0  0.26264  0.98663  0.78429  1.0000
+  C   C118      1.0  0.26950  0.92286  0.80414  1.0000
+  C   C119      1.0  0.29250  0.92129  0.84241  1.0000
+  C   C120      1.0  0.27570  0.11842  0.78241  1.0000
+  C   C121      1.0  0.25530  0.85448  0.78415  1.0000
+  C   C122      1.0  0.57453  0.02268  0.96553  1.0000
+  C   C123      1.0  0.64426  0.04693  0.96533  1.0000
+  C   C124      1.0  0.68187  0.06129  0.92812  1.0000
+  C   C125      1.0  0.68980  0.01557  0.86092  1.0000
+  C   C126      1.0  0.69405  0.95179  0.84077  1.0000
+  C   C127      1.0  0.71811  0.95069  0.80275  1.0000
+  C   C128      1.0  0.73747  0.01338  0.78429  1.0000
+  C   C129      1.0  0.73070  0.07713  0.80420  1.0000
+  C   C130      1.0  0.70757  0.07871  0.84244  1.0000
+  C   C131      1.0  0.72430  0.88157  0.78240  1.0000
+  C   C132      1.0  0.74486  0.14556  0.78422  1.0000
+  C   C133      1.0  0.52268  0.07453  0.53447  1.0000
+  C   C134      1.0  0.54693  0.14426  0.53467  1.0000
+  C   C135      1.0  0.56129  0.18187  0.57188  1.0000
+  C   C136      1.0  0.51557  0.18979  0.63908  1.0000
+  C   C137      1.0  0.45179  0.19406  0.65922  1.0000
+  C   C138      1.0  0.45069  0.21813  0.69725  1.0000
+  C   C139      1.0  0.51337  0.23739  0.71573  1.0000
+  C   C140      1.0  0.57713  0.23058  0.69583  1.0000
+  C   C141      1.0  0.57871  0.20752  0.65757  1.0000
+  C   C142      1.0  0.38157  0.22430  0.71760  1.0000
+  C   C143      1.0  0.64554  0.24485  0.71581  1.0000
+  C   C144      1.0  0.47731  0.92547  0.53446  1.0000
+  C   C145      1.0  0.45307  0.85574  0.53467  1.0000
+  C   C146      1.0  0.43873  0.81812  0.57188  1.0000
+  C   C147      1.0  0.48445  0.81019  0.63909  1.0000
+  C   C148      1.0  0.54824  0.80591  0.65921  1.0000
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21383.json b/tests/testresources/refs/MOF_descriptors/odac-21383.json
new file mode 100644
index 00000000..ebf0883d
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21383.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "f-Gval-0-all", "f-Gval-1-all", "f-Gval-2-all", "f-Gval-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "mc-Gval-0-all", "mc-Gval-1-all", "mc-Gval-2-all", "mc-Gval-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", 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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21433.json b/tests/testresources/refs/MOF_descriptors/odac-21433.json
new file mode 100644
index 00000000..1b10bc94
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21433.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "f-Gval-0-all", "f-Gval-1-all", "f-Gval-2-all", "f-Gval-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "mc-Gval-0-all", "mc-Gval-1-all", "mc-Gval-2-all", "mc-Gval-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "D_mc-Gval-0-all", "D_mc-Gval-1-all", "D_mc-Gval-2-all", "D_mc-Gval-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "f-lig-Gval-0", "f-lig-Gval-1", "f-lig-Gval-2", "f-lig-Gval-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "lc-Gval-0-all", "lc-Gval-1-all", "lc-Gval-2-all", "lc-Gval-3-all", "lc-alpha-0-all", "lc-alpha-1-all", "lc-alpha-2-all", "lc-alpha-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "D_lc-Gval-0-all", "D_lc-Gval-1-all", "D_lc-Gval-2-all", "D_lc-Gval-3-all", "D_lc-alpha-0-all", "D_lc-alpha-1-all", "D_lc-alpha-2-all", "D_lc-alpha-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "func-Gval-0-all", "func-Gval-1-all", "func-Gval-2-all", "func-Gval-3-all", "func-alpha-0-all", "func-alpha-1-all", "func-alpha-2-all", "func-alpha-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all", "D_func-Gval-0-all", "D_func-Gval-1-all", "D_func-Gval-2-all", "D_func-Gval-3-all", "D_func-alpha-0-all", "D_func-alpha-1-all", "D_func-alpha-2-all", "D_func-alpha-3-all"], "descriptors": [69.11089999999997, 104.57600000000002, 170.21039999999996, 180.80639999999997, 1325.0, 1792.0, 2328.0, 2880.0, 9.0, 16.0, 20.0, 24.0, 36.0, 80.0, 80.0, 48.0, 8.213599999999994, 13.5488, 17.07960000000001, 18.57119999999999, 253.0, 384.0, 552.0, 720.0, 2.5921000000000016, 22.153599999999987, 14.103600000000007, 66.46080000000005, 169.0, 416.0, 780.0, 1248.0, 1.0, 4.0, 4.0, 12.0, 16.0, 32.0, 64.0, 96.0, 1.5876000000000017, 3.6791999999999985, 5.342399999999999, 11.0376, 9.0, 72.0, 60.0, 216.0, 0.0, -7.319999999999994, -2.32, -21.959999999999983, 0.0, 20.0, -8.0, 60.0, 0.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 24.0, 0.0, 2.119999999999999, 0.8000000000000006, 6.360000000000002, 0.0, -12.0, -8.0, -36.0, 52.13049999999999, 60.268800000000034, 142.00320000000008, 0.0, 481.0, 960.0, 768.0, 0.0, 5.0, 8.0, 12.0, 0.0, 20.0, 32.0, 12.0, 0.0, 3.2552000000000008, 6.1904, 6.394800000000001, 0.0, 169.0, 240.0, 432.0, 0.0, 11.833600000000011, 7.533599999999988, 35.500799999999934, 0.0, 64.0, 120.0, 192.0, 0.0, 1.0, 1.0, 3.0, 0.0, 1.0, 4.0, 3.0, 0.0, 0.5328999999999996, 0.7738, 1.598699999999999, 0.0, 36.0, 30.0, 108.0, 0.0, 28.090000000000007, 132.5, 84.27000000000021, 0.0, 0.0, 1.25, 0.0, 0.0, 0.0, -7.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -3.0, 0.0, 0.0, 0.0, -0.3299999999999992, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -19.70000000000003, 0.0, 0.0, 4.796100000000009, 30.134399999999953, 0.0, 0.0, 225.0, 480.0, 0.0, 0.0, 1.0, 4.0, 0.0, 0.0, 16.0, 16.0, 0.0, 0.0, 1.1235999999999993, 3.0952, 0.0, 0.0, 25.0, 120.0, 0.0, 0.0, 625.0, 530.0, 0.0, 0.0, 0.0, -5.0, 0.0, 0.0, 0.0, 28.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 12.0, 0.0, 0.0, 0.0, 1.3199999999999967, 0.0, 0.0, 0.0, -4.0, 0.0, 0.0, 0.0, 78.80000000000013, 0.0, 0.0]}
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21478.json b/tests/testresources/refs/MOF_descriptors/odac-21478.json
new file mode 100644
index 00000000..34d79043
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21478.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "f-Gval-0-all", "f-Gval-1-all", "f-Gval-2-all", "f-Gval-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "mc-Gval-0-all", "mc-Gval-1-all", "mc-Gval-2-all", "mc-Gval-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "D_mc-Gval-0-all", "D_mc-Gval-1-all", "D_mc-Gval-2-all", "D_mc-Gval-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "f-lig-Gval-0", "f-lig-Gval-1", "f-lig-Gval-2", "f-lig-Gval-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "lc-Gval-0-all", "lc-Gval-1-all", "lc-Gval-2-all", "lc-Gval-3-all", "lc-alpha-0-all", "lc-alpha-1-all", "lc-alpha-2-all", "lc-alpha-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "D_lc-Gval-0-all", "D_lc-Gval-1-all", "D_lc-Gval-2-all", "D_lc-Gval-3-all", "D_lc-alpha-0-all", "D_lc-alpha-1-all", "D_lc-alpha-2-all", "D_lc-alpha-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "func-Gval-0-all", "func-Gval-1-all", "func-Gval-2-all", "func-Gval-3-all", "func-alpha-0-all", "func-alpha-1-all", "func-alpha-2-all", "func-alpha-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all", "D_func-Gval-0-all", "D_func-Gval-1-all", "D_func-Gval-2-all", "D_func-Gval-3-all", "D_func-alpha-0-all", "D_func-alpha-1-all", "D_func-alpha-2-all", "D_func-alpha-3-all"], "descriptors": [69.24129999999998, 105.67680000000001, 170.91119999999998, 180.80639999999997, 2056.0, 2880.0, 4368.0, 2880.0, 9.0, 16.0, 20.0, 24.0, 36.0, 80.0, 80.0, 48.0, 8.342099999999997, 13.8408, 17.503600000000002, 18.57119999999999, 388.0, 816.0, 912.0, 720.0, 2.722499999999997, 22.704000000000004, 14.454000000000006, 59.92800000000005, 900.0, 960.0, 1800.0, 2040.0, 1.0, 4.0, 4.0, 12.0, 16.0, 32.0, 64.0, 80.0, 1.7161, 3.825199999999999, 5.5544, 9.589200000000003, 144.0, 288.0, 240.0, 624.0, 0.0, -7.1599999999999975, -2.1599999999999984, -16.519999999999985, 0.0, 88.0, 60.0, 292.0, 0.0, 0.0, 0.0, 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510.1777500000006, 0.0, 0.0, 0.0, -3.759999999999995, 0.0, 0.0, 0.0, 35.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 12.0, 0.0, 0.0, 0.0, 1.680000000000004, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 79.59288999999991, 0.0, 0.0]}
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21735.json b/tests/testresources/refs/MOF_descriptors/odac-21735.json
new file mode 100644
index 00000000..e339690e
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21735.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "f-Gval-0-all", "f-Gval-1-all", "f-Gval-2-all", "f-Gval-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "mc-Gval-0-all", "mc-Gval-1-all", "mc-Gval-2-all", "mc-Gval-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "D_mc-Gval-0-all", "D_mc-Gval-1-all", "D_mc-Gval-2-all", "D_mc-Gval-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "f-lig-Gval-0", "f-lig-Gval-1", "f-lig-Gval-2", "f-lig-Gval-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "lc-Gval-0-all", "lc-Gval-1-all", "lc-Gval-2-all", "lc-Gval-3-all", "lc-alpha-0-all", "lc-alpha-1-all", "lc-alpha-2-all", "lc-alpha-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "D_lc-Gval-0-all", "D_lc-Gval-1-all", "D_lc-Gval-2-all", "D_lc-Gval-3-all", "D_lc-alpha-0-all", "D_lc-alpha-1-all", "D_lc-alpha-2-all", "D_lc-alpha-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "func-Gval-0-all", "func-Gval-1-all", "func-Gval-2-all", "func-Gval-3-all", "func-alpha-0-all", "func-alpha-1-all", "func-alpha-2-all", "func-alpha-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all", "D_func-Gval-0-all", "D_func-Gval-1-all", "D_func-Gval-2-all", "D_func-Gval-3-all", "D_func-alpha-0-all", "D_func-alpha-1-all", "D_func-alpha-2-all", "D_func-alpha-3-all"], "descriptors": [486.6785999999997, 920.8192000000006, 4251.559199999997, 4714.176000000003, 12084.0, 33088.0, 72384.0, 91776.0, 54.0, 152.0, 432.0, 672.0, 632.0, 2336.0, 4812.0, 6360.0, 38.94480000000001, 137.0648000000001, 306.56640000000027, 470.5872000000002, 1444.0, 3504.0, 13344.0, 13536.0, 1.7689000000000001, 36.60160000000001, 26.493600000000004, 105.06999999999998, 1600.0, 2560.0, 7440.0, 7360.0, 1.0, 8.0, 10.0, 24.0, 64.0, 176.0, 368.0, 464.0, 2.3716000000000004, 8.9936, 15.369200000000005, 27.227200000000014, 16.0, 192.0, 136.0, 544.0, 0.0, -16.88, -6.619999999999998, -47.07999999999999, 0.0, 256.0, 214.0, 776.0, 0.0, 0.0, 0.0, 0.0, 0.0, 42.0, 34.0, 134.0, 0.0, 6.480000000000003, 5.420000000000001, 19.28, 0.0, -16.0, 6.0, -40.0, 118.7144, 219.096, 337.3204, 385.387, 548.0, 1008.0, 1456.0, 1420.0, 16.0, 32.0, 48.0, 58.0, 80.0, 192.0, 256.0, 250.0, 7.422399999999999, 16.262400000000003, 23.044800000000006, 24.6794, 276.0, 480.0, 720.0, 708.0, 11.833599999999999, 8.771999999999998, 20.605599999999995, 17.543999999999997, 64.0, 48.0, 112.0, 96.0, 1.0, 1.0, 2.0, 2.0, 1.0, 3.0, 4.0, 6.0, 0.5328999999999998, 0.5621, 1.095, 1.1242, 36.0, 24.0, 60.0, 48.0, 28.09, 59.88999999999999, 87.98, 119.77999999999999, 0.0, 0.8900000000000002, 0.8900000000000002, 1.7800000000000005, 0.0, 2.0, 2.0, 4.0, 0.0, 0.0, 0.0, 0.0, 0.0, -2.0, -2.0, -4.0, 0.0, -0.040000000000000036, -0.040000000000000036, -0.08000000000000007, 0.0, 2.0, 2.0, 4.0, 0.0, -6.000000000000001, -6.000000000000001, -12.000000000000002, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]}
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21816.json b/tests/testresources/refs/MOF_descriptors/odac-21816.json
new file mode 100644
index 00000000..cbb3741f
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21816.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "f-Gval-0-all", "f-Gval-1-all", "f-Gval-2-all", "f-Gval-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "mc-Gval-0-all", "mc-Gval-1-all", "mc-Gval-2-all", "mc-Gval-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "D_mc-Gval-0-all", "D_mc-Gval-1-all", "D_mc-Gval-2-all", "D_mc-Gval-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "f-lig-Gval-0", "f-lig-Gval-1", "f-lig-Gval-2", "f-lig-Gval-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "lc-Gval-0-all", "lc-Gval-1-all", "lc-Gval-2-all", "lc-Gval-3-all", "lc-alpha-0-all", "lc-alpha-1-all", "lc-alpha-2-all", "lc-alpha-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "D_lc-Gval-0-all", "D_lc-Gval-1-all", "D_lc-Gval-2-all", "D_lc-Gval-3-all", "D_lc-alpha-0-all", "D_lc-alpha-1-all", "D_lc-alpha-2-all", "D_lc-alpha-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "func-Gval-0-all", "func-Gval-1-all", "func-Gval-2-all", "func-Gval-3-all", "func-alpha-0-all", "func-alpha-1-all", "func-alpha-2-all", "func-alpha-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all", "D_func-Gval-0-all", "D_func-Gval-1-all", "D_func-Gval-2-all", "D_func-Gval-3-all", "D_func-alpha-0-all", "D_func-alpha-1-all", "D_func-alpha-2-all", "D_func-alpha-3-all"], "descriptors": [127.89880000000002, 244.9279999999999, 456.19520000000006, 525.632, 2338.0, 4480.0, 4832.0, 6016.0, 14.0, 32.0, 48.0, 64.0, 80.0, 192.0, 256.0, 320.0, 10.4436, 25.112000000000002, 34.054399999999994, 43.099199999999996, 594.0, 1440.0, 1856.0, 2208.0, 3.61, 26.144000000000002, 19.38, 45.524, 841.0, 928.0, 696.0, 1624.0, 1.0, 4.0, 4.0, 8.0, 16.0, 32.0, 48.0, 80.0, 1.9043999999999992, 4.029600000000001, 4.2504, 8.28, 121.0, 264.0, 176.0, 440.0, 0.0, -6.1599999999999975, -2.600000000000001, -8.76, 0.0, 84.0, 92.0, 176.0, 0.0, 0.0, 0.0, 0.0, 0.0, 8.0, 4.0, 12.0, 0.0, 2.600000000000001, 2.439999999999998, 5.039999999999998, 0.0, 20.0, 28.0, 48.0, 692.2384000000012, 1367.6209999999999, 2187.9464000000007, 2846.5820000000003, 3226.0, 6392.0, 9824.0, 11120.0, 94.0, 198.0, 312.0, 420.0, 510.0, 1278.0, 1864.0, 2180.0, 44.379000000000026, 102.30460000000001, 154.956, 191.3699999999999, 1610.0, 3032.0, 4784.0, 5472.0, 11.833599999999992, 8.771999999999993, 20.605599999999985, 17.543999999999986, 64.0, 48.0, 112.0, 96.0, 1.0, 1.0, 2.0, 2.0, 1.0, 3.0, 4.0, 6.0, 0.5328999999999998, 0.5621000000000005, 1.0949999999999998, 1.124200000000001, 36.0, 24.0, 60.0, 48.0, 28.09, 59.89000000000004, 87.98, 119.78000000000009, 0.0, 0.8900000000000005, 0.8900000000000005, 1.780000000000001, 0.0, 2.0, 2.0, 4.0, 0.0, 0.0, 0.0, 0.0, 0.0, -2.0, -2.0, -4.0, 0.0, -0.040000000000000036, -0.040000000000000036, -0.08000000000000007, 0.0, 2.0, 2.0, 4.0, 0.0, -6.000000000000001, -6.000000000000001, -12.000000000000002, 10.5376, 15.481999999999985, 26.471599999999995, 39.13400000000001, 56.5, 69.5, 143.0, 167.0, 1.0, 2.0, 3.0, 5.0, 5.0, 12.0, 18.0, 26.0, 0.5476999999999994, 0.9972999999999994, 1.6948000000000005, 2.4107000000000003, 30.5, 34.5, 72.0, 84.0, 41.424999999999976, 130.24130700000012, 194.59500000000003, 302.37145549999997, 0.0, 1.3550000000000013, 1.18, 3.775000000000002, 0.0, 5.0, 2.5, 14.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.15, -0.050000000000000044, 0.4599999999999995, 0.0, 4.0, 2.5, 11.5, 0.0, -5.453554999999997, -8.85, -13.510665000000005]}

From 91d0b45a9ed4bcea6623cd43b3a6c4aa4417efd7 Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Sat, 16 Dec 2023 20:14:55 -0500
Subject: [PATCH 09/19] Remove checkpoint file

---
 .../MOF_RAC_example-checkpoint.ipynb          | 391 ------------------
 1 file changed, 391 deletions(-)
 delete mode 100644 molSimplify/Informatics/MOF/.ipynb_checkpoints/MOF_RAC_example-checkpoint.ipynb

diff --git a/molSimplify/Informatics/MOF/.ipynb_checkpoints/MOF_RAC_example-checkpoint.ipynb b/molSimplify/Informatics/MOF/.ipynb_checkpoints/MOF_RAC_example-checkpoint.ipynb
deleted file mode 100644
index a84b7bd4..00000000
--- a/molSimplify/Informatics/MOF/.ipynb_checkpoints/MOF_RAC_example-checkpoint.ipynb
+++ /dev/null
@@ -1,391 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "ename": "ModuleNotFoundError",
-     "evalue": "No module named 'pymatgen'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-1-3fad17901d6c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mmolSimplify\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mInformatics\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mMOF\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mMOF_descriptors\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mget_MOF_descriptors\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpandas\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;31m### Defining pymatgen function for getting primitive, since molSimplify does not depend on pymatgen\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/molSimplify/molSimplify/Informatics/MOF/MOF_descriptors.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     26\u001b[0m \u001b[0;31m# Pymatgen is used to get the primitive cell.                                           #\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     27\u001b[0m \u001b[0;31m#########################################################################################\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 28\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mpymatgen\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mio\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcif\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mCifParser\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     29\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     30\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'pymatgen'"
-     ]
-    }
-   ],
-   "source": [
-    "import os\n",
-    "from molSimplify.Informatics.MOF.MOF_descriptors import get_MOF_descriptors, get_primitive\n",
-    "import pandas as pd"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "alpha , beta , gama = 119.96277134, 90.0 ,90.0\n",
-      "[16.58, 0, 0]\n",
-      "[2.447456628095985e-15, 39.97, 0]\n",
-      "[2.4483756299962953e-15, -19.96999999721939, 34.64101615221368]\n",
-      "[0. 0. 0. 0.]\n",
-      "[  1.7689  36.6016  26.4936 105.07  ]\n",
-      "[  3.5378  73.2032  54.9822 203.357 ]\n",
-      "[  5.3067 109.8048  83.4708 301.644 ]\n",
-      "[  7.0756 146.4064 111.9594 399.931 ]\n",
-      "[  8.8445 183.008  138.453  505.001 ]\n",
-      "[ 10.6134 219.6096 166.9416 603.288 ]\n",
-      "[ 12.3823 256.2112 193.4352 708.358 ]\n",
-      "[ 14.1512 292.8128 221.9238 806.645 ]\n",
-      "[ 15.9201 329.4144 250.4124 904.932 ]\n",
-      "[  17.689  366.016  278.901 1003.219]\n",
-      "[  19.4579  402.6176  305.3946 1108.289 ]\n",
-      "[  21.2268  439.2192  333.8832 1206.576 ]\n",
-      "[  22.9957  475.8208  360.3768 1311.646 ]\n",
-      "[  24.7646  512.4224  388.8654 1409.933 ]\n",
-      "[  26.5335  549.024   417.354  1508.22  ]\n",
-      "[  28.3024  585.6256  445.8426 1606.507 ]\n",
-      "[  30.0713  622.2272  472.3362 1711.577 ]\n",
-      "[0. 0. 0. 0.]\n",
-      "[1600. 2560. 7440. 7360.]\n",
-      "[ 3200.  5120. 14520. 14240.]\n",
-      "[ 4800.  7680. 21600. 21120.]\n",
-      "[ 6400. 10240. 28680. 28000.]\n",
-      "[ 8000. 12800. 36120. 35360.]\n",
-      "[ 9600. 15360. 43200. 42240.]\n",
-      "[11200. 17920. 50640. 49600.]\n",
-      "[12800. 20480. 57720. 56480.]\n",
-      "[14400. 23040. 64800. 63360.]\n",
-      "[16000. 25600. 71880. 70240.]\n",
-      "[17600. 28160. 79320. 77600.]\n",
-      "[19200. 30720. 86400. 84480.]\n",
-      "[20800. 33280. 93840. 91840.]\n",
-      "[ 22400.  35840. 100920.  98720.]\n",
-      "[ 24000.  38400. 108000. 105600.]\n",
-      "[ 25600.  40960. 115080. 112480.]\n",
-      "[ 27200.  43520. 122520. 119840.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 1.  8. 10. 24.]\n",
-      "[ 2. 16. 21. 46.]\n",
-      "[ 3. 24. 32. 68.]\n",
-      "[ 4. 32. 43. 90.]\n",
-      "[  5.  40.  53. 114.]\n",
-      "[  6.  48.  64. 136.]\n",
-      "[  7.  56.  74. 160.]\n",
-      "[  8.  64.  85. 182.]\n",
-      "[  9.  72.  96. 204.]\n",
-      "[ 10.  80. 107. 226.]\n",
-      "[ 11.  88. 117. 250.]\n",
-      "[ 12.  96. 128. 272.]\n",
-      "[ 13. 104. 138. 296.]\n",
-      "[ 14. 112. 149. 318.]\n",
-      "[ 15. 120. 160. 340.]\n",
-      "[ 16. 128. 171. 362.]\n",
-      "[ 17. 136. 181. 386.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 64. 176. 368. 496.]\n",
-      "[128. 360. 712. 928.]\n",
-      "[ 192.  544. 1056. 1360.]\n",
-      "[ 256.  728. 1400. 1792.]\n",
-      "[ 320.  904. 1768. 2288.]\n",
-      "[ 384. 1088. 2112. 2720.]\n",
-      "[ 448. 1264. 2480. 3216.]\n",
-      "[ 512. 1448. 2824. 3648.]\n",
-      "[ 576. 1632. 3168. 4080.]\n",
-      "[ 640. 1816. 3512. 4512.]\n",
-      "[ 704. 1992. 3880. 5008.]\n",
-      "[ 768. 2176. 4224. 5440.]\n",
-      "[ 832. 2352. 4592. 5936.]\n",
-      "[ 896. 2536. 4936. 6368.]\n",
-      "[ 960. 2720. 5280. 6800.]\n",
-      "[1024. 2904. 5624. 7232.]\n",
-      "[1088. 3080. 5992. 7728.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 2.3716  8.9936 15.3692 27.2272]\n",
-      "[ 4.7432 17.9872 30.0762 52.0828]\n",
-      "[ 7.1148 26.9808 44.7832 76.9384]\n",
-      "[  9.4864  35.9744  59.4902 101.794 ]\n",
-      "[ 11.858   44.968   74.8594 129.0212]\n",
-      "[ 14.2296  53.9616  89.5664 153.8768]\n",
-      "[ 16.6012  62.9552 104.9356 181.104 ]\n",
-      "[ 18.9728  71.9488 119.6426 205.9596]\n",
-      "[ 21.3444  80.9424 134.3496 230.8152]\n",
-      "[ 23.716   89.936  149.0566 255.6708]\n",
-      "[ 26.0876  98.9296 164.4258 282.898 ]\n",
-      "[ 28.4592 107.9232 179.1328 307.7536]\n",
-      "[ 30.8308 116.9168 194.502  334.9808]\n",
-      "[ 33.2024 125.9104 209.209  359.8364]\n",
-      "[ 35.574 134.904 223.916 384.692]\n",
-      "[ 37.9456 143.8976 238.623  409.5476]\n",
-      "[ 40.3172 152.8912 253.9922 436.7748]\n",
-      "[0. 0. 0. 0.]\n",
-      "[  1.7689  36.6016  26.4936 105.07  ]\n",
-      "[  3.5378  73.2032  54.9822 203.357 ]\n",
-      "[  5.3067 109.8048  83.4708 301.644 ]\n",
-      "[  7.0756 146.4064 111.9594 399.931 ]\n",
-      "[  8.8445 183.008  138.453  505.001 ]\n",
-      "[ 10.6134 219.6096 166.9416 603.288 ]\n",
-      "[ 12.3823 256.2112 193.4352 708.358 ]\n",
-      "[ 14.1512 292.8128 221.9238 806.645 ]\n",
-      "[ 15.9201 329.4144 250.4124 904.932 ]\n",
-      "[  17.689  366.016  278.901 1003.219]\n",
-      "[  19.4579  402.6176  305.3946 1108.289 ]\n",
-      "[  21.2268  439.2192  333.8832 1206.576 ]\n",
-      "[  22.9957  475.8208  360.3768 1311.646 ]\n",
-      "[  24.7646  512.4224  388.8654 1409.933 ]\n",
-      "[  26.5335  549.024   417.354  1508.22  ]\n",
-      "[  28.3024  585.6256  445.8426 1606.507 ]\n",
-      "[  30.0713  622.2272  472.3362 1711.577 ]\n",
-      "[0. 0. 0. 0.]\n",
-      "[1600. 2560. 7440. 7360.]\n",
-      "[ 3200.  5120. 14520. 14240.]\n",
-      "[ 4800.  7680. 21600. 21120.]\n",
-      "[ 6400. 10240. 28680. 28000.]\n",
-      "[ 8000. 12800. 36120. 35360.]\n",
-      "[ 9600. 15360. 43200. 42240.]\n",
-      "[11200. 17920. 50640. 49600.]\n",
-      "[12800. 20480. 57720. 56480.]\n",
-      "[14400. 23040. 64800. 63360.]\n",
-      "[16000. 25600. 71880. 70240.]\n",
-      "[17600. 28160. 79320. 77600.]\n",
-      "[19200. 30720. 86400. 84480.]\n",
-      "[20800. 33280. 93840. 91840.]\n",
-      "[ 22400.  35840. 100920.  98720.]\n",
-      "[ 24000.  38400. 108000. 105600.]\n",
-      "[ 25600.  40960. 115080. 112480.]\n",
-      "[ 27200.  43520. 122520. 119840.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 1.  8. 10. 24.]\n",
-      "[ 2. 16. 21. 46.]\n",
-      "[ 3. 24. 32. 68.]\n",
-      "[ 4. 32. 43. 90.]\n",
-      "[  5.  40.  53. 114.]\n",
-      "[  6.  48.  64. 136.]\n",
-      "[  7.  56.  74. 160.]\n",
-      "[  8.  64.  85. 182.]\n",
-      "[  9.  72.  96. 204.]\n",
-      "[ 10.  80. 107. 226.]\n",
-      "[ 11.  88. 117. 250.]\n",
-      "[ 12.  96. 128. 272.]\n",
-      "[ 13. 104. 138. 296.]\n",
-      "[ 14. 112. 149. 318.]\n",
-      "[ 15. 120. 160. 340.]\n",
-      "[ 16. 128. 171. 362.]\n",
-      "[ 17. 136. 181. 386.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 64. 176. 368. 496.]\n",
-      "[128. 360. 712. 928.]\n",
-      "[ 192.  544. 1056. 1360.]\n",
-      "[ 256.  728. 1400. 1792.]\n",
-      "[ 320.  904. 1768. 2288.]\n",
-      "[ 384. 1088. 2112. 2720.]\n",
-      "[ 448. 1264. 2480. 3216.]\n",
-      "[ 512. 1448. 2824. 3648.]\n",
-      "[ 576. 1632. 3168. 4080.]\n",
-      "[ 640. 1816. 3512. 4512.]\n",
-      "[ 704. 1992. 3880. 5008.]\n",
-      "[ 768. 2176. 4224. 5440.]\n",
-      "[ 832. 2352. 4592. 5936.]\n",
-      "[ 896. 2536. 4936. 6368.]\n",
-      "[ 960. 2720. 5280. 6800.]\n",
-      "[1024. 2904. 5624. 7232.]\n",
-      "[1088. 3080. 5992. 7728.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 2.3716  8.9936 15.3692 27.2272]\n",
-      "[ 4.7432 17.9872 30.0762 52.0828]\n",
-      "[ 7.1148 26.9808 44.7832 76.9384]\n",
-      "[  9.4864  35.9744  59.4902 101.794 ]\n",
-      "[ 11.858   44.968   74.8594 129.0212]\n",
-      "[ 14.2296  53.9616  89.5664 153.8768]\n",
-      "[ 16.6012  62.9552 104.9356 181.104 ]\n",
-      "[ 18.9728  71.9488 119.6426 205.9596]\n",
-      "[ 21.3444  80.9424 134.3496 230.8152]\n",
-      "[ 23.716   89.936  149.0566 255.6708]\n",
-      "[ 26.0876  98.9296 164.4258 282.898 ]\n",
-      "[ 28.4592 107.9232 179.1328 307.7536]\n",
-      "[ 30.8308 116.9168 194.502  334.9808]\n",
-      "[ 33.2024 125.9104 209.209  359.8364]\n",
-      "[ 35.574 134.904 223.916 384.692]\n",
-      "[ 37.9456 143.8976 238.623  409.5476]\n",
-      "[ 40.3172 152.8912 253.9922 436.7748]\n",
-      "[0. 0. 0. 0.]\n",
-      "[  1.7689  36.6016  26.4936 105.07  ]\n",
-      "[  3.5378  73.2032  54.9822 203.357 ]\n",
-      "[  5.3067 109.8048  83.4708 301.644 ]\n",
-      "[  7.0756 146.4064 111.9594 399.931 ]\n",
-      "[  8.8445 183.008  138.453  505.001 ]\n",
-      "[ 10.6134 219.6096 166.9416 603.288 ]\n",
-      "[ 12.3823 256.2112 193.4352 708.358 ]\n",
-      "[ 14.1512 292.8128 221.9238 806.645 ]\n",
-      "[ 15.9201 329.4144 250.4124 904.932 ]\n",
-      "[  17.689  366.016  278.901 1003.219]\n",
-      "[  19.4579  402.6176  305.3946 1108.289 ]\n",
-      "[  21.2268  439.2192  333.8832 1206.576 ]\n",
-      "[  22.9957  475.8208  360.3768 1311.646 ]\n",
-      "[  24.7646  512.4224  388.8654 1409.933 ]\n",
-      "[  26.5335  549.024   417.354  1508.22  ]\n",
-      "[  28.3024  585.6256  445.8426 1606.507 ]\n",
-      "[  30.0713  622.2272  472.3362 1711.577 ]\n",
-      "[0. 0. 0. 0.]\n",
-      "[1600. 2560. 7440. 7360.]\n",
-      "[ 3200.  5120. 14520. 14240.]\n",
-      "[ 4800.  7680. 21600. 21120.]\n",
-      "[ 6400. 10240. 28680. 28000.]\n",
-      "[ 8000. 12800. 36120. 35360.]\n",
-      "[ 9600. 15360. 43200. 42240.]\n",
-      "[11200. 17920. 50640. 49600.]\n",
-      "[12800. 20480. 57720. 56480.]\n",
-      "[14400. 23040. 64800. 63360.]\n",
-      "[16000. 25600. 71880. 70240.]\n",
-      "[17600. 28160. 79320. 77600.]\n",
-      "[19200. 30720. 86400. 84480.]\n",
-      "[20800. 33280. 93840. 91840.]\n",
-      "[ 22400.  35840. 100920.  98720.]\n",
-      "[ 24000.  38400. 108000. 105600.]\n",
-      "[ 25600.  40960. 115080. 112480.]\n",
-      "[ 27200.  43520. 122520. 119840.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 1.  8. 10. 24.]\n",
-      "[ 2. 16. 21. 46.]\n",
-      "[ 3. 24. 32. 68.]\n",
-      "[ 4. 32. 43. 90.]\n",
-      "[  5.  40.  53. 114.]\n",
-      "[  6.  48.  64. 136.]\n",
-      "[  7.  56.  74. 160.]\n",
-      "[  8.  64.  85. 182.]\n",
-      "[  9.  72.  96. 204.]\n",
-      "[ 10.  80. 107. 226.]\n",
-      "[ 11.  88. 117. 250.]\n",
-      "[ 12.  96. 128. 272.]\n",
-      "[ 13. 104. 138. 296.]\n",
-      "[ 14. 112. 149. 318.]\n",
-      "[ 15. 120. 160. 340.]\n",
-      "[ 16. 128. 171. 362.]\n",
-      "[ 17. 136. 181. 386.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 64. 176. 368. 496.]\n",
-      "[128. 360. 712. 928.]\n",
-      "[ 192.  544. 1056. 1360.]\n",
-      "[ 256.  728. 1400. 1792.]\n",
-      "[ 320.  904. 1768. 2288.]\n",
-      "[ 384. 1088. 2112. 2720.]\n",
-      "[ 448. 1264. 2480. 3216.]\n",
-      "[ 512. 1448. 2824. 3648.]\n",
-      "[ 576. 1632. 3168. 4080.]\n",
-      "[ 640. 1816. 3512. 4512.]\n",
-      "[ 704. 1992. 3880. 5008.]\n",
-      "[ 768. 2176. 4224. 5440.]\n",
-      "[ 832. 2352. 4592. 5936.]\n",
-      "[ 896. 2536. 4936. 6368.]\n",
-      "[ 960. 2720. 5280. 6800.]\n",
-      "[1024. 2904. 5624. 7232.]\n",
-      "[1088. 3080. 5992. 7728.]\n",
-      "[0. 0. 0. 0.]\n",
-      "[ 2.3716  8.9936 15.3692 27.2272]\n",
-      "[ 4.7432 17.9872 30.0762 52.0828]\n",
-      "[ 7.1148 26.9808 44.7832 76.9384]\n",
-      "[  9.4864  35.9744  59.4902 101.794 ]\n",
-      "[ 11.858   44.968   74.8594 129.0212]\n",
-      "[ 14.2296  53.9616  89.5664 153.8768]\n",
-      "[ 16.6012  62.9552 104.9356 181.104 ]\n",
-      "[ 18.9728  71.9488 119.6426 205.9596]\n",
-      "[ 21.3444  80.9424 134.3496 230.8152]\n",
-      "[ 23.716   89.936  149.0566 255.6708]\n",
-      "[ 26.0876  98.9296 164.4258 282.898 ]\n",
-      "[ 28.4592 107.9232 179.1328 307.7536]\n",
-      "[ 30.8308 116.9168 194.502  334.9808]\n",
-      "[ 33.2024 125.9104 209.209  359.8364]\n",
-      "[ 35.574 134.904 223.916 384.692]\n",
-      "[ 37.9456 143.8976 238.623  409.5476]\n",
-      "[ 40.3172 152.8912 253.9922 436.7748]\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "(176, 176)\n"
-     ]
-    }
-   ],
-   "source": [
-    "featurization_list = []\n",
-    "#### Adapt this directory for your use.\n",
-    "featurization_directory = '/Users/<your username>/Desktop/example_MOF/'\n",
-    "\n",
-    "#### Place your clean cif files of interest inside of this directory, under cif/\n",
-    "#### Thus, the path where the cif file should be is: /Users/<your username>/Desktop/example_MOF/cif/\n",
-    "\n",
-    "### The code expects to look for a directory called /cif/ in the example directory\n",
-    "for cif_file in os.listdir(featurization_directory+'/cif/'):\n",
-    "    #### This first part gets the primitive cells ####\n",
-    "    if not os.path.exists(featurization_directory+'/primitive/'):\n",
-    "        os.mkdir(featurization_directory+'/primitive/')\n",
-    "    get_primitive(featurization_directory+'/cif/'+cif_file, featurization_directory+'/primitive/'+cif_file)\n",
-    "    #### With the primitive cells, we can generate descriptors and write them\n",
-    "    full_names, full_descriptors = get_MOF_descriptors(featurization_directory+'/primitive/'+cif_file,3,path=featurization_directory+'/',\n",
-    "        xyzpath=featurization_directory+'/xyz/'+cif_file.replace('cif','xyz'))\n",
-    "    full_names.append('filename')\n",
-    "    full_descriptors.append(cif_file)\n",
-    "    featurization = dict(zip(full_names, full_descriptors))\n",
-    "    featurization_list.append(featurization)\n",
-    "df = pd.DataFrame(featurization_list) \n",
-    "### Write the RACs to the directory. Full featurization frame contains everything.\n",
-    "df.to_csv(featurization_directory+'/full_featurization_frame.csv',index=False) \n",
-    "\n",
-    "\n",
-    "#### The full featurization frame contains all features. \n",
-    "# The following table can help decode features:\n",
-    "# mc --> metal centered products \n",
-    "# D_mc --> metal centered differences\n",
-    "# lc --> linker connecting atom centered products\n",
-    "# D_lc --> linker connecting atom centered differences\n",
-    "# f- --> full MOF unit cell (not used in https://www.nature.com/articles/s41467-020-17755-8)\n",
-    "# f-lig --> full linker RACs\n",
-    "# func --> functional group centered products\n",
-    "# D_func --> functional group centered differences\n",
-    "\n",
-    "# All Zeo++ features should be computed separately."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.6.8"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}

From 450c8dda39173e18bc51354f54700aaa604de31e Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Sat, 16 Dec 2023 20:38:49 -0500
Subject: [PATCH 10/19] Move pymatgen import to get_primitive() function

---
 molSimplify/Informatics/MOF/MOF_descriptors.py            | 5 ++---
 .../MOF/MOF_descriptors_alternate_functional.py           | 8 ++++++--
 molSimplify/Informatics/MOF/cluster_extraction.py         | 2 +-
 tests/informatics/test_MOF_descriptors.py                 | 8 ++++----
 4 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/molSimplify/Informatics/MOF/MOF_descriptors.py b/molSimplify/Informatics/MOF/MOF_descriptors.py
index 6224276b..003e4da0 100644
--- a/molSimplify/Informatics/MOF/MOF_descriptors.py
+++ b/molSimplify/Informatics/MOF/MOF_descriptors.py
@@ -54,7 +54,6 @@
 
 ### Defining pymatgen function for getting primitive, since molSimplify does not depend on pymatgen.
 # This function is commented out and should be uncommented if used.
-from pymatgen.io.cif import CifParser
 
 
 def get_primitive(datapath, writepath, occupancy_tolerance=1):
@@ -75,10 +74,10 @@ def get_primitive(datapath, writepath, occupancy_tolerance=1):
     None
 
     """
-
+    from pymatgen.io.cif import CifParser
     s = CifParser(datapath, occupancy_tolerance=occupancy_tolerance).get_structures()[0]
     sprim = s.get_primitive_structure()
-    sprim.to("cif", writepath)  # Output structure to a file.
+    sprim.to(writepath, "cif")  # Output structure to a file.
 
 
 '''<<<< END OF CODE TO COMPUTE PRIMITIVE UNIT CELLS >>>>'''
diff --git a/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py b/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py
index ede9df0d..bc5a42ec 100644
--- a/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py
+++ b/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py
@@ -23,11 +23,15 @@
 # This MOF RAC generator assumes that pymatgen is installed.                            #
 # Pymatgen is used to get the primitive cell.                                           #
 #########################################################################################
-from pymatgen.io.cif import CifParser
+
+
 def get_primitive(datapath, writepath):
+    from pymatgen.io.cif import CifParser
     s = CifParser(datapath, occupancy_tolerance=1).get_structures()[0]
     sprim = s.get_primitive_structure()
-    sprim.to("cif",writepath)
+    sprim.to("cif", writepath)
+
+
 '''<<<< END OF CODE TO COMPUTE PRIMITIVE UNIT CELLS >>>>'''
 
 #########################################################################################
diff --git a/molSimplify/Informatics/MOF/cluster_extraction.py b/molSimplify/Informatics/MOF/cluster_extraction.py
index 747ce665..f7941db5 100644
--- a/molSimplify/Informatics/MOF/cluster_extraction.py
+++ b/molSimplify/Informatics/MOF/cluster_extraction.py
@@ -19,10 +19,10 @@
 # This MOF RAC generator assumes that pymatgen is installed.                            #
 # Pymatgen is used to get the primitive cell.                                           #
 #########################################################################################
-from pymatgen.io.cif import CifParser
 
 
 def get_primitive(datapath, writepath):
+    from pymatgen.io.cif import CifParser
     s = CifParser(datapath, occupancy_tolerance=1).get_structures()[0]
     sprim = s.get_primitive_structure()
     sprim.to("cif", writepath)
diff --git a/tests/informatics/test_MOF_descriptors.py b/tests/informatics/test_MOF_descriptors.py
index 22bc518a..510012b7 100644
--- a/tests/informatics/test_MOF_descriptors.py
+++ b/tests/informatics/test_MOF_descriptors.py
@@ -33,16 +33,16 @@ def RACs_names(starts, properties, depth, scope="all"):
 
 
 @pytest.mark.parametrize(
-    "name",
+    "cif_file",
     ["odac-21383.cif",
      "odac-21433.cif",
      "odac-21478.cif",
      "odac-21735.cif",
      "odac-21816.cif"])
-def test_get_MOF_descriptors(resource_path_root, tmpdir, name, ref_names):
+def test_get_MOF_descriptors(resource_path_root, tmpdir, cif_file, ref_names):
     with DebugTimer("get_MOF_descriptors()"):
         full_names, full_descriptors = get_MOF_descriptors(
-            str(resource_path_root / "inputs" / "cif_files" / name),
+            str(resource_path_root / "inputs" / "cif_files" / cif_file),
             depth=3,
             path=str(tmpdir),
             xyzpath=str(tmpdir / "test.xyz"),
@@ -50,7 +50,7 @@ def test_get_MOF_descriptors(resource_path_root, tmpdir, name, ref_names):
         )
 
     with open(resource_path_root / "refs" / "MOF_descriptors"
-              / name.replace("cif", "json"), "r") as fin:
+              / cif_file.replace("cif", "json"), "r") as fin:
         ref = json.load(fin)
 
     assert full_names == ref_names

From 8f3ed8fe1c51f6c291ffd11e1ac5e484604cb805 Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Sun, 17 Dec 2023 14:23:18 -0500
Subject: [PATCH 11/19] Added more type hints

---
 molSimplify/Informatics/MOF/MOF_descriptors.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/molSimplify/Informatics/MOF/MOF_descriptors.py b/molSimplify/Informatics/MOF/MOF_descriptors.py
index 003e4da0..83027ce2 100644
--- a/molSimplify/Informatics/MOF/MOF_descriptors.py
+++ b/molSimplify/Informatics/MOF/MOF_descriptors.py
@@ -5,6 +5,7 @@
 from scipy import sparse
 import numpy as np
 import pandas as pd
+from typing import Tuple, List, Dict
 from molSimplify.Classes.atom3D import atom3D
 from molSimplify.Classes.mol3D import mol3D
 from molSimplify.Scripts.cellbuilder_tools import import_from_cif
@@ -83,7 +84,7 @@ def get_primitive(datapath, writepath, occupancy_tolerance=1):
 '''<<<< END OF CODE TO COMPUTE PRIMITIVE UNIT CELLS >>>>'''
 
 
-def load_sbu_lc_descriptors(sbupath):
+def load_sbu_lc_descriptors(sbupath: str) -> Tuple[str, pd.DataFrame, pd.DataFrame]:
     """
     Loads the sbu and lc descriptors.
 
@@ -101,19 +102,21 @@ def load_sbu_lc_descriptors(sbupath):
 
     """
     sbu_descriptor_path = os.path.dirname(sbupath)
-    if os.path.getsize(sbu_descriptor_path+'/sbu_descriptors.csv') > 0:  # Checking if there is a file there.
-        sbu_descriptors = pd.read_csv(sbu_descriptor_path+'/sbu_descriptors.csv')
+    if os.path.getsize(sbu_descriptor_path + '/sbu_descriptors.csv') > 0:  # Checking if there is a file there.
+        sbu_descriptors = pd.read_csv(sbu_descriptor_path + '/sbu_descriptors.csv')
     else:
         sbu_descriptors = pd.DataFrame()
-    if os.path.getsize(sbu_descriptor_path+'/lc_descriptors.csv') > 0:  # Checking if there is a file there.
-        lc_descriptors = pd.read_csv(sbu_descriptor_path+'/lc_descriptors.csv')
+    if os.path.getsize(sbu_descriptor_path + '/lc_descriptors.csv') > 0:  # Checking if there is a file there.
+        lc_descriptors = pd.read_csv(sbu_descriptor_path + '/lc_descriptors.csv')
     else:
         lc_descriptors = pd.DataFrame()
 
     return sbu_descriptor_path, sbu_descriptors, lc_descriptors
 
 
-def gen_and_append_desc(temp_mol, target_list, depth, descriptor_names, descriptors, Gval, feature_type):
+def gen_and_append_desc(
+        temp_mol: mol3D, target_list, depth: int, descriptor_names: List[str],
+        descriptors: List[float], Gval: bool, feature_type: str) -> Tuple[Dict, List[str], List[float]]:
     """
     Generate and append descriptors, both standard and delta.
 

From 877481dcc9e61557801fbaeb442dd2a9b2bf719d Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Sun, 17 Dec 2023 15:15:35 -0500
Subject: [PATCH 12/19] Convert .cif files to primitive unit cell

---
 .../inputs/cif_files/odac-21383.cif           | 519 +++++------
 .../inputs/cif_files/odac-21433.cif           | 335 +++----
 .../inputs/cif_files/odac-21478.cif           | 415 ++++-----
 .../inputs/cif_files/odac-21735.cif           | 275 +++---
 .../inputs/cif_files/odac-21816.cif           | 831 +++++++++---------
 5 files changed, 1190 insertions(+), 1185 deletions(-)

diff --git a/tests/testresources/inputs/cif_files/odac-21383.cif b/tests/testresources/inputs/cif_files/odac-21383.cif
index 1d3ed003..c226c1d5 100644
--- a/tests/testresources/inputs/cif_files/odac-21383.cif
+++ b/tests/testresources/inputs/cif_files/odac-21383.cif
@@ -1,261 +1,262 @@
-data_image0
-_chemical_formula_structural       Ga36P36O148F16
-_chemical_formula_sum              "Ga36 P36 O148 F16"
-_cell_length_a       17.7002
-_cell_length_b       32.7061
-_cell_length_c       10.1684
-_cell_angle_alpha    90
-_cell_angle_beta     90
-_cell_angle_gamma    90
-
-_space_group_name_H-M_alt    "P 1"
-_space_group_IT_number       1
-
+# generated using pymatgen
+data_Ga9P9O37F4
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   10.16840000
+_cell_length_b   17.70020000
+_cell_length_c   32.70610000
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Ga9P9O37F4
+_chemical_formula_sum   'Ga36 P36 O148 F16'
+_cell_volume   5886.53263189
+_cell_formula_units_Z   4
 loop_
-  _space_group_symop_operation_xyz
-  'x, y, z'
-
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
 loop_
-  _atom_site_type_symbol
-  _atom_site_label
-  _atom_site_symmetry_multiplicity
-  _atom_site_fract_x
-  _atom_site_fract_y
-  _atom_site_fract_z
-  _atom_site_occupancy
-  Ga  Ga1       1.0  0.43059  0.92287  0.05643  1.0000
-  Ga  Ga2       1.0  0.48410  0.02595  0.02197  1.0000
-  Ga  Ga3       1.0  0.15815  0.98867  0.88183  1.0000
-  Ga  Ga4       1.0  0.34659  0.50676  0.58670  1.0000
-  Ga  Ga5       1.0  0.08393  0.57961  0.42319  1.0000
-  Ga  Ga6       1.0  0.02252  0.47611  0.45525  1.0000
-  Ga  Ga7       1.0  0.34114  0.66620  0.58927  1.0000
-  Ga  Ga8       1.0  0.17185  0.82627  0.88792  1.0000
-  Ga  Ga9       1.0  0.30408  0.75647  0.92147  1.0000
-  Ga  Ga10      1.0  0.57037  0.07744  0.55502  1.0000
-  Ga  Ga11      1.0  0.51611  0.97446  0.52138  1.0000
-  Ga  Ga12      1.0  0.84196  0.01129  0.38288  1.0000
-  Ga  Ga13      1.0  0.65341  0.49313  0.08664  1.0000
-  Ga  Ga14      1.0  0.91594  0.42029  0.92329  1.0000
-  Ga  Ga15      1.0  0.97747  0.52383  0.95523  1.0000
-  Ga  Ga16      1.0  0.65877  0.33342  0.08974  1.0000
-  Ga  Ga17      1.0  0.82830  0.17378  0.38821  1.0000
-  Ga  Ga18      1.0  0.69648  0.24360  0.42307  1.0000
-  Ga  Ga19      1.0  0.92996  0.07736  0.05544  1.0000
-  Ga  Ga20      1.0  0.98407  0.97427  0.02212  1.0000
-  Ga  Ga21      1.0  0.65807  0.01135  0.88314  1.0000
-  Ga  Ga22      1.0  0.84658  0.49311  0.58664  1.0000
-  Ga  Ga23      1.0  0.58408  0.42027  0.42331  1.0000
-  Ga  Ga24      1.0  0.52254  0.52381  0.45523  1.0000
-  Ga  Ga25      1.0  0.84123  0.33342  0.58976  1.0000
-  Ga  Ga26      1.0  0.67187  0.17378  0.88815  1.0000
-  Ga  Ga27      1.0  0.80356  0.24360  0.92309  1.0000
-  Ga  Ga28      1.0  0.07041  0.92272  0.55490  1.0000
-  Ga  Ga29      1.0  0.01582  0.02574  0.52223  1.0000
-  Ga  Ga30      1.0  0.34172  0.98885  0.38206  1.0000
-  Ga  Ga31      1.0  0.15340  0.50686  0.08665  1.0000
-  Ga  Ga32      1.0  0.41599  0.57969  0.92325  1.0000
-  Ga  Ga33      1.0  0.47749  0.47615  0.95522  1.0000
-  Ga  Ga34      1.0  0.15876  0.66660  0.08951  1.0000
-  Ga  Ga35      1.0  0.32817  0.82575  0.38620  1.0000
-  Ga  Ga36      1.0  0.19617  0.75627  0.42252  1.0000
-  P   P1        1.0  0.31337  0.99434  0.05803  1.0000
-  P   P2        1.0  0.52467  0.95466  0.82822  1.0000
-  P   P3        1.0  0.06651  0.90510  0.84888  1.0000
-  P   P4        1.0  0.98376  0.54782  0.64882  1.0000
-  P   P5        1.0  0.19351  0.50343  0.40645  1.0000
-  P   P6        1.0  0.43845  0.59028  0.62901  1.0000
-  P   P7        1.0  0.34400  0.75646  0.60991  1.0000
-  P   P8        1.0  0.32414  0.83918  0.05928  1.0000
-  P   P9        1.0  0.30802  0.66116  0.89815  1.0000
-  P   P10       1.0  0.68688  0.00560  0.55914  1.0000
-  P   P11       1.0  0.47548  0.04576  0.32815  1.0000
-  P   P12       1.0  0.93349  0.09497  0.34958  1.0000
-  P   P13       1.0  0.01619  0.45214  0.14882  1.0000
-  P   P14       1.0  0.80646  0.49652  0.90645  1.0000
-  P   P15       1.0  0.56162  0.40957  0.12895  1.0000
-  P   P16       1.0  0.65635  0.24318  0.11197  1.0000
-  P   P17       1.0  0.67615  0.16085  0.56051  1.0000
-  P   P18       1.0  0.69209  0.33884  0.39813  1.0000
-  P   P19       1.0  0.81321  0.00562  0.05928  1.0000
-  P   P20       1.0  0.02477  0.04560  0.82869  1.0000
-  P   P21       1.0  0.56658  0.09505  0.84935  1.0000
-  P   P22       1.0  0.48383  0.45210  0.64886  1.0000
-  P   P23       1.0  0.69355  0.49651  0.40640  1.0000
-  P   P24       1.0  0.93839  0.40956  0.62898  1.0000
-  P   P25       1.0  0.84372  0.24318  0.61195  1.0000
-  P   P26       1.0  0.82395  0.16081  0.06056  1.0000
-  P   P27       1.0  0.80794  0.33884  0.89816  1.0000
-  P   P28       1.0  0.18650  0.99472  0.55712  1.0000
-  P   P29       1.0  0.97498  0.95435  0.32876  1.0000
-  P   P30       1.0  0.43347  0.90507  0.34924  1.0000
-  P   P31       1.0  0.51619  0.54784  0.14887  1.0000
-  P   P32       1.0  0.30646  0.50345  0.90646  1.0000
-  P   P33       1.0  0.06160  0.59043  0.12887  1.0000
-  P   P34       1.0  0.15658  0.75695  0.11105  1.0000
-  P   P35       1.0  0.17591  0.83898  0.55953  1.0000
-  P   P36       1.0  0.19176  0.66107  0.39794  1.0000
-  O   O1        1.0  0.36930  0.56124  0.63882  1.0000
-  O   O2        1.0  0.13538  0.93385  0.83366  1.0000
-  O   O3        1.0  0.13323  0.47188  0.45118  1.0000
-  O   O4        1.0  0.35030  0.77223  0.75240  1.0000
-  O   O5        1.0  0.02578  0.50758  0.62007  1.0000
-  O   O6        1.0  0.20934  0.77214  0.83963  1.0000
-  O   O7        1.0  0.37244  0.02727  0.02004  1.0000
-  O   O8        1.0  0.48241  0.99468  0.85946  1.0000
-  O   O9        1.0  0.26051  0.74525  0.58022  1.0000
-  O   O10       1.0  0.25240  0.85096  0.98186  1.0000
-  O   O11       1.0  0.26725  0.49188  0.47540  1.0000
-  O   O12       1.0  0.34503  0.70353  0.92025  1.0000
-  O   O13       1.0  0.24142  0.00420  0.98193  1.0000
-  O   O14       1.0  0.00114  0.92187  0.93177  1.0000
-  O   O15       1.0  0.35517  0.79645  0.02209  1.0000
-  O   O16       1.0  0.50873  0.57242  0.56275  1.0000
-  O   O17       1.0  0.49419  0.91819  0.90872  1.0000
-  O   O18       1.0  0.02066  0.58375  0.57395  1.0000
-  O   O19       1.0  0.61031  0.95927  0.85926  1.0000
-  O   O20       1.0  0.33849  0.95034  0.02262  1.0000
-  O   O21       1.0  0.17320  0.54790  0.44401  1.0000
-  O   O22       1.0  0.89885  0.54430  0.60927  1.0000
-  O   O23       1.0  0.29692  0.65271  0.74928  1.0000
-  O   O24       1.0  0.51714  0.94311  0.68271  1.0000
-  O   O25       1.0  0.29712  0.99885  0.20677  1.0000
-  O   O26       1.0  0.20409  0.49766  0.25662  1.0000
-  O   O27       1.0  0.30596  0.84210  0.20712  1.0000
-  O   O28       1.0  0.45944  0.60410  0.77088  1.0000
-  O   O29       1.0  0.98309  0.55794  0.79664  1.0000
-  O   O30       1.0  0.41696  0.62880  0.54922  1.0000
-  O   O31       1.0  0.03144  0.89719  0.71005  1.0000
-  O   O32       1.0  0.09016  0.86348  0.90607  1.0000
-  O   O33       1.0  0.38689  0.86952  0.02345  1.0000
-  O   O34       1.0  0.35971  0.62936  0.96217  1.0000
-  O   O35       1.0  0.37646  0.78989  0.51811  1.0000
-  O   O36       1.0  0.22762  0.65917  0.95502  1.0000
-  O   O37       1.0  0.39109  0.71673  0.59096  1.0000
-  O   O38       1.0  0.63080  0.43859  0.13845  1.0000
-  O   O39       1.0  0.86463  0.06617  0.33478  1.0000
-  O   O40       1.0  0.86677  0.52806  0.95121  1.0000
-  O   O41       1.0  0.65035  0.22706  0.25425  1.0000
-  O   O42       1.0  0.97419  0.49239  0.12012  1.0000
-  O   O43       1.0  0.79109  0.22794  0.34040  1.0000
-  O   O44       1.0  0.62792  0.97264  0.52061  1.0000
-  O   O45       1.0  0.51828  0.00588  0.35879  1.0000
-  O   O46       1.0  0.73962  0.25472  0.08150  1.0000
-  O   O47       1.0  0.74868  0.14943  0.48499  1.0000
-  O   O48       1.0  0.73273  0.50809  0.97540  1.0000
-  O   O49       1.0  0.65515  0.29645  0.42014  1.0000
-  O   O50       1.0  0.75906  0.99570  0.48383  1.0000
-  O   O51       1.0  0.99891  0.07817  0.43222  1.0000
-  O   O52       1.0  0.64543  0.20379  0.52464  1.0000
-  O   O53       1.0  0.49140  0.42745  0.06253  1.0000
-  O   O54       1.0  0.50551  0.08228  0.40883  1.0000
-  O   O55       1.0  0.97927  0.41620  0.07401  1.0000
-  O   O56       1.0  0.38972  0.04098  0.35840  1.0000
-  O   O57       1.0  0.66225  0.04962  0.52348  1.0000
-  O   O58       1.0  0.82674  0.45206  0.94402  1.0000
-  O   O59       1.0  0.10110  0.45567  0.10921  1.0000
-  O   O60       1.0  0.70310  0.34730  0.24929  1.0000
-  O   O61       1.0  0.48190  0.05759  0.18258  1.0000
-  O   O62       1.0  0.70271  0.00112  0.70804  1.0000
-  O   O63       1.0  0.79589  0.50230  0.75663  1.0000
-  O   O64       1.0  0.69299  0.15733  0.70856  1.0000
-  O   O65       1.0  0.54054  0.39589  0.27094  1.0000
-  O   O66       1.0  0.01692  0.44200  0.29663  1.0000
-  O   O67       1.0  0.58300  0.37090  0.04979  1.0000
-  O   O68       1.0  0.96869  0.10281  0.21083  1.0000
-  O   O69       1.0  0.90998  0.13662  0.40655  1.0000
-  O   O70       1.0  0.61388  0.13072  0.52021  1.0000
-  O   O71       1.0  0.64035  0.37061  0.46216  1.0000
-  O   O72       1.0  0.62400  0.20954  0.02083  1.0000
-  O   O73       1.0  0.77248  0.34088  0.45509  1.0000
-  O   O74       1.0  0.60895  0.28284  0.09347  1.0000
-  O   O75       1.0  0.86921  0.43858  0.63850  1.0000
-  O   O76       1.0  0.63547  0.06626  0.83488  1.0000
-  O   O77       1.0  0.63325  0.52804  0.45116  1.0000
-  O   O78       1.0  0.84968  0.22707  0.75423  1.0000
-  O   O79       1.0  0.52585  0.49234  0.62010  1.0000
-  O   O80       1.0  0.70899  0.22793  0.84042  1.0000
-  O   O81       1.0  0.87235  0.97278  0.02073  1.0000
-  O   O82       1.0  0.98231  0.00562  0.85957  1.0000
-  O   O83       1.0  0.76046  0.25473  0.58146  1.0000
-  O   O84       1.0  0.75143  0.14937  0.98501  1.0000
-  O   O85       1.0  0.76727  0.50808  0.47539  1.0000
-  O   O86       1.0  0.84486  0.29644  0.92017  1.0000
-  O   O87       1.0  0.74119  0.99564  0.98348  1.0000
-  O   O88       1.0  0.50101  0.07834  0.93188  1.0000
-  O   O89       1.0  0.85465  0.20374  0.02451  1.0000
-  O   O90       1.0  0.00861  0.42743  0.56256  1.0000
-  O   O91       1.0  0.99443  0.08214  0.90892  1.0000
-  O   O92       1.0  0.52079  0.41616  0.57408  1.0000
-  O   O93       1.0  0.11043  0.04089  0.85990  1.0000
-  O   O94       1.0  0.83796  0.04964  0.02387  1.0000
-  O   O95       1.0  0.67328  0.45204  0.44394  1.0000
-  O   O96       1.0  0.39893  0.45560  0.60918  1.0000
-  O   O97       1.0  0.79690  0.34730  0.74932  1.0000
-  O   O98       1.0  0.01811  0.05723  0.68309  1.0000
-  O   O99       1.0  0.79723  0.00104  0.20807  1.0000
-  O   O100      1.0  0.70412  0.50230  0.25658  1.0000
-  O   O101      1.0  0.80705  0.15737  0.20863  1.0000
-  O   O102      1.0  0.95948  0.39588  0.77098  1.0000
-  O   O103      1.0  0.48312  0.44200  0.79669  1.0000
-  O   O104      1.0  0.91700  0.37090  0.54982  1.0000
-  O   O105      1.0  0.53158  0.10289  0.71045  1.0000
-  O   O106      1.0  0.59001  0.13674  0.90626  1.0000
-  O   O107      1.0  0.88625  0.13064  0.02064  1.0000
-  O   O108      1.0  0.85968  0.37061  0.96216  1.0000
-  O   O109      1.0  0.87609  0.20956  0.52077  1.0000
-  O   O110      1.0  0.72755  0.34089  0.95513  1.0000
-  O   O111      1.0  0.89111  0.28285  0.59352  1.0000
-  O   O112      1.0  0.13077  0.56141  0.13839  1.0000
-  O   O113      1.0  0.36486  0.93401  0.33335  1.0000
-  O   O114      1.0  0.36679  0.47193  0.95124  1.0000
-  O   O115      1.0  0.15043  0.77288  0.25355  1.0000
-  O   O116      1.0  0.47419  0.50759  0.12012  1.0000
-  O   O117      1.0  0.29075  0.77159  0.33906  1.0000
-  O   O118      1.0  0.12760  0.02776  0.51858  1.0000
-  O   O119      1.0  0.01726  0.99438  0.35953  1.0000
-  O   O120      1.0  0.23993  0.74567  0.08037  1.0000
-  O   O121      1.0  0.24902  0.85001  0.48481  1.0000
-  O   O122      1.0  0.23275  0.49191  0.97548  1.0000
-  O   O123      1.0  0.15479  0.70345  0.41987  1.0000
-  O   O124      1.0  0.25878  0.00476  0.48239  1.0000
-  O   O125      1.0  0.49850  0.92183  0.43293  1.0000
-  O   O126      1.0  0.14485  0.79620  0.52319  1.0000
-  O   O127      1.0  0.99139  0.57256  0.06240  1.0000
-  O   O128      1.0  0.00537  0.91783  0.40898  1.0000
-  O   O129      1.0  0.47925  0.58378  0.07409  1.0000
-  O   O130      1.0  0.88932  0.95902  0.35999  1.0000
-  O   O131      1.0  0.16143  0.95090  0.52064  1.0000
-  O   O132      1.0  0.32676  0.54793  0.94387  1.0000
-  O   O133      1.0  0.60110  0.54432  0.10925  1.0000
-  O   O134      1.0  0.20291  0.65263  0.24910  1.0000
-  O   O135      1.0  0.98165  0.94277  0.18305  1.0000
-  O   O136      1.0  0.20119  0.99946  0.70616  1.0000
-  O   O137      1.0  0.29586  0.49760  0.75667  1.0000
-  O   O138      1.0  0.19274  0.84238  0.70777  1.0000
-  O   O139      1.0  0.04040  0.60406  0.27087  1.0000
-  O   O140      1.0  0.51691  0.55794  0.29670  1.0000
-  O   O141      1.0  0.08297  0.62912  0.04986  1.0000
-  O   O142      1.0  0.46941  0.89718  0.21113  1.0000
-  O   O143      1.0  0.40903  0.86353  0.40577  1.0000
-  O   O144      1.0  0.11446  0.86961  0.51959  1.0000
-  O   O145      1.0  0.13998  0.62932  0.46198  1.0000
-  O   O146      1.0  0.12400  0.79067  0.02045  1.0000
-  O   O147      1.0  0.27211  0.65893  0.45496  1.0000
-  O   O148      1.0  0.10925  0.71727  0.09222  1.0000
-  F   F1        1.0  0.59454  0.01931  0.03888  1.0000
-  F   F2        1.0  0.03282  0.52842  0.36063  1.0000
-  F   F3        1.0  0.47617  0.97356  0.12043  1.0000
-  F   F4        1.0  0.41305  0.51613  0.43540  1.0000
-  F   F5        1.0  0.40605  0.98157  0.53697  1.0000
-  F   F6        1.0  0.96715  0.47151  0.86070  1.0000
-  F   F7        1.0  0.52466  0.02671  0.61962  1.0000
-  F   F8        1.0  0.58697  0.48383  0.93532  1.0000
-  F   F9        1.0  0.09449  0.98073  0.03817  1.0000
-  F   F10       1.0  0.53286  0.47150  0.36075  1.0000
-  F   F11       1.0  0.97607  0.02672  0.11986  1.0000
-  F   F12       1.0  0.91305  0.48380  0.43533  1.0000
-  F   F13       1.0  0.90545  0.01913  0.53909  1.0000
-  F   F14       1.0  0.46722  0.52847  0.86074  1.0000
-  F   F15       1.0  0.02440  0.97339  0.61988  1.0000
-  F   F16       1.0  0.08695  0.51615  0.93532  1.0000
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Ga  Ga0  1  0.05643000  0.43059000  0.92287000  1.0
+  Ga  Ga1  1  0.02197000  0.48410000  0.02595000  1.0
+  Ga  Ga2  1  0.88183000  0.15815000  0.98867000  1.0
+  Ga  Ga3  1  0.58670000  0.34659000  0.50676000  1.0
+  Ga  Ga4  1  0.42319000  0.08393000  0.57961000  1.0
+  Ga  Ga5  1  0.45525000  0.02252000  0.47611000  1.0
+  Ga  Ga6  1  0.58927000  0.34114000  0.66620000  1.0
+  Ga  Ga7  1  0.88792000  0.17185000  0.82627000  1.0
+  Ga  Ga8  1  0.92147000  0.30408000  0.75647000  1.0
+  Ga  Ga9  1  0.55502000  0.57037000  0.07744000  1.0
+  Ga  Ga10  1  0.52138000  0.51611000  0.97446000  1.0
+  Ga  Ga11  1  0.38288000  0.84196000  0.01129000  1.0
+  Ga  Ga12  1  0.08664000  0.65341000  0.49313000  1.0
+  Ga  Ga13  1  0.92329000  0.91594000  0.42029000  1.0
+  Ga  Ga14  1  0.95523000  0.97747000  0.52383000  1.0
+  Ga  Ga15  1  0.08974000  0.65877000  0.33342000  1.0
+  Ga  Ga16  1  0.38821000  0.82830000  0.17378000  1.0
+  Ga  Ga17  1  0.42307000  0.69648000  0.24360000  1.0
+  Ga  Ga18  1  0.05544000  0.92996000  0.07736000  1.0
+  Ga  Ga19  1  0.02212000  0.98407000  0.97427000  1.0
+  Ga  Ga20  1  0.88314000  0.65807000  0.01135000  1.0
+  Ga  Ga21  1  0.58664000  0.84658000  0.49311000  1.0
+  Ga  Ga22  1  0.42331000  0.58408000  0.42027000  1.0
+  Ga  Ga23  1  0.45523000  0.52254000  0.52381000  1.0
+  Ga  Ga24  1  0.58976000  0.84123000  0.33342000  1.0
+  Ga  Ga25  1  0.88815000  0.67187000  0.17378000  1.0
+  Ga  Ga26  1  0.92309000  0.80356000  0.24360000  1.0
+  Ga  Ga27  1  0.55490000  0.07041000  0.92272000  1.0
+  Ga  Ga28  1  0.52223000  0.01582000  0.02574000  1.0
+  Ga  Ga29  1  0.38206000  0.34172000  0.98885000  1.0
+  Ga  Ga30  1  0.08665000  0.15340000  0.50686000  1.0
+  Ga  Ga31  1  0.92325000  0.41599000  0.57969000  1.0
+  Ga  Ga32  1  0.95522000  0.47749000  0.47615000  1.0
+  Ga  Ga33  1  0.08951000  0.15876000  0.66666667  1.0
+  Ga  Ga34  1  0.38620000  0.32817000  0.82575000  1.0
+  Ga  Ga35  1  0.42252000  0.19617000  0.75627000  1.0
+  P  P36  1  0.05803000  0.31337000  0.99434000  1.0
+  P  P37  1  0.82822000  0.52467000  0.95466000  1.0
+  P  P38  1  0.84888000  0.06651000  0.90510000  1.0
+  P  P39  1  0.64882000  0.98376000  0.54782000  1.0
+  P  P40  1  0.40645000  0.19351000  0.50343000  1.0
+  P  P41  1  0.62901000  0.43845000  0.59028000  1.0
+  P  P42  1  0.60991000  0.34400000  0.75646000  1.0
+  P  P43  1  0.05928000  0.32414000  0.83918000  1.0
+  P  P44  1  0.89815000  0.30802000  0.66116000  1.0
+  P  P45  1  0.55914000  0.68688000  0.00560000  1.0
+  P  P46  1  0.32815000  0.47548000  0.04576000  1.0
+  P  P47  1  0.34958000  0.93349000  0.09497000  1.0
+  P  P48  1  0.14882000  0.01619000  0.45214000  1.0
+  P  P49  1  0.90645000  0.80646000  0.49652000  1.0
+  P  P50  1  0.12895000  0.56162000  0.40957000  1.0
+  P  P51  1  0.11197000  0.65635000  0.24318000  1.0
+  P  P52  1  0.56051000  0.67615000  0.16085000  1.0
+  P  P53  1  0.39813000  0.69209000  0.33884000  1.0
+  P  P54  1  0.05928000  0.81321000  0.00562000  1.0
+  P  P55  1  0.82869000  0.02477000  0.04560000  1.0
+  P  P56  1  0.84935000  0.56658000  0.09505000  1.0
+  P  P57  1  0.64886000  0.48383000  0.45210000  1.0
+  P  P58  1  0.40640000  0.69355000  0.49651000  1.0
+  P  P59  1  0.62898000  0.93839000  0.40956000  1.0
+  P  P60  1  0.61195000  0.84372000  0.24318000  1.0
+  P  P61  1  0.06056000  0.82395000  0.16081000  1.0
+  P  P62  1  0.89816000  0.80794000  0.33884000  1.0
+  P  P63  1  0.55712000  0.18650000  0.99472000  1.0
+  P  P64  1  0.32876000  0.97498000  0.95435000  1.0
+  P  P65  1  0.34924000  0.43347000  0.90507000  1.0
+  P  P66  1  0.14887000  0.51619000  0.54784000  1.0
+  P  P67  1  0.90646000  0.30646000  0.50345000  1.0
+  P  P68  1  0.12887000  0.06160000  0.59043000  1.0
+  P  P69  1  0.11105000  0.15658000  0.75695000  1.0
+  P  P70  1  0.55953000  0.17591000  0.83898000  1.0
+  P  P71  1  0.39794000  0.19176000  0.66107000  1.0
+  O  O72  1  0.63882000  0.36930000  0.56124000  1.0
+  O  O73  1  0.83366000  0.13538000  0.93385000  1.0
+  O  O74  1  0.45118000  0.13323000  0.47188000  1.0
+  O  O75  1  0.75240000  0.35030000  0.77223000  1.0
+  O  O76  1  0.62007000  0.02578000  0.50758000  1.0
+  O  O77  1  0.83963000  0.20934000  0.77214000  1.0
+  O  O78  1  0.02004000  0.37244000  0.02727000  1.0
+  O  O79  1  0.85946000  0.48241000  0.99468000  1.0
+  O  O80  1  0.58022000  0.26051000  0.74525000  1.0
+  O  O81  1  0.98186000  0.25240000  0.85096000  1.0
+  O  O82  1  0.47540000  0.26725000  0.49188000  1.0
+  O  O83  1  0.92025000  0.34503000  0.70353000  1.0
+  O  O84  1  0.98193000  0.24142000  0.00420000  1.0
+  O  O85  1  0.93177000  0.00114000  0.92187000  1.0
+  O  O86  1  0.02209000  0.35517000  0.79645000  1.0
+  O  O87  1  0.56275000  0.50873000  0.57242000  1.0
+  O  O88  1  0.90872000  0.49419000  0.91819000  1.0
+  O  O89  1  0.57395000  0.02066000  0.58375000  1.0
+  O  O90  1  0.85926000  0.61031000  0.95927000  1.0
+  O  O91  1  0.02262000  0.33849000  0.95034000  1.0
+  O  O92  1  0.44401000  0.17320000  0.54790000  1.0
+  O  O93  1  0.60927000  0.89885000  0.54430000  1.0
+  O  O94  1  0.74928000  0.29692000  0.65271000  1.0
+  O  O95  1  0.68271000  0.51714000  0.94311000  1.0
+  O  O96  1  0.20677000  0.29712000  0.99885000  1.0
+  O  O97  1  0.25662000  0.20409000  0.49766000  1.0
+  O  O98  1  0.20712000  0.30596000  0.84210000  1.0
+  O  O99  1  0.77088000  0.45944000  0.60410000  1.0
+  O  O100  1  0.79664000  0.98309000  0.55794000  1.0
+  O  O101  1  0.54922000  0.41696000  0.62880000  1.0
+  O  O102  1  0.71005000  0.03144000  0.89719000  1.0
+  O  O103  1  0.90607000  0.09016000  0.86348000  1.0
+  O  O104  1  0.02345000  0.38689000  0.86952000  1.0
+  O  O105  1  0.96217000  0.35971000  0.62936000  1.0
+  O  O106  1  0.51811000  0.37646000  0.78989000  1.0
+  O  O107  1  0.95502000  0.22762000  0.65917000  1.0
+  O  O108  1  0.59096000  0.39109000  0.71673000  1.0
+  O  O109  1  0.13845000  0.63080000  0.43859000  1.0
+  O  O110  1  0.33478000  0.86463000  0.06617000  1.0
+  O  O111  1  0.95121000  0.86677000  0.52806000  1.0
+  O  O112  1  0.25425000  0.65035000  0.22706000  1.0
+  O  O113  1  0.12012000  0.97419000  0.49239000  1.0
+  O  O114  1  0.34040000  0.79109000  0.22794000  1.0
+  O  O115  1  0.52061000  0.62792000  0.97264000  1.0
+  O  O116  1  0.35879000  0.51828000  0.00588000  1.0
+  O  O117  1  0.08150000  0.73962000  0.25472000  1.0
+  O  O118  1  0.48499000  0.74868000  0.14943000  1.0
+  O  O119  1  0.97540000  0.73273000  0.50809000  1.0
+  O  O120  1  0.42014000  0.65515000  0.29645000  1.0
+  O  O121  1  0.48383000  0.75906000  0.99570000  1.0
+  O  O122  1  0.43222000  0.99891000  0.07817000  1.0
+  O  O123  1  0.52464000  0.64543000  0.20379000  1.0
+  O  O124  1  0.06253000  0.49140000  0.42745000  1.0
+  O  O125  1  0.40883000  0.50551000  0.08228000  1.0
+  O  O126  1  0.07401000  0.97927000  0.41620000  1.0
+  O  O127  1  0.35840000  0.38972000  0.04098000  1.0
+  O  O128  1  0.52348000  0.66225000  0.04962000  1.0
+  O  O129  1  0.94402000  0.82674000  0.45206000  1.0
+  O  O130  1  0.10921000  0.10110000  0.45567000  1.0
+  O  O131  1  0.24929000  0.70310000  0.34730000  1.0
+  O  O132  1  0.18258000  0.48190000  0.05759000  1.0
+  O  O133  1  0.70804000  0.70271000  0.00112000  1.0
+  O  O134  1  0.75663000  0.79589000  0.50230000  1.0
+  O  O135  1  0.70856000  0.69299000  0.15733000  1.0
+  O  O136  1  0.27094000  0.54054000  0.39589000  1.0
+  O  O137  1  0.29663000  0.01692000  0.44200000  1.0
+  O  O138  1  0.04979000  0.58300000  0.37090000  1.0
+  O  O139  1  0.21083000  0.96869000  0.10281000  1.0
+  O  O140  1  0.40655000  0.90998000  0.13662000  1.0
+  O  O141  1  0.52021000  0.61388000  0.13072000  1.0
+  O  O142  1  0.46216000  0.64035000  0.37061000  1.0
+  O  O143  1  0.02083000  0.62400000  0.20954000  1.0
+  O  O144  1  0.45509000  0.77248000  0.34088000  1.0
+  O  O145  1  0.09347000  0.60895000  0.28284000  1.0
+  O  O146  1  0.63850000  0.86921000  0.43858000  1.0
+  O  O147  1  0.83488000  0.63547000  0.06626000  1.0
+  O  O148  1  0.45116000  0.63325000  0.52804000  1.0
+  O  O149  1  0.75423000  0.84968000  0.22707000  1.0
+  O  O150  1  0.62010000  0.52585000  0.49234000  1.0
+  O  O151  1  0.84042000  0.70899000  0.22793000  1.0
+  O  O152  1  0.02073000  0.87235000  0.97278000  1.0
+  O  O153  1  0.85957000  0.98231000  0.00562000  1.0
+  O  O154  1  0.58146000  0.76046000  0.25473000  1.0
+  O  O155  1  0.98501000  0.75143000  0.14937000  1.0
+  O  O156  1  0.47539000  0.76727000  0.50808000  1.0
+  O  O157  1  0.92017000  0.84486000  0.29644000  1.0
+  O  O158  1  0.98348000  0.74119000  0.99564000  1.0
+  O  O159  1  0.93188000  0.50101000  0.07834000  1.0
+  O  O160  1  0.02451000  0.85465000  0.20374000  1.0
+  O  O161  1  0.56256000  0.00861000  0.42743000  1.0
+  O  O162  1  0.90892000  0.99443000  0.08214000  1.0
+  O  O163  1  0.57408000  0.52079000  0.41616000  1.0
+  O  O164  1  0.85990000  0.11043000  0.04089000  1.0
+  O  O165  1  0.02387000  0.83796000  0.04964000  1.0
+  O  O166  1  0.44394000  0.67328000  0.45204000  1.0
+  O  O167  1  0.60918000  0.39893000  0.45560000  1.0
+  O  O168  1  0.74932000  0.79690000  0.34730000  1.0
+  O  O169  1  0.68309000  0.01811000  0.05723000  1.0
+  O  O170  1  0.20807000  0.79723000  0.00104000  1.0
+  O  O171  1  0.25658000  0.70412000  0.50230000  1.0
+  O  O172  1  0.20863000  0.80705000  0.15737000  1.0
+  O  O173  1  0.77098000  0.95948000  0.39588000  1.0
+  O  O174  1  0.79669000  0.48312000  0.44200000  1.0
+  O  O175  1  0.54982000  0.91700000  0.37090000  1.0
+  O  O176  1  0.71045000  0.53158000  0.10289000  1.0
+  O  O177  1  0.90626000  0.59001000  0.13674000  1.0
+  O  O178  1  0.02064000  0.88625000  0.13064000  1.0
+  O  O179  1  0.96216000  0.85968000  0.37061000  1.0
+  O  O180  1  0.52077000  0.87609000  0.20956000  1.0
+  O  O181  1  0.95513000  0.72755000  0.34089000  1.0
+  O  O182  1  0.59352000  0.89111000  0.28285000  1.0
+  O  O183  1  0.13839000  0.13077000  0.56141000  1.0
+  O  O184  1  0.33333333  0.36486000  0.93401000  1.0
+  O  O185  1  0.95124000  0.36679000  0.47193000  1.0
+  O  O186  1  0.25355000  0.15043000  0.77288000  1.0
+  O  O187  1  0.12012000  0.47419000  0.50759000  1.0
+  O  O188  1  0.33906000  0.29075000  0.77159000  1.0
+  O  O189  1  0.51858000  0.12760000  0.02776000  1.0
+  O  O190  1  0.35953000  0.01726000  0.99438000  1.0
+  O  O191  1  0.08037000  0.23993000  0.74567000  1.0
+  O  O192  1  0.48481000  0.24902000  0.85001000  1.0
+  O  O193  1  0.97548000  0.23275000  0.49191000  1.0
+  O  O194  1  0.41987000  0.15479000  0.70345000  1.0
+  O  O195  1  0.48239000  0.25878000  0.00476000  1.0
+  O  O196  1  0.43293000  0.49850000  0.92183000  1.0
+  O  O197  1  0.52319000  0.14485000  0.79620000  1.0
+  O  O198  1  0.06240000  0.99139000  0.57256000  1.0
+  O  O199  1  0.40898000  0.00537000  0.91783000  1.0
+  O  O200  1  0.07409000  0.47925000  0.58378000  1.0
+  O  O201  1  0.35999000  0.88932000  0.95902000  1.0
+  O  O202  1  0.52064000  0.16143000  0.95090000  1.0
+  O  O203  1  0.94387000  0.32676000  0.54793000  1.0
+  O  O204  1  0.10925000  0.60110000  0.54432000  1.0
+  O  O205  1  0.24910000  0.20291000  0.65263000  1.0
+  O  O206  1  0.18305000  0.98165000  0.94277000  1.0
+  O  O207  1  0.70616000  0.20119000  0.99946000  1.0
+  O  O208  1  0.75667000  0.29586000  0.49760000  1.0
+  O  O209  1  0.70777000  0.19274000  0.84238000  1.0
+  O  O210  1  0.27087000  0.04040000  0.60406000  1.0
+  O  O211  1  0.29670000  0.51691000  0.55794000  1.0
+  O  O212  1  0.04986000  0.08297000  0.62912000  1.0
+  O  O213  1  0.21113000  0.46941000  0.89718000  1.0
+  O  O214  1  0.40577000  0.40903000  0.86353000  1.0
+  O  O215  1  0.51959000  0.11446000  0.86961000  1.0
+  O  O216  1  0.46198000  0.13998000  0.62932000  1.0
+  O  O217  1  0.02045000  0.12400000  0.79067000  1.0
+  O  O218  1  0.45496000  0.27211000  0.65893000  1.0
+  O  O219  1  0.09222000  0.10925000  0.71727000  1.0
+  F  F220  1  0.03888000  0.59454000  0.01931000  1.0
+  F  F221  1  0.36063000  0.03282000  0.52842000  1.0
+  F  F222  1  0.12043000  0.47617000  0.97356000  1.0
+  F  F223  1  0.43540000  0.41305000  0.51613000  1.0
+  F  F224  1  0.53697000  0.40605000  0.98157000  1.0
+  F  F225  1  0.86070000  0.96715000  0.47151000  1.0
+  F  F226  1  0.61962000  0.52466000  0.02671000  1.0
+  F  F227  1  0.93532000  0.58697000  0.48383000  1.0
+  F  F228  1  0.03817000  0.09449000  0.98073000  1.0
+  F  F229  1  0.36075000  0.53286000  0.47150000  1.0
+  F  F230  1  0.11986000  0.97607000  0.02672000  1.0
+  F  F231  1  0.43533000  0.91305000  0.48380000  1.0
+  F  F232  1  0.53909000  0.90545000  0.01913000  1.0
+  F  F233  1  0.86074000  0.46722000  0.52847000  1.0
+  F  F234  1  0.61988000  0.02440000  0.97339000  1.0
+  F  F235  1  0.93532000  0.08695000  0.51615000  1.0
diff --git a/tests/testresources/inputs/cif_files/odac-21433.cif b/tests/testresources/inputs/cif_files/odac-21433.cif
index b3554cbd..2829ddf7 100644
--- a/tests/testresources/inputs/cif_files/odac-21433.cif
+++ b/tests/testresources/inputs/cif_files/odac-21433.cif
@@ -1,169 +1,170 @@
-data_image0
-_chemical_formula_structural       Al24P24O96
-_chemical_formula_sum              "Al24 P24 O96"
-_cell_length_a       18.7247
-_cell_length_b       18.7247
-_cell_length_c       9.4862
-_cell_angle_alpha    90
-_cell_angle_beta     90
-_cell_angle_gamma    90.0001
-
-_space_group_name_H-M_alt    "P 1"
-_space_group_IT_number       1
-
+# generated using pymatgen
+data_AlPO4
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   9.48620000
+_cell_length_b   18.72470000
+_cell_length_c   18.72470000
+_cell_angle_alpha   89.99990000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   AlPO4
+_chemical_formula_sum   'Al24 P24 O96'
+_cell_volume   3325.99822727
+_cell_formula_units_Z   24
 loop_
-  _space_group_symop_operation_xyz
-  'x, y, z'
-
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
 loop_
-  _atom_site_type_symbol
-  _atom_site_label
-  _atom_site_symmetry_multiplicity
-  _atom_site_fract_x
-  _atom_site_fract_y
-  _atom_site_fract_z
-  _atom_site_occupancy
-  Al  Al1       1.0  0.95507  0.83477  0.84024  1.0000
-  Al  Al2       1.0  0.16576  0.93612  0.91662  1.0000
-  Al  Al3       1.0  0.06583  0.94694  0.33735  1.0000
-  Al  Al4       1.0  0.54508  0.66527  0.83989  1.0000
-  Al  Al5       1.0  0.33427  0.56385  0.91669  1.0000
-  Al  Al6       1.0  0.43405  0.55299  0.33746  1.0000
-  Al  Al7       1.0  0.66518  0.95501  0.84012  1.0000
-  Al  Al8       1.0  0.56381  0.16567  0.91648  1.0000
-  Al  Al9       1.0  0.55294  0.06572  0.33734  1.0000
-  Al  Al10      1.0  0.83478  0.54492  0.84010  1.0000
-  Al  Al11      1.0  0.93619  0.33432  0.91650  1.0000
-  Al  Al12      1.0  0.94709  0.43432  0.33731  1.0000
-  Al  Al13      1.0  0.04498  0.16528  0.15993  1.0000
-  Al  Al14      1.0  0.83431  0.06384  0.08358  1.0000
-  Al  Al15      1.0  0.93429  0.05297  0.66264  1.0000
-  Al  Al16      1.0  0.45505  0.33472  0.15992  1.0000
-  Al  Al17      1.0  0.66567  0.43615  0.08362  1.0000
-  Al  Al18      1.0  0.56571  0.44701  0.66262  1.0000
-  Al  Al19      1.0  0.33476  0.04486  0.15998  1.0000
-  Al  Al20      1.0  0.43584  0.83431  0.08383  1.0000
-  Al  Al21      1.0  0.44704  0.93429  0.66265  1.0000
-  Al  Al22      1.0  0.16529  0.45519  0.16007  1.0000
-  Al  Al23      1.0  0.06367  0.66554  0.08351  1.0000
-  Al  Al24      1.0  0.05303  0.56570  0.66263  1.0000
-  P   P1        1.0  0.06553  0.83448  0.09144  1.0000
-  P   P2        1.0  0.83432  0.95131  0.84001  1.0000
-  P   P3        1.0  0.05645  0.93368  0.66221  1.0000
-  P   P4        1.0  0.43486  0.66519  0.09112  1.0000
-  P   P5        1.0  0.66569  0.54866  0.84000  1.0000
-  P   P6        1.0  0.44356  0.56634  0.66222  1.0000
-  P   P7        1.0  0.66531  0.06534  0.09135  1.0000
-  P   P8        1.0  0.54855  0.83433  0.84023  1.0000
-  P   P9        1.0  0.56631  0.05640  0.66210  1.0000
-  P   P10       1.0  0.83470  0.43466  0.09137  1.0000
-  P   P11       1.0  0.95127  0.66568  0.83986  1.0000
-  P   P12       1.0  0.93370  0.44359  0.66209  1.0000
-  P   P13       1.0  0.93466  0.16531  0.90868  1.0000
-  P   P14       1.0  0.16567  0.04871  0.16002  1.0000
-  P   P15       1.0  0.94364  0.06626  0.33786  1.0000
-  P   P16       1.0  0.56534  0.33468  0.90868  1.0000
-  P   P17       1.0  0.33435  0.45122  0.16004  1.0000
-  P   P18       1.0  0.55633  0.43378  0.33784  1.0000
-  P   P19       1.0  0.33470  0.93462  0.90842  1.0000
-  P   P20       1.0  0.45128  0.16564  0.16000  1.0000
-  P   P21       1.0  0.43369  0.94351  0.33798  1.0000
-  P   P22       1.0  0.16534  0.56554  0.90885  1.0000
-  P   P23       1.0  0.04874  0.33439  0.15998  1.0000
-  P   P24       1.0  0.06634  0.55647  0.33801  1.0000
-  O   O1        1.0  0.99702  0.84563  0.00411  1.0000
-  O   O2        1.0  0.05535  0.87068  0.23465  1.0000
-  O   O3        1.0  0.13060  0.86521  0.01367  1.0000
-  O   O4        1.0  0.07989  0.75515  0.11712  1.0000
-  O   O5        1.0  0.87340  0.87943  0.83702  1.0000
-  O   O6        1.0  0.84495  0.98470  0.98711  1.0000
-  O   O7        1.0  0.75516  0.93785  0.80993  1.0000
-  O   O8        1.0  0.86300  0.00156  0.72489  1.0000
-  O   O9        1.0  0.12251  0.94211  0.75543  1.0000
-  O   O10       1.0  0.01277  0.00297  0.67165  1.0000
-  O   O11       1.0  0.01125  0.86919  0.70897  1.0000
-  O   O12       1.0  0.08168  0.92068  0.51068  1.0000
-  O   O13       1.0  0.50322  0.65370  0.00367  1.0000
-  O   O14       1.0  0.44472  0.62910  0.23447  1.0000
-  O   O15       1.0  0.36937  0.63492  0.01375  1.0000
-  O   O16       1.0  0.42073  0.74448  0.11697  1.0000
-  O   O17       1.0  0.62670  0.62057  0.83690  1.0000
-  O   O18       1.0  0.65506  0.51529  0.98711  1.0000
-  O   O19       1.0  0.74485  0.56212  0.80992  1.0000
-  O   O20       1.0  0.63699  0.49842  0.72487  1.0000
-  O   O21       1.0  0.37751  0.55793  0.75554  1.0000
-  O   O22       1.0  0.48722  0.49704  0.67163  1.0000
-  O   O23       1.0  0.48875  0.63084  0.70887  1.0000
-  O   O24       1.0  0.41833  0.57942  0.51073  1.0000
-  O   O25       1.0  0.65376  0.99697  0.00380  1.0000
-  O   O26       1.0  0.62912  0.05522  0.23457  1.0000
-  O   O27       1.0  0.63467  0.13070  0.01418  1.0000
-  O   O28       1.0  0.74466  0.07909  0.11661  1.0000
-  O   O29       1.0  0.62043  0.87340  0.83724  1.0000
-  O   O30       1.0  0.51506  0.84467  0.98726  1.0000
-  O   O31       1.0  0.56211  0.75521  0.80990  1.0000
-  O   O32       1.0  0.49836  0.86302  0.72501  1.0000
-  O   O33       1.0  0.55786  0.12249  0.75529  1.0000
-  O   O34       1.0  0.49701  0.01275  0.67166  1.0000
-  O   O35       1.0  0.63079  0.01121  0.70882  1.0000
-  O   O36       1.0  0.57921  0.08165  0.51058  1.0000
-  O   O37       1.0  0.84625  0.50303  0.00382  1.0000
-  O   O38       1.0  0.87089  0.44479  0.23457  1.0000
-  O   O39       1.0  0.86532  0.36931  0.01417  1.0000
-  O   O40       1.0  0.75534  0.42093  0.11661  1.0000
-  O   O41       1.0  0.87941  0.62662  0.83681  1.0000
-  O   O42       1.0  0.98460  0.65513  0.98710  1.0000
-  O   O43       1.0  0.93786  0.74483  0.80977  1.0000
-  O   O44       1.0  0.00161  0.63701  0.72491  1.0000
-  O   O45       1.0  0.94215  0.37751  0.75530  1.0000
-  O   O46       1.0  0.00301  0.48726  0.67169  1.0000
-  O   O47       1.0  0.86922  0.48878  0.70879  1.0000
-  O   O48       1.0  0.92081  0.41837  0.51056  1.0000
-  O   O49       1.0  0.00302  0.15376  0.99624  1.0000
-  O   O50       1.0  0.94479  0.12914  0.76544  1.0000
-  O   O51       1.0  0.86929  0.13466  0.98579  1.0000
-  O   O52       1.0  0.92090  0.24467  0.88341  1.0000
-  O   O53       1.0  0.12664  0.12060  0.16298  1.0000
-  O   O54       1.0  0.15504  0.01528  0.01294  1.0000
-  O   O55       1.0  0.24482  0.06220  0.19004  1.0000
-  O   O56       1.0  0.13697  0.99848  0.27516  1.0000
-  O   O57       1.0  0.87754  0.05780  0.24468  1.0000
-  O   O58       1.0  0.98731  0.99695  0.32837  1.0000
-  O   O59       1.0  0.98881  0.13075  0.29113  1.0000
-  O   O60       1.0  0.91837  0.07919  0.48937  1.0000
-  O   O61       1.0  0.49699  0.34625  0.99624  1.0000
-  O   O62       1.0  0.55521  0.37086  0.76545  1.0000
-  O   O63       1.0  0.63071  0.36534  0.98578  1.0000
-  O   O64       1.0  0.57910  0.25533  0.88342  1.0000
-  O   O65       1.0  0.37333  0.37931  0.16283  1.0000
-  O   O66       1.0  0.34499  0.48472  0.01298  1.0000
-  O   O67       1.0  0.25521  0.43770  0.18996  1.0000
-  O   O68       1.0  0.36311  0.50131  0.27525  1.0000
-  O   O69       1.0  0.62242  0.44224  0.24467  1.0000
-  O   O70       1.0  0.51266  0.50308  0.32841  1.0000
-  O   O71       1.0  0.51117  0.36929  0.29111  1.0000
-  O   O72       1.0  0.58161  0.42085  0.48934  1.0000
-  O   O73       1.0  0.34621  0.00291  0.99621  1.0000
-  O   O74       1.0  0.37077  0.94496  0.76512  1.0000
-  O   O75       1.0  0.36555  0.86918  0.98486  1.0000
-  O   O76       1.0  0.25535  0.92083  0.88312  1.0000
-  O   O77       1.0  0.37943  0.12657  0.16302  1.0000
-  O   O78       1.0  0.48467  0.15505  0.01289  1.0000
-  O   O79       1.0  0.43784  0.24479  0.19007  1.0000
-  O   O80       1.0  0.50156  0.13699  0.27509  1.0000
-  O   O81       1.0  0.44233  0.87742  0.24484  1.0000
-  O   O82       1.0  0.50298  0.98720  0.32856  1.0000
-  O   O83       1.0  0.36929  0.98878  0.29125  1.0000
-  O   O84       1.0  0.42075  0.91821  0.48946  1.0000
-  O   O85       1.0  0.15379  0.49721  0.99639  1.0000
-  O   O86       1.0  0.12914  0.55535  0.76567  1.0000
-  O   O87       1.0  0.13471  0.63101  0.98572  1.0000
-  O   O88       1.0  0.24469  0.57939  0.88358  1.0000
-  O   O89       1.0  0.12058  0.37347  0.16295  1.0000
-  O   O90       1.0  0.01533  0.34497  0.01288  1.0000
-  O   O91       1.0  0.06218  0.25523  0.19006  1.0000
-  O   O92       1.0  0.99846  0.36305  0.27509  1.0000
-  O   O93       1.0  0.05782  0.62258  0.24482  1.0000
-  O   O94       1.0  0.99694  0.51294  0.32853  1.0000
-  O   O95       1.0  0.13056  0.51102  0.29139  1.0000
-  O   O96       1.0  0.07926  0.58184  0.48946  1.0000
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Al  Al0  1  0.84024000  0.16523000  0.95507000  1.0
+  Al  Al1  1  0.91662000  0.06388000  0.16576000  1.0
+  Al  Al2  1  0.33735000  0.05306000  0.06583000  1.0
+  Al  Al3  1  0.83989000  0.33473000  0.54508000  1.0
+  Al  Al4  1  0.91669000  0.43615000  0.33427000  1.0
+  Al  Al5  1  0.33746000  0.44701000  0.43405000  1.0
+  Al  Al6  1  0.84012000  0.04499000  0.66518000  1.0
+  Al  Al7  1  0.91648000  0.83433000  0.56381000  1.0
+  Al  Al8  1  0.33734000  0.93428000  0.55294000  1.0
+  Al  Al9  1  0.84010000  0.45508000  0.83478000  1.0
+  Al  Al10  1  0.91650000  0.66568000  0.93619000  1.0
+  Al  Al11  1  0.33731000  0.56568000  0.94709000  1.0
+  Al  Al12  1  0.15993000  0.83472000  0.04498000  1.0
+  Al  Al13  1  0.08358000  0.93616000  0.83431000  1.0
+  Al  Al14  1  0.66264000  0.94703000  0.93429000  1.0
+  Al  Al15  1  0.15992000  0.66528000  0.45505000  1.0
+  Al  Al16  1  0.08362000  0.56385000  0.66567000  1.0
+  Al  Al17  1  0.66262000  0.55299000  0.56571000  1.0
+  Al  Al18  1  0.15998000  0.95514000  0.33476000  1.0
+  Al  Al19  1  0.08383000  0.16569000  0.43584000  1.0
+  Al  Al20  1  0.66265000  0.06571000  0.44704000  1.0
+  Al  Al21  1  0.16007000  0.54481000  0.16529000  1.0
+  Al  Al22  1  0.08351000  0.33446000  0.06367000  1.0
+  Al  Al23  1  0.66263000  0.43430000  0.05303000  1.0
+  P  P24  1  0.09144000  0.16552000  0.06553000  1.0
+  P  P25  1  0.84001000  0.04869000  0.83432000  1.0
+  P  P26  1  0.66221000  0.06632000  0.05645000  1.0
+  P  P27  1  0.09112000  0.33481000  0.43486000  1.0
+  P  P28  1  0.84000000  0.45134000  0.66569000  1.0
+  P  P29  1  0.66222000  0.43366000  0.44356000  1.0
+  P  P30  1  0.09135000  0.93466000  0.66531000  1.0
+  P  P31  1  0.84023000  0.16567000  0.54855000  1.0
+  P  P32  1  0.66210000  0.94360000  0.56631000  1.0
+  P  P33  1  0.09137000  0.56534000  0.83470000  1.0
+  P  P34  1  0.83986000  0.33432000  0.95127000  1.0
+  P  P35  1  0.66209000  0.55641000  0.93370000  1.0
+  P  P36  1  0.90868000  0.83469000  0.93466000  1.0
+  P  P37  1  0.16002000  0.95129000  0.16567000  1.0
+  P  P38  1  0.33786000  0.93374000  0.94364000  1.0
+  P  P39  1  0.90868000  0.66532000  0.56534000  1.0
+  P  P40  1  0.16004000  0.54878000  0.33435000  1.0
+  P  P41  1  0.33784000  0.56622000  0.55633000  1.0
+  P  P42  1  0.90842000  0.06538000  0.33470000  1.0
+  P  P43  1  0.16000000  0.83436000  0.45128000  1.0
+  P  P44  1  0.33798000  0.05649000  0.43369000  1.0
+  P  P45  1  0.90885000  0.43446000  0.16534000  1.0
+  P  P46  1  0.15998000  0.66561000  0.04874000  1.0
+  P  P47  1  0.33801000  0.44353000  0.06634000  1.0
+  O  O48  1  0.00411000  0.15437000  0.99702000  1.0
+  O  O49  1  0.23465000  0.12932000  0.05535000  1.0
+  O  O50  1  0.01367000  0.13479000  0.13060000  1.0
+  O  O51  1  0.11712000  0.24485000  0.07989000  1.0
+  O  O52  1  0.83702000  0.12057000  0.87340000  1.0
+  O  O53  1  0.98711000  0.01530000  0.84495000  1.0
+  O  O54  1  0.80993000  0.06215000  0.75516000  1.0
+  O  O55  1  0.72489000  0.99844000  0.86300000  1.0
+  O  O56  1  0.75543000  0.05789000  0.12251000  1.0
+  O  O57  1  0.67165000  0.99703000  0.01277000  1.0
+  O  O58  1  0.70897000  0.13081000  0.01125000  1.0
+  O  O59  1  0.51068000  0.07932000  0.08168000  1.0
+  O  O60  1  0.00367000  0.34630000  0.50322000  1.0
+  O  O61  1  0.23447000  0.37090000  0.44472000  1.0
+  O  O62  1  0.01375000  0.36508000  0.36937000  1.0
+  O  O63  1  0.11697000  0.25552000  0.42073000  1.0
+  O  O64  1  0.83690000  0.37943000  0.62670000  1.0
+  O  O65  1  0.98711000  0.48471000  0.65506000  1.0
+  O  O66  1  0.80992000  0.43788000  0.74485000  1.0
+  O  O67  1  0.72487000  0.50158000  0.63699000  1.0
+  O  O68  1  0.75554000  0.44207000  0.37751000  1.0
+  O  O69  1  0.67163000  0.50296000  0.48722000  1.0
+  O  O70  1  0.70887000  0.36916000  0.48875000  1.0
+  O  O71  1  0.51073000  0.42058000  0.41833000  1.0
+  O  O72  1  0.00380000  0.00303000  0.65376000  1.0
+  O  O73  1  0.23457000  0.94478000  0.62912000  1.0
+  O  O74  1  0.01418000  0.86930000  0.63467000  1.0
+  O  O75  1  0.11661000  0.92091000  0.74466000  1.0
+  O  O76  1  0.83724000  0.12660000  0.62043000  1.0
+  O  O77  1  0.98726000  0.15533000  0.51506000  1.0
+  O  O78  1  0.80990000  0.24479000  0.56211000  1.0
+  O  O79  1  0.72501000  0.13698000  0.49836000  1.0
+  O  O80  1  0.75529000  0.87751000  0.55786000  1.0
+  O  O81  1  0.67166000  0.98725000  0.49701000  1.0
+  O  O82  1  0.70882000  0.98879000  0.63079000  1.0
+  O  O83  1  0.51058000  0.91835000  0.57921000  1.0
+  O  O84  1  0.00382000  0.49697000  0.84625000  1.0
+  O  O85  1  0.23457000  0.55521000  0.87089000  1.0
+  O  O86  1  0.01417000  0.63069000  0.86532000  1.0
+  O  O87  1  0.11661000  0.57907000  0.75534000  1.0
+  O  O88  1  0.83681000  0.37338000  0.87941000  1.0
+  O  O89  1  0.98710000  0.34487000  0.98460000  1.0
+  O  O90  1  0.80977000  0.25517000  0.93786000  1.0
+  O  O91  1  0.72491000  0.36299000  0.00161000  1.0
+  O  O92  1  0.75530000  0.62249000  0.94215000  1.0
+  O  O93  1  0.67169000  0.51274000  0.00301000  1.0
+  O  O94  1  0.70879000  0.51122000  0.86922000  1.0
+  O  O95  1  0.51056000  0.58163000  0.92081000  1.0
+  O  O96  1  0.99624000  0.84624000  0.00302000  1.0
+  O  O97  1  0.76544000  0.87086000  0.94479000  1.0
+  O  O98  1  0.98579000  0.86534000  0.86929000  1.0
+  O  O99  1  0.88341000  0.75533000  0.92090000  1.0
+  O  O100  1  0.16298000  0.87940000  0.12664000  1.0
+  O  O101  1  0.01294000  0.98472000  0.15504000  1.0
+  O  O102  1  0.19004000  0.93780000  0.24482000  1.0
+  O  O103  1  0.27516000  0.00152000  0.13697000  1.0
+  O  O104  1  0.24468000  0.94220000  0.87754000  1.0
+  O  O105  1  0.32837000  0.00305000  0.98731000  1.0
+  O  O106  1  0.29113000  0.86925000  0.98881000  1.0
+  O  O107  1  0.48937000  0.92081000  0.91837000  1.0
+  O  O108  1  0.99624000  0.65375000  0.49699000  1.0
+  O  O109  1  0.76545000  0.62914000  0.55521000  1.0
+  O  O110  1  0.98578000  0.63466000  0.63071000  1.0
+  O  O111  1  0.88342000  0.74467000  0.57910000  1.0
+  O  O112  1  0.16283000  0.62069000  0.37333000  1.0
+  O  O113  1  0.01298000  0.51528000  0.34499000  1.0
+  O  O114  1  0.18996000  0.56230000  0.25521000  1.0
+  O  O115  1  0.27525000  0.49869000  0.36311000  1.0
+  O  O116  1  0.24467000  0.55776000  0.62242000  1.0
+  O  O117  1  0.32841000  0.49692000  0.51266000  1.0
+  O  O118  1  0.29111000  0.63071000  0.51117000  1.0
+  O  O119  1  0.48934000  0.57915000  0.58161000  1.0
+  O  O120  1  0.99621000  0.99709000  0.34621000  1.0
+  O  O121  1  0.76512000  0.05504000  0.37077000  1.0
+  O  O122  1  0.98486000  0.13082000  0.36555000  1.0
+  O  O123  1  0.88312000  0.07917000  0.25535000  1.0
+  O  O124  1  0.16302000  0.87343000  0.37943000  1.0
+  O  O125  1  0.01289000  0.84495000  0.48467000  1.0
+  O  O126  1  0.19007000  0.75521000  0.43784000  1.0
+  O  O127  1  0.27509000  0.86301000  0.50156000  1.0
+  O  O128  1  0.24484000  0.12258000  0.44233000  1.0
+  O  O129  1  0.32856000  0.01280000  0.50298000  1.0
+  O  O130  1  0.29125000  0.01122000  0.36929000  1.0
+  O  O131  1  0.48946000  0.08179000  0.42075000  1.0
+  O  O132  1  0.99639000  0.50279000  0.15379000  1.0
+  O  O133  1  0.76567000  0.44465000  0.12914000  1.0
+  O  O134  1  0.98572000  0.36899000  0.13471000  1.0
+  O  O135  1  0.88358000  0.42061000  0.24469000  1.0
+  O  O136  1  0.16295000  0.62653000  0.12058000  1.0
+  O  O137  1  0.01288000  0.65503000  0.01533000  1.0
+  O  O138  1  0.19006000  0.74477000  0.06218000  1.0
+  O  O139  1  0.27509000  0.63695000  0.99846000  1.0
+  O  O140  1  0.24482000  0.37742000  0.05782000  1.0
+  O  O141  1  0.32853000  0.48706000  0.99694000  1.0
+  O  O142  1  0.29139000  0.48898000  0.13056000  1.0
+  O  O143  1  0.48946000  0.41816000  0.07926000  1.0
diff --git a/tests/testresources/inputs/cif_files/odac-21478.cif b/tests/testresources/inputs/cif_files/odac-21478.cif
index 81afed13..6168919a 100644
--- a/tests/testresources/inputs/cif_files/odac-21478.cif
+++ b/tests/testresources/inputs/cif_files/odac-21478.cif
@@ -1,209 +1,210 @@
-data_image0
-_chemical_formula_structural       Zn24P32H32O96
-_chemical_formula_sum              "Zn24 P32 H32 O96"
-_cell_length_a       17.0323
-_cell_length_b       9.06338
-_cell_length_c       24.5579
-_cell_angle_alpha    89.9998
-_cell_angle_beta     107.472
-_cell_angle_gamma    90
-
-_space_group_name_H-M_alt    "P 1"
-_space_group_IT_number       1
-
+# generated using pymatgen
+data_Zn3P4(HO3)4
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   9.06338000
+_cell_length_b   17.03230000
+_cell_length_c   24.55790000
+_cell_angle_alpha   107.47200000
+_cell_angle_beta   89.99980000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Zn3P4(HO3)4
+_chemical_formula_sum   'Zn24 P32 H32 O96'
+_cell_volume   3616.10536228
+_cell_formula_units_Z   8
 loop_
-  _space_group_symop_operation_xyz
-  'x, y, z'
-
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
 loop_
-  _atom_site_type_symbol
-  _atom_site_label
-  _atom_site_symmetry_multiplicity
-  _atom_site_fract_x
-  _atom_site_fract_y
-  _atom_site_fract_z
-  _atom_site_occupancy
-  Zn  Zn1       1.0  0.10629  0.75801  0.27142  1.0000
-  Zn  Zn2       1.0  0.75579  0.72476  0.16434  1.0000
-  Zn  Zn3       1.0  0.22745  0.48941  0.49468  1.0000
-  Zn  Zn4       1.0  0.29113  0.98105  0.49893  1.0000
-  Zn  Zn5       1.0  0.29105  0.29821  0.17638  1.0000
-  Zn  Zn6       1.0  0.38342  0.74294  0.72159  1.0000
-  Zn  Zn7       1.0  0.89323  0.25726  0.22752  1.0000
-  Zn  Zn8       1.0  0.24335  0.22443  0.33461  1.0000
-  Zn  Zn9       1.0  0.77121  0.99023  0.00498  1.0000
-  Zn  Zn10      1.0  0.70923  0.48529  0.00071  1.0000
-  Zn  Zn11      1.0  0.70883  0.79879  0.32336  1.0000
-  Zn  Zn12      1.0  0.61671  0.24284  0.77848  1.0000
-  Zn  Zn13      1.0  0.89319  0.24283  0.72816  1.0000
-  Zn  Zn14      1.0  0.24398  0.27586  0.83543  1.0000
-  Zn  Zn15      1.0  0.77180  0.51106  0.50487  1.0000
-  Zn  Zn16      1.0  0.70859  0.01894  0.50086  1.0000
-  Zn  Zn17      1.0  0.70910  0.70244  0.82375  1.0000
-  Zn  Zn18      1.0  0.61649  0.25672  0.27818  1.0000
-  Zn  Zn19      1.0  0.10662  0.74250  0.77230  1.0000
-  Zn  Zn20      1.0  0.75602  0.77523  0.66485  1.0000
-  Zn  Zn21      1.0  0.22688  0.00881  0.99562  1.0000
-  Zn  Zn22      1.0  0.28961  0.51504  0.99903  1.0000
-  Zn  Zn23      1.0  0.29135  0.20090  0.67666  1.0000
-  Zn  Zn24      1.0  0.38393  0.75667  0.22232  1.0000
-  P   P1        1.0  0.92717  0.59618  0.25294  1.0000
-  P   P2        1.0  0.19101  0.48165  0.24440  1.0000
-  P   P3        1.0  0.16720  0.76977  0.41317  1.0000
-  P   P4        1.0  0.65055  0.77972  0.03503  1.0000
-  P   P5        1.0  0.18043  0.19978  0.54651  1.0000
-  P   P6        1.0  0.32245  0.71635  0.58862  1.0000
-  P   P7        1.0  0.44264  0.43047  0.27043  1.0000
-  P   P8        1.0  0.65617  0.55040  0.23040  1.0000
-  P   P9        1.0  0.07236  0.09565  0.24466  1.0000
-  P   P10       1.0  0.80897  0.98124  0.25521  1.0000
-  P   P11       1.0  0.83042  0.26858  0.08595  1.0000
-  P   P12       1.0  0.34804  0.27848  0.46396  1.0000
-  P   P13       1.0  0.82114  0.70454  0.95396  1.0000
-  P   P14       1.0  0.67750  0.21864  0.91144  1.0000
-  P   P15       1.0  0.55717  0.93151  0.22952  1.0000
-  P   P16       1.0  0.34375  0.05029  0.26952  1.0000
-  P   P17       1.0  0.07262  0.40365  0.74671  1.0000
-  P   P18       1.0  0.80872  0.51879  0.75566  1.0000
-  P   P19       1.0  0.83232  0.23083  0.58642  1.0000
-  P   P20       1.0  0.34816  0.22023  0.96495  1.0000
-  P   P21       1.0  0.81940  0.80028  0.45346  1.0000
-  P   P22       1.0  0.67725  0.28350  0.41108  1.0000
-  P   P23       1.0  0.55765  0.56922  0.72990  1.0000
-  P   P24       1.0  0.34380  0.44946  0.76954  1.0000
-  P   P25       1.0  0.92716  0.90369  0.75364  1.0000
-  P   P26       1.0  0.19144  0.01856  0.74513  1.0000
-  P   P27       1.0  0.16737  0.73021  0.91405  1.0000
-  P   P28       1.0  0.65097  0.72130  0.53531  1.0000
-  P   P29       1.0  0.17863  0.29685  0.04666  1.0000
-  P   P30       1.0  0.32343  0.78009  0.08921  1.0000
-  P   P31       1.0  0.44311  0.06806  0.77053  1.0000
-  P   P32       1.0  0.65611  0.94990  0.73026  1.0000
-  H   H1        1.0  0.91814  0.68659  0.29737  1.0000
-  H   H2        1.0  0.11086  0.43129  0.23912  1.0000
-  H   H3        1.0  0.11732  0.81275  0.44689  1.0000
-  H   H4        1.0  0.58512  0.81258  0.05681  1.0000
-  H   H5        1.0  0.11417  0.17164  0.56811  1.0000
-  H   H6        1.0  0.38491  0.60883  0.60176  1.0000
-  H   H7        1.0  0.39656  0.38397  0.30626  1.0000
-  H   H8        1.0  0.57656  0.58850  0.23169  1.0000
-  H   H9        1.0  0.08112  0.18536  0.20001  1.0000
-  H   H10       1.0  0.88900  0.93080  0.26015  1.0000
-  H   H11       1.0  0.88015  0.30503  0.05139  1.0000
-  H   H12       1.0  0.41332  0.31127  0.44192  1.0000
-  H   H13       1.0  0.88813  0.67700  0.93311  1.0000
-  H   H14       1.0  0.61444  0.11233  0.89899  1.0000
-  H   H15       1.0  0.60284  0.88444  0.19350  1.0000
-  H   H16       1.0  0.42330  0.08855  0.26816  1.0000
-  H   H17       1.0  0.08155  0.31322  0.70226  1.0000
-  H   H18       1.0  0.88882  0.56944  0.76099  1.0000
-  H   H19       1.0  0.88216  0.18808  0.55265  1.0000
-  H   H20       1.0  0.41368  0.18674  0.94326  1.0000
-  H   H21       1.0  0.88564  0.82831  0.43184  1.0000
-  H   H22       1.0  0.61467  0.39077  0.39781  1.0000
-  H   H23       1.0  0.60353  0.61539  0.69389  1.0000
-  H   H24       1.0  0.42343  0.41118  0.76835  1.0000
-  H   H25       1.0  0.91810  0.81351  0.79810  1.0000
-  H   H26       1.0  0.11139  0.06904  0.74008  1.0000
-  H   H27       1.0  0.11754  0.68984  0.94803  1.0000
-  H   H28       1.0  0.58538  0.68863  0.55705  1.0000
-  H   H29       1.0  0.11286  0.32684  0.06855  1.0000
-  H   H30       1.0  0.38724  0.88498  0.10185  1.0000
-  H   H31       1.0  0.39703  0.11382  0.80645  1.0000
-  H   H32       1.0  0.57652  0.91145  0.73152  1.0000
-  O   O1        1.0  0.01335  0.61855  0.24681  1.0000
-  O   O2        1.0  0.86336  0.64019  0.19667  1.0000
-  O   O3        1.0  0.91534  0.43790  0.27098  1.0000
-  O   O4        1.0  0.19214  0.65029  0.25078  1.0000
-  O   O5        1.0  0.21076  0.43647  0.18976  1.0000
-  O   O6        1.0  0.25070  0.41342  0.29840  1.0000
-  O   O7        1.0  0.11465  0.79078  0.35109  1.0000
-  O   O8        1.0  0.24367  0.86997  0.42780  1.0000
-  O   O9        1.0  0.18990  0.60571  0.42487  1.0000
-  O   O10       1.0  0.66054  0.91036  0.99769  1.0000
-  O   O11       1.0  0.73155  0.76041  0.08387  1.0000
-  O   O12       1.0  0.62757  0.63454  0.00182  1.0000
-  O   O13       1.0  0.19243  0.05928  0.51505  1.0000
-  O   O14       1.0  0.15591  0.33516  0.50732  1.0000
-  O   O15       1.0  0.25879  0.23394  0.59585  1.0000
-  O   O16       1.0  0.24142  0.64382  0.55333  1.0000
-  O   O17       1.0  0.31223  0.77937  0.64439  1.0000
-  O   O18       1.0  0.35100  0.83788  0.55517  1.0000
-  O   O19       1.0  0.53016  0.37313  0.29720  1.0000
-  O   O20       1.0  0.44091  0.59928  0.26977  1.0000
-  O   O21       1.0  0.40355  0.36564  0.21024  1.0000
-  O   O22       1.0  0.66408  0.61081  0.17376  1.0000
-  O   O23       1.0  0.66489  0.38199  0.23275  1.0000
-  O   O24       1.0  0.71977  0.61876  0.28276  1.0000
-  O   O25       1.0  0.98644  0.11820  0.25123  1.0000
-  O   O26       1.0  0.13634  0.13961  0.30087  1.0000
-  O   O27       1.0  0.08419  0.93709  0.22683  1.0000
-  O   O28       1.0  0.80799  0.14986  0.24886  1.0000
-  O   O29       1.0  0.78957  0.93604  0.30998  1.0000
-  O   O30       1.0  0.74894  0.91289  0.20139  1.0000
-  O   O31       1.0  0.88413  0.28965  0.14767  1.0000
-  O   O32       1.0  0.75605  0.37384  0.07170  1.0000
-  O   O33       1.0  0.80363  0.10596  0.07517  1.0000
-  O   O34       1.0  0.33789  0.41069  0.50054  1.0000
-  O   O35       1.0  0.26703  0.25786  0.41517  1.0000
-  O   O36       1.0  0.37091  0.13391  0.49758  1.0000
-  O   O37       1.0  0.80811  0.56446  0.98524  1.0000
-  O   O38       1.0  0.84558  0.83980  0.99340  1.0000
-  O   O39       1.0  0.74343  0.73967  0.90431  1.0000
-  O   O40       1.0  0.75825  0.14536  0.94677  1.0000
-  O   O41       1.0  0.68793  0.27953  0.85543  1.0000
-  O   O42       1.0  0.64961  0.34218  0.94432  1.0000
-  O   O43       1.0  0.46946  0.87476  0.20305  1.0000
-  O   O44       1.0  0.55955  0.10028  0.23014  1.0000
-  O   O45       1.0  0.59634  0.86662  0.28968  1.0000
-  O   O46       1.0  0.33578  0.11124  0.32608  1.0000
-  O   O47       1.0  0.33524  0.88183  0.26752  1.0000
-  O   O48       1.0  0.28006  0.11816  0.21710  1.0000
-  O   O49       1.0  0.98641  0.38179  0.75283  1.0000
-  O   O50       1.0  0.13630  0.35934  0.80298  1.0000
-  O   O51       1.0  0.08492  0.56183  0.72876  1.0000
-  O   O52       1.0  0.80769  0.35016  0.74923  1.0000
-  O   O53       1.0  0.78892  0.56336  0.81033  1.0000
-  O   O54       1.0  0.74903  0.58708  0.70167  1.0000
-  O   O55       1.0  0.88501  0.21036  0.64847  1.0000
-  O   O56       1.0  0.75606  0.13014  0.57194  1.0000
-  O   O57       1.0  0.80925  0.39471  0.57466  1.0000
-  O   O58       1.0  0.33718  0.08882  0.00159  1.0000
-  O   O59       1.0  0.26751  0.24164  0.91595  1.0000
-  O   O60       1.0  0.37129  0.36487  0.99851  1.0000
-  O   O61       1.0  0.80739  0.94087  0.48485  1.0000
-  O   O62       1.0  0.84387  0.66501  0.49270  1.0000
-  O   O63       1.0  0.74105  0.76582  0.40415  1.0000
-  O   O64       1.0  0.75819  0.35643  0.44633  1.0000
-  O   O65       1.0  0.68766  0.22018  0.35541  1.0000
-  O   O66       1.0  0.64878  0.16206  0.44460  1.0000
-  O   O67       1.0  0.46992  0.62555  0.70302  1.0000
-  O   O68       1.0  0.55993  0.40043  0.73083  1.0000
-  O   O69       1.0  0.59670  0.63473  0.78998  1.0000
-  O   O70       1.0  0.33586  0.38935  0.82623  1.0000
-  O   O71       1.0  0.33506  0.61787  0.76711  1.0000
-  O   O72       1.0  0.28021  0.38096  0.71722  1.0000
-  O   O73       1.0  0.01339  0.88148  0.74759  1.0000
-  O   O74       1.0  0.86349  0.85962  0.69733  1.0000
-  O   O75       1.0  0.91499  0.06190  0.77161  1.0000
-  O   O76       1.0  0.19251  0.84997  0.75164  1.0000
-  O   O77       1.0  0.21094  0.06341  0.69037  1.0000
-  O   O78       1.0  0.25135  0.08713  0.79897  1.0000
-  O   O79       1.0  0.11457  0.70986  0.85199  1.0000
-  O   O80       1.0  0.24314  0.62817  0.92837  1.0000
-  O   O81       1.0  0.19182  0.89376  0.92543  1.0000
-  O   O82       1.0  0.66115  0.58929  0.49862  1.0000
-  O   O83       1.0  0.73180  0.74103  0.58430  1.0000
-  O   O84       1.0  0.62860  0.86623  0.50186  1.0000
-  O   O85       1.0  0.19053  0.43491  0.01387  1.0000
-  O   O86       1.0  0.15317  0.15896  0.00882  1.0000
-  O   O87       1.0  0.25755  0.26405  0.09570  1.0000
-  O   O88       1.0  0.24289  0.85511  0.05461  1.0000
-  O   O89       1.0  0.31319  0.71857  0.14520  1.0000
-  O   O90       1.0  0.35011  0.65656  0.05572  1.0000
-  O   O91       1.0  0.53062  0.12536  0.79736  1.0000
-  O   O92       1.0  0.44111  0.89927  0.76938  1.0000
-  O   O93       1.0  0.40400  0.13366  0.71047  1.0000
-  O   O94       1.0  0.66418  0.88980  0.67362  1.0000
-  O   O95       1.0  0.66475  0.11832  0.73271  1.0000
-  O   O96       1.0  0.71986  0.88156  0.78252  1.0000
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Zn  Zn0  1  0.24199000  0.89371000  0.72858000  1.0
+  Zn  Zn1  1  0.27524000  0.24421000  0.83566000  1.0
+  Zn  Zn2  1  0.51059000  0.77255000  0.50532000  1.0
+  Zn  Zn3  1  0.01895000  0.70887000  0.50107000  1.0
+  Zn  Zn4  1  0.70179000  0.70895000  0.82362000  1.0
+  Zn  Zn5  1  0.25706000  0.61658000  0.27841000  1.0
+  Zn  Zn6  1  0.74274000  0.10677000  0.77248000  1.0
+  Zn  Zn7  1  0.77557000  0.75665000  0.66539000  1.0
+  Zn  Zn8  1  0.00977000  0.22879000  0.99502000  1.0
+  Zn  Zn9  1  0.51471000  0.29077000  0.99929000  1.0
+  Zn  Zn10  1  0.20121000  0.29117000  0.67664000  1.0
+  Zn  Zn11  1  0.75716000  0.38329000  0.22152000  1.0
+  Zn  Zn12  1  0.75717000  0.10681000  0.27184000  1.0
+  Zn  Zn13  1  0.72414000  0.75602000  0.16457000  1.0
+  Zn  Zn14  1  0.48894000  0.22820000  0.49513000  1.0
+  Zn  Zn15  1  0.98106000  0.29141000  0.49914000  1.0
+  Zn  Zn16  1  0.29756000  0.29090000  0.17625000  1.0
+  Zn  Zn17  1  0.74328000  0.38351000  0.72182000  1.0
+  Zn  Zn18  1  0.25750000  0.89338000  0.22770000  1.0
+  Zn  Zn19  1  0.22477000  0.24398000  0.33515000  1.0
+  Zn  Zn20  1  0.99119000  0.77312000  0.00438000  1.0
+  Zn  Zn21  1  0.48496000  0.71039000  0.00097000  1.0
+  Zn  Zn22  1  0.79910000  0.70865000  0.32334000  1.0
+  Zn  Zn23  1  0.24333000  0.61607000  0.77768000  1.0
+  P  P24  1  0.40382000  0.07283000  0.74706000  1.0
+  P  P25  1  0.51835000  0.80899000  0.75560000  1.0
+  P  P26  1  0.23023000  0.83280000  0.58683000  1.0
+  P  P27  1  0.22028000  0.34945000  0.96497000  1.0
+  P  P28  1  0.80022000  0.81957000  0.45349000  1.0
+  P  P29  1  0.28365000  0.67755000  0.41138000  1.0
+  P  P30  1  0.56953000  0.55736000  0.72957000  1.0
+  P  P31  1  0.44960000  0.34383000  0.76960000  1.0
+  P  P32  1  0.90435000  0.92764000  0.75534000  1.0
+  P  P33  1  0.01876000  0.19103000  0.74479000  1.0
+  P  P34  1  0.73142000  0.16958000  0.91405000  1.0
+  P  P35  1  0.72152000  0.65196000  0.53604000  1.0
+  P  P36  1  0.29546000  0.17886000  0.04604000  1.0
+  P  P37  1  0.78136000  0.32250000  0.08856000  1.0
+  P  P38  1  0.06849000  0.44283000  0.77048000  1.0
+  P  P39  1  0.94971000  0.65625000  0.73048000  1.0
+  P  P40  1  0.59635000  0.92738000  0.25329000  1.0
+  P  P41  1  0.48121000  0.19128000  0.24434000  1.0
+  P  P42  1  0.76917000  0.16768000  0.41358000  1.0
+  P  P43  1  0.77977000  0.65184000  0.03505000  1.0
+  P  P44  1  0.19972000  0.18060000  0.54654000  1.0
+  P  P45  1  0.71650000  0.32275000  0.58892000  1.0
+  P  P46  1  0.43078000  0.44235000  0.27010000  1.0
+  P  P47  1  0.55054000  0.65620000  0.23046000  1.0
+  P  P48  1  0.09631000  0.07284000  0.24636000  1.0
+  P  P49  1  0.98144000  0.80856000  0.25487000  1.0
+  P  P50  1  0.26979000  0.83263000  0.08595000  1.0
+  P  P51  1  0.27870000  0.34903000  0.46469000  1.0
+  P  P52  1  0.70315000  0.82137000  0.95334000  1.0
+  P  P53  1  0.21991000  0.67657000  0.91079000  1.0
+  P  P54  1  0.93194000  0.55689000  0.22947000  1.0
+  P  P55  1  0.05010000  0.34389000  0.26974000  1.0
+  H  H56  1  0.31341000  0.08186000  0.70263000  1.0
+  H  H57  1  0.56871000  0.88914000  0.76088000  1.0
+  H  H58  1  0.18725000  0.88268000  0.55311000  1.0
+  H  H59  1  0.18742000  0.41488000  0.94319000  1.0
+  H  H60  1  0.82836000  0.88583000  0.43189000  1.0
+  H  H61  1  0.39117000  0.61509000  0.39824000  1.0
+  H  H62  1  0.61603000  0.60344000  0.69374000  1.0
+  H  H63  1  0.41150000  0.42344000  0.76831000  1.0
+  H  H64  1  0.81464000  0.91888000  0.79999000  1.0
+  H  H65  1  0.06920000  0.11100000  0.73985000  1.0
+  H  H66  1  0.69497000  0.11985000  0.94861000  1.0
+  H  H67  1  0.68873000  0.58668000  0.55808000  1.0
+  H  H68  1  0.32300000  0.11187000  0.06689000  1.0
+  H  H69  1  0.88767000  0.38556000  0.10101000  1.0
+  H  H70  1  0.11556000  0.39716000  0.80650000  1.0
+  H  H71  1  0.91145000  0.57670000  0.73184000  1.0
+  H  H72  1  0.68678000  0.91845000  0.29774000  1.0
+  H  H73  1  0.43056000  0.11118000  0.23901000  1.0
+  H  H74  1  0.81192000  0.11784000  0.44735000  1.0
+  H  H75  1  0.81326000  0.58632000  0.05674000  1.0
+  H  H76  1  0.17169000  0.11436000  0.56816000  1.0
+  H  H77  1  0.60923000  0.38533000  0.60219000  1.0
+  H  H78  1  0.38461000  0.39647000  0.30611000  1.0
+  H  H79  1  0.58882000  0.57657000  0.23165000  1.0
+  H  H80  1  0.18649000  0.08190000  0.20190000  1.0
+  H  H81  1  0.93096000  0.88861000  0.25992000  1.0
+  H  H82  1  0.31016000  0.88246000  0.05197000  1.0
+  H  H83  1  0.31137000  0.41462000  0.44295000  1.0
+  H  H84  1  0.67316000  0.88714000  0.93145000  1.0
+  H  H85  1  0.11502000  0.61276000  0.89815000  1.0
+  H  H86  1  0.88618000  0.60297000  0.19355000  1.0
+  H  H87  1  0.08855000  0.42348000  0.26848000  1.0
+  O  O88  1  0.38145000  0.98665000  0.75319000  1.0
+  O  O89  1  0.35981000  0.13664000  0.80333000  1.0
+  O  O90  1  0.56210000  0.08466000  0.72902000  1.0
+  O  O91  1  0.34971000  0.80786000  0.74922000  1.0
+  O  O92  1  0.56353000  0.78924000  0.81024000  1.0
+  O  O93  1  0.58658000  0.74930000  0.70160000  1.0
+  O  O94  1  0.20922000  0.88535000  0.64891000  1.0
+  O  O95  1  0.13003000  0.75633000  0.57220000  1.0
+  O  O96  1  0.39429000  0.81010000  0.57513000  1.0
+  O  O97  1  0.08964000  0.33946000  0.00231000  1.0
+  O  O98  1  0.23959000  0.26845000  0.91613000  1.0
+  O  O99  1  0.36546000  0.37243000  0.99818000  1.0
+  O  O100  1  0.94072000  0.80757000  0.48495000  1.0
+  O  O101  1  0.66484000  0.84409000  0.49268000  1.0
+  O  O102  1  0.76606000  0.74121000  0.40415000  1.0
+  O  O103  1  0.35618000  0.75858000  0.44667000  1.0
+  O  O104  1  0.22063000  0.68777000  0.35561000  1.0
+  O  O105  1  0.16212000  0.64900000  0.44483000  1.0
+  O  O106  1  0.62687000  0.46984000  0.70280000  1.0
+  O  O107  1  0.40072000  0.55909000  0.73023000  1.0
+  O  O108  1  0.63436000  0.59645000  0.78976000  1.0
+  O  O109  1  0.38919000  0.33592000  0.82624000  1.0
+  O  O110  1  0.61801000  0.33511000  0.76725000  1.0
+  O  O111  1  0.38124000  0.28023000  0.71724000  1.0
+  O  O112  1  0.88180000  0.01356000  0.74877000  1.0
+  O  O113  1  0.86039000  0.86366000  0.69913000  1.0
+  O  O114  1  0.06291000  0.91581000  0.77317000  1.0
+  O  O115  1  0.85014000  0.19201000  0.75114000  1.0
+  O  O116  1  0.06396000  0.21043000  0.69002000  1.0
+  O  O117  1  0.08711000  0.25106000  0.79861000  1.0
+  O  O118  1  0.71035000  0.11587000  0.85233000  1.0
+  O  O119  1  0.62616000  0.24395000  0.92830000  1.0
+  O  O120  1  0.89404000  0.19637000  0.92483000  1.0
+  O  O121  1  0.58931000  0.66211000  0.49946000  1.0
+  O  O122  1  0.74214000  0.73297000  0.58483000  1.0
+  O  O123  1  0.86609000  0.62909000  0.50242000  1.0
+  O  O124  1  0.43554000  0.19189000  0.01476000  1.0
+  O  O125  1  0.16020000  0.15442000  0.00660000  1.0
+  O  O126  1  0.26033000  0.25657000  0.09569000  1.0
+  O  O127  1  0.85464000  0.24175000  0.05323000  1.0
+  O  O128  1  0.72047000  0.31207000  0.14457000  1.0
+  O  O129  1  0.65782000  0.35039000  0.05568000  1.0
+  O  O130  1  0.12524000  0.53054000  0.79695000  1.0
+  O  O131  1  0.89972000  0.44045000  0.76986000  1.0
+  O  O132  1  0.13338000  0.40366000  0.71032000  1.0
+  O  O133  1  0.88876000  0.66422000  0.67392000  1.0
+  O  O134  1  0.11817000  0.66476000  0.73248000  1.0
+  O  O135  1  0.88184000  0.71994000  0.78290000  1.0
+  O  O136  1  0.61821000  0.01359000  0.24717000  1.0
+  O  O137  1  0.64066000  0.86370000  0.19702000  1.0
+  O  O138  1  0.43817000  0.91508000  0.27124000  1.0
+  O  O139  1  0.64984000  0.19231000  0.25077000  1.0
+  O  O140  1  0.43664000  0.21108000  0.18967000  1.0
+  O  O141  1  0.41292000  0.25097000  0.29833000  1.0
+  O  O142  1  0.78964000  0.11499000  0.35153000  1.0
+  O  O143  1  0.86986000  0.24394000  0.42806000  1.0
+  O  O144  1  0.60529000  0.19075000  0.42534000  1.0
+  O  O145  1  0.91118000  0.66282000  0.99841000  1.0
+  O  O146  1  0.75836000  0.73249000  0.08405000  1.0
+  O  O147  1  0.63513000  0.62871000  0.00149000  1.0
+  O  O148  1  0.05913000  0.19261000  0.51515000  1.0
+  O  O149  1  0.33499000  0.15613000  0.50730000  1.0
+  O  O150  1  0.23418000  0.25895000  0.59585000  1.0
+  O  O151  1  0.64357000  0.24181000  0.55367000  1.0
+  O  O152  1  0.77982000  0.31234000  0.64459000  1.0
+  O  O153  1  0.83794000  0.35122000  0.55540000  1.0
+  O  O154  1  0.37445000  0.53008000  0.29698000  1.0
+  O  O155  1  0.59957000  0.44007000  0.26917000  1.0
+  O  O156  1  0.36527000  0.40330000  0.21002000  1.0
+  O  O157  1  0.61065000  0.66414000  0.17377000  1.0
+  O  O158  1  0.38213000  0.66494000  0.23289000  1.0
+  O  O159  1  0.61904000  0.71979000  0.28278000  1.0
+  O  O160  1  0.11852000  0.98661000  0.25241000  1.0
+  O  O161  1  0.14038000  0.13651000  0.30267000  1.0
+  O  O162  1  0.93810000  0.08501000  0.22839000  1.0
+  O  O163  1  0.15003000  0.80749000  0.24836000  1.0
+  O  O164  1  0.93659000  0.78906000  0.30963000  1.0
+  O  O165  1  0.91287000  0.74865000  0.20103000  1.0
+  O  O166  1  0.29014000  0.88543000  0.14801000  1.0
+  O  O167  1  0.37183000  0.75686000  0.07163000  1.0
+  O  O168  1  0.10624000  0.80818000  0.07457000  1.0
+  O  O169  1  0.41071000  0.33885000  0.50138000  1.0
+  O  O170  1  0.25897000  0.26820000  0.41570000  1.0
+  O  O171  1  0.13377000  0.37140000  0.49814000  1.0
+  O  O172  1  0.56509000  0.80947000  0.98613000  1.0
+  O  O173  1  0.84104000  0.84683000  0.99118000  1.0
+  O  O174  1  0.73595000  0.74245000  0.90430000  1.0
+  O  O175  1  0.14489000  0.75711000  0.94539000  1.0
+  O  O176  1  0.28143000  0.68681000  0.85480000  1.0
+  O  O177  1  0.34344000  0.64989000  0.94428000  1.0
+  O  O178  1  0.87464000  0.46938000  0.20264000  1.0
+  O  O179  1  0.10073000  0.55889000  0.23062000  1.0
+  O  O180  1  0.86634000  0.59600000  0.28953000  1.0
+  O  O181  1  0.11020000  0.33582000  0.32638000  1.0
+  O  O182  1  0.88168000  0.33525000  0.26729000  1.0
+  O  O183  1  0.11844000  0.28014000  0.21748000  1.0
diff --git a/tests/testresources/inputs/cif_files/odac-21735.cif b/tests/testresources/inputs/cif_files/odac-21735.cif
index 04257992..ecaeefc3 100644
--- a/tests/testresources/inputs/cif_files/odac-21735.cif
+++ b/tests/testresources/inputs/cif_files/odac-21735.cif
@@ -1,139 +1,140 @@
-data_image0
-_chemical_formula_structural       Zr6H28C48O32
-_chemical_formula_sum              "Zr6 H28 C48 O32"
-_cell_length_a       14.7589
-_cell_length_b       14.7589
-_cell_length_c       14.7589
-_cell_angle_alpha    60
-_cell_angle_beta     60
-_cell_angle_gamma    60
-
-_space_group_name_H-M_alt    "P 1"
-_space_group_IT_number       1
-
+# generated using pymatgen
+data_Zr3H14(C3O2)8
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   14.75890000
+_cell_length_b   14.75890000
+_cell_length_c   14.75890000
+_cell_angle_alpha   60.00000000
+_cell_angle_beta   60.00000000
+_cell_angle_gamma   60.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Zr3H14(C3O2)8
+_chemical_formula_sum   'Zr6 H28 C48 O32'
+_cell_volume   2273.24881124
+_cell_formula_units_Z   2
 loop_
-  _space_group_symop_operation_xyz
-  'x, y, z'
-
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
 loop_
-  _atom_site_type_symbol
-  _atom_site_label
-  _atom_site_symmetry_multiplicity
-  _atom_site_fract_x
-  _atom_site_fract_y
-  _atom_site_fract_z
-  _atom_site_occupancy
-  Zr  Zr1       1.0  0.88062  0.11969  0.11996  1.0000
-  Zr  Zr2       1.0  0.12013  0.88017  0.88056  1.0000
-  Zr  Zr3       1.0  0.12016  0.88015  0.12009  1.0000
-  Zr  Zr4       1.0  0.88064  0.11977  0.88045  1.0000
-  Zr  Zr5       1.0  0.12023  0.11965  0.88039  1.0000
-  Zr  Zr6       1.0  0.88068  0.88010  0.12005  1.0000
-  H   H1        1.0  0.84757  0.13815  0.42213  1.0000
-  H   H2        1.0  0.13788  0.84700  0.59344  1.0000
-  H   H3        1.0  0.42387  0.59399  0.84593  1.0000
-  H   H4        1.0  0.59268  0.42201  0.13852  1.0000
-  H   H5        1.0  0.42413  0.84540  0.13697  1.0000
-  H   H6        1.0  0.59269  0.13826  0.84776  1.0000
-  H   H7        1.0  0.84752  0.42194  0.59324  1.0000
-  H   H8        1.0  0.13673  0.59430  0.42380  1.0000
-  H   H9        1.0  0.14064  0.41983  0.84925  1.0000
-  H   H10       1.0  0.84564  0.59468  0.13590  1.0000
-  H   H11       1.0  0.59265  0.84762  0.42169  1.0000
-  H   H12       1.0  0.42175  0.13851  0.59242  1.0000
-  H   H13       1.0  0.13802  0.84688  0.42275  1.0000
-  H   H14       1.0  0.84746  0.13835  0.59276  1.0000
-  H   H15       1.0  0.59471  0.42348  0.84588  1.0000
-  H   H16       1.0  0.42215  0.59267  0.13829  1.0000
-  H   H17       1.0  0.84496  0.42476  0.13513  1.0000
-  H   H18       1.0  0.14171  0.58942  0.85040  1.0000
-  H   H19       1.0  0.42195  0.84756  0.59238  1.0000
-  H   H20       1.0  0.59241  0.13860  0.42173  1.0000
-  H   H21       1.0  0.42207  0.13802  0.84789  1.0000
-  H   H22       1.0  0.59467  0.84563  0.13689  1.0000
-  H   H23       1.0  0.84721  0.59266  0.42270  1.0000
-  H   H24       1.0  0.13680  0.42375  0.59451  1.0000
-  H   H25       1.0  0.09476  0.09447  0.09434  1.0000
-  H   H26       1.0  0.09454  0.09444  0.71734  1.0000
-  H   H27       1.0  0.09490  0.71699  0.09501  1.0000
-  H   H28       1.0  0.71748  0.09426  0.09440  1.0000
-  C   C1        1.0  0.91052  0.07496  0.46055  1.0000
-  C   C2        1.0  0.07483  0.91013  0.55508  1.0000
-  C   C3        1.0  0.46183  0.55557  0.90931  1.0000
-  C   C4        1.0  0.55488  0.46050  0.07501  1.0000
-  C   C5        1.0  0.46184  0.90899  0.07423  1.0000
-  C   C6        1.0  0.55491  0.07469  0.91050  1.0000
-  C   C7        1.0  0.91027  0.46057  0.55527  1.0000
-  C   C8        1.0  0.07397  0.55569  0.46178  1.0000
-  C   C9        1.0  0.07685  0.45886  0.91155  1.0000
-  C   C10       1.0  0.90968  0.55553  0.07373  1.0000
-  C   C11       1.0  0.55441  0.91066  0.46003  1.0000
-  C   C12       1.0  0.46012  0.07531  0.55423  1.0000
-  C   C13       1.0  0.07491  0.91008  0.46089  1.0000
-  C   C14       1.0  0.91045  0.07504  0.55473  1.0000
-  C   C15       1.0  0.55607  0.46147  0.90927  1.0000
-  C   C16       1.0  0.46073  0.55467  0.07493  1.0000
-  C   C17       1.0  0.90937  0.46169  0.07332  1.0000
-  C   C18       1.0  0.07726  0.55255  0.91208  1.0000
-  C   C19       1.0  0.46024  0.91062  0.55422  1.0000
-  C   C20       1.0  0.55429  0.07537  0.46005  1.0000
-  C   C21       1.0  0.46076  0.07458  0.91058  1.0000
-  C   C22       1.0  0.55602  0.90907  0.07416  1.0000
-  C   C23       1.0  0.91009  0.55482  0.46116  1.0000
-  C   C24       1.0  0.07408  0.46148  0.55590  1.0000
-  C   C25       1.0  0.99579  0.99553  0.30909  1.0000
-  C   C26       1.0  0.99328  0.99303  0.41269  1.0000
-  C   C27       1.0  0.99550  0.99547  0.70064  1.0000
-  C   C28       1.0  0.99311  0.99310  0.60190  1.0000
-  C   C29       1.0  0.30945  0.70036  0.99542  1.0000
-  C   C30       1.0  0.41319  0.60197  0.99274  1.0000
-  C   C31       1.0  0.70062  0.30903  0.99560  1.0000
-  C   C32       1.0  0.60239  0.41290  0.99278  1.0000
-  C   C33       1.0  0.30949  0.99499  0.99571  1.0000
-  C   C34       1.0  0.41320  0.99233  0.99304  1.0000
-  C   C35       1.0  0.70091  0.99512  0.99539  1.0000
-  C   C36       1.0  0.60241  0.99248  0.99287  1.0000
-  C   C37       1.0  0.99564  0.30917  0.70075  1.0000
-  C   C38       1.0  0.99292  0.41288  0.60240  1.0000
-  C   C39       1.0  0.99535  0.70049  0.30958  1.0000
-  C   C40       1.0  0.99258  0.60217  0.41335  1.0000
-  C   C41       1.0  0.99575  0.30905  0.99515  1.0000
-  C   C42       1.0  -0.00651  0.41240  -0.00717  1.0000
-  C   C43       1.0  0.99649  0.69948  0.99615  1.0000
-  C   C44       1.0  0.99412  0.60084  0.99363  1.0000
-  C   C45       1.0  0.70029  0.99568  0.30883  1.0000
-  C   C46       1.0  0.60139  0.99347  0.41211  1.0000
-  C   C47       1.0  0.30899  0.99550  0.70017  1.0000
-  C   C48       1.0  0.41226  0.99339  0.60127  1.0000
-  O   O1        1.0  0.92048  0.07421  0.26786  1.0000
-  O   O2        1.0  0.07371  0.91969  0.73896  1.0000
-  O   O3        1.0  0.26847  0.73847  0.91985  1.0000
-  O   O4        1.0  0.73838  0.26782  0.07437  1.0000
-  O   O5        1.0  0.26822  0.91968  0.07433  1.0000
-  O   O6        1.0  0.73859  0.07398  0.92022  1.0000
-  O   O7        1.0  0.92019  0.26801  0.73887  1.0000
-  O   O8        1.0  0.07413  0.73827  0.26823  1.0000
-  O   O9        1.0  0.07461  0.26766  0.92002  1.0000
-  O   O10       1.0  0.92091  0.73751  0.07465  1.0000
-  O   O11       1.0  0.73820  0.92028  0.26768  1.0000
-  O   O12       1.0  0.26821  0.07374  0.73851  1.0000
-  O   O13       1.0  0.07427  0.91999  0.26813  1.0000
-  O   O14       1.0  0.92029  0.07429  0.73835  1.0000
-  O   O15       1.0  0.73846  0.26782  0.92029  1.0000
-  O   O16       1.0  0.26811  0.73802  0.07429  1.0000
-  O   O17       1.0  0.91983  0.26845  0.07332  1.0000
-  O   O18       1.0  0.07508  0.73744  0.92073  1.0000
-  O   O19       1.0  0.26784  0.92014  0.73805  1.0000
-  O   O20       1.0  0.73860  0.07392  0.26804  1.0000
-  O   O21       1.0  0.26825  0.07370  0.92034  1.0000
-  O   O22       1.0  0.73917  0.91951  0.07378  1.0000
-  O   O23       1.0  0.91995  0.73852  0.26835  1.0000
-  O   O24       1.0  0.07459  0.26762  0.73840  1.0000
-  O   O25       1.0  0.95066  0.14914  0.95049  1.0000
-  O   O26       1.0  0.06794  0.79746  0.06791  1.0000
-  O   O27       1.0  0.14956  0.95018  0.95055  1.0000
-  O   O28       1.0  0.79796  0.06743  0.06766  1.0000
-  O   O29       1.0  0.95067  0.95010  0.95055  1.0000
-  O   O30       1.0  0.06782  0.06759  0.06769  1.0000
-  O   O31       1.0  0.95058  0.95027  0.14950  1.0000
-  O   O32       1.0  0.06780  0.06740  0.79781  1.0000
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Zr  Zr0  1  0.12027000  0.88004000  0.11938000  1.0
+  Zr  Zr1  1  0.88086000  0.11944000  0.87987000  1.0
+  Zr  Zr2  1  0.12040000  0.87991000  0.87984000  1.0
+  Zr  Zr3  1  0.88086000  0.11955000  0.11936000  1.0
+  Zr  Zr4  1  0.12027000  0.11961000  0.87977000  1.0
+  Zr  Zr5  1  0.88083000  0.87995000  0.11932000  1.0
+  H  H6  1  0.40785000  0.57787000  0.15243000  1.0
+  H  H7  1  0.57832000  0.40656000  0.86212000  1.0
+  H  H8  1  0.86379000  0.15407000  0.57613000  1.0
+  H  H9  1  0.15321000  0.86148000  0.40732000  1.0
+  H  H10  1  0.40650000  0.86303000  0.57587000  1.0
+  H  H11  1  0.57871000  0.15224000  0.40731000  1.0
+  H  H12  1  0.86270000  0.40676000  0.15248000  1.0
+  H  H13  1  0.15483000  0.57620000  0.86327000  1.0
+  H  H14  1  0.40972000  0.15075000  0.85936000  1.0
+  H  H15  1  0.57622000  0.86410000  0.15436000  1.0
+  H  H16  1  0.86196000  0.57831000  0.40735000  1.0
+  H  H17  1  0.15268000  0.40758000  0.57825000  1.0
+  H  H18  1  0.40765000  0.57725000  0.86198000  1.0
+  H  H19  1  0.57857000  0.40724000  0.15254000  1.0
+  H  H20  1  0.86407000  0.15412000  0.40529000  1.0
+  H  H21  1  0.15311000  0.86171000  0.57785000  1.0
+  H  H22  1  0.40485000  0.86487000  0.15504000  1.0
+  H  H23  1  0.58153000  0.14960000  0.85829000  1.0
+  H  H24  1  0.86189000  0.40762000  0.57805000  1.0
+  H  H25  1  0.15274000  0.57827000  0.40759000  1.0
+  H  H26  1  0.40798000  0.15211000  0.57793000  1.0
+  H  H27  1  0.57719000  0.86311000  0.40533000  1.0
+  H  H28  1  0.86257000  0.57730000  0.15279000  1.0
+  H  H29  1  0.15506000  0.40549000  0.86320000  1.0
+  H  H30  1  0.28357000  0.90566000  0.90524000  1.0
+  H  H31  1  0.90632000  0.28266000  0.90546000  1.0
+  H  H32  1  0.90690000  0.90499000  0.90510000  1.0
+  H  H33  1  0.90614000  0.90560000  0.28252000  1.0
+  C  C34  1  0.44603000  0.53945000  0.08948000  1.0
+  C  C35  1  0.54004000  0.44492000  0.92517000  1.0
+  C  C36  1  0.92671000  0.09069000  0.53817000  1.0
+  C  C37  1  0.09039000  0.92499000  0.44512000  1.0
+  C  C38  1  0.44506000  0.92577000  0.53816000  1.0
+  C  C39  1  0.54010000  0.08950000  0.44509000  1.0
+  C  C40  1  0.92611000  0.44473000  0.08973000  1.0
+  C  C41  1  0.09144000  0.53822000  0.92603000  1.0
+  C  C42  1  0.44726000  0.08845000  0.92315000  1.0
+  C  C43  1  0.53894000  0.92627000  0.09032000  1.0
+  C  C44  1  0.92510000  0.53997000  0.44559000  1.0
+  C  C45  1  0.08966000  0.44577000  0.53988000  1.0
+  C  C46  1  0.44588000  0.53911000  0.92509000  1.0
+  C  C47  1  0.54022000  0.44527000  0.08955000  1.0
+  C  C48  1  0.92681000  0.09073000  0.44393000  1.0
+  C  C49  1  0.09033000  0.92507000  0.53927000  1.0
+  C  C50  1  0.44438000  0.92668000  0.09063000  1.0
+  C  C51  1  0.54189000  0.08792000  0.92274000  1.0
+  C  C52  1  0.92508000  0.44578000  0.53976000  1.0
+  C  C53  1  0.08971000  0.53995000  0.44571000  1.0
+  C  C54  1  0.44592000  0.08942000  0.53924000  1.0
+  C  C55  1  0.53925000  0.92584000  0.44398000  1.0
+  C  C56  1  0.92607000  0.53884000  0.08991000  1.0
+  C  C57  1  0.09146000  0.44410000  0.92592000  1.0
+  C  C58  1  0.30041000  0.69091000  0.00421000  1.0
+  C  C59  1  0.39900000  0.58731000  0.00672000  1.0
+  C  C60  1  0.69161000  0.29936000  0.00450000  1.0
+  C  C61  1  0.58811000  0.39810000  0.00689000  1.0
+  C  C62  1  0.00523000  0.00458000  0.69055000  1.0
+  C  C63  1  0.00790000  0.00726000  0.58681000  1.0
+  C  C64  1  0.00525000  0.00440000  0.29938000  1.0
+  C  C65  1  0.00807000  0.00722000  0.39761000  1.0
+  C  C66  1  0.30019000  0.00429000  0.69051000  1.0
+  C  C67  1  0.39857000  0.00696000  0.58680000  1.0
+  C  C68  1  0.69142000  0.00461000  0.29909000  1.0
+  C  C69  1  0.58776000  0.00713000  0.39759000  1.0
+  C  C70  1  0.00556000  0.29925000  0.00436000  1.0
+  C  C71  1  0.00820000  0.39760000  0.00708000  1.0
+  C  C72  1  0.00542000  0.69042000  0.00465000  1.0
+  C  C73  1  0.00810000  0.58665000  0.00742000  1.0
+  C  C74  1  0.29995000  0.00485000  0.00425000  1.0
+  C  C75  1  0.39872000  0.00717000  0.00651000  1.0
+  C  C76  1  0.69212000  0.00385000  0.00351000  1.0
+  C  C77  1  0.58859000  0.00637000  0.00588000  1.0
+  C  C78  1  0.00480000  0.69117000  0.29971000  1.0
+  C  C79  1  0.00697000  0.58789000  0.39861000  1.0
+  C  C80  1  0.00466000  0.29983000  0.69101000  1.0
+  C  C81  1  0.00692000  0.39873000  0.58774000  1.0
+  O  O82  1  0.26255000  0.73214000  0.07952000  1.0
+  O  O83  1  0.73236000  0.26104000  0.92629000  1.0
+  O  O84  1  0.92679000  0.08015000  0.73153000  1.0
+  O  O85  1  0.08057000  0.92563000  0.26162000  1.0
+  O  O86  1  0.26223000  0.92567000  0.73178000  1.0
+  O  O87  1  0.73279000  0.07978000  0.26141000  1.0
+  O  O88  1  0.92707000  0.26113000  0.07981000  1.0
+  O  O89  1  0.08063000  0.73177000  0.92587000  1.0
+  O  O90  1  0.26229000  0.07998000  0.92539000  1.0
+  O  O91  1  0.73307000  0.92535000  0.07909000  1.0
+  O  O92  1  0.92616000  0.73232000  0.26180000  1.0
+  O  O93  1  0.08046000  0.26149000  0.73179000  1.0
+  O  O94  1  0.26239000  0.73187000  0.92573000  1.0
+  O  O95  1  0.73293000  0.26165000  0.07971000  1.0
+  O  O96  1  0.92657000  0.07971000  0.26154000  1.0
+  O  O97  1  0.08042000  0.92571000  0.73189000  1.0
+  O  O98  1  0.26160000  0.92668000  0.08017000  1.0
+  O  O99  1  0.73325000  0.07927000  0.92492000  1.0
+  O  O100  1  0.92603000  0.26195000  0.73216000  1.0
+  O  O101  1  0.08056000  0.73196000  0.26140000  1.0
+  O  O102  1  0.26229000  0.07966000  0.73175000  1.0
+  O  O103  1  0.73246000  0.92622000  0.26083000  1.0
+  O  O104  1  0.92682000  0.73165000  0.08005000  1.0
+  O  O105  1  0.08061000  0.26160000  0.92541000  1.0
+  O  O106  1  0.05029000  0.04951000  0.04934000  1.0
+  O  O107  1  0.93331000  0.93209000  0.93206000  1.0
+  O  O108  1  0.05029000  0.04945000  0.85044000  1.0
+  O  O109  1  0.93305000  0.93234000  0.20204000  1.0
+  O  O110  1  0.85132000  0.04945000  0.04933000  1.0
+  O  O111  1  0.20310000  0.93231000  0.93218000  1.0
+  O  O112  1  0.05035000  0.85050000  0.04942000  1.0
+  O  O113  1  0.93301000  0.20219000  0.93220000  1.0
diff --git a/tests/testresources/inputs/cif_files/odac-21816.cif b/tests/testresources/inputs/cif_files/odac-21816.cif
index 0fd41b5d..8d5644bc 100644
--- a/tests/testresources/inputs/cif_files/odac-21816.cif
+++ b/tests/testresources/inputs/cif_files/odac-21816.cif
@@ -1,417 +1,418 @@
-data_image0
-_chemical_formula_structural       Cu16H88C192N16O80
-_chemical_formula_sum              "Cu16 H88 C192 N16 O80"
-_cell_length_a       18.9609
-_cell_length_b       18.9609
-_cell_length_c       34.7406
-_cell_angle_alpha    90
-_cell_angle_beta     90
-_cell_angle_gamma    90.0002
-
-_space_group_name_H-M_alt    "P 1"
-_space_group_IT_number       1
-
+# generated using pymatgen
+data_Cu2H11C24(NO5)2
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   18.96090000
+_cell_length_b   18.96090000
+_cell_length_c   34.74060000
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   89.99980000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Cu2H11C24(NO5)2
+_chemical_formula_sum   'Cu16 H88 C192 N16 O80'
+_cell_volume   12489.79212822
+_cell_formula_units_Z   8
 loop_
-  _space_group_symop_operation_xyz
-  'x, y, z'
-
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
 loop_
-  _atom_site_type_symbol
-  _atom_site_label
-  _atom_site_symmetry_multiplicity
-  _atom_site_fract_x
-  _atom_site_fract_y
-  _atom_site_fract_z
-  _atom_site_occupancy
-  Cu  Cu1       1.0  0.73250  0.29250  0.22324  1.0000
-  Cu  Cu2       1.0  0.26750  0.70750  0.22324  1.0000
-  Cu  Cu3       1.0  0.70750  0.73250  0.22324  1.0000
-  Cu  Cu4       1.0  0.29250  0.26750  0.22324  1.0000
-  Cu  Cu5       1.0  0.76750  0.79250  0.27676  1.0000
-  Cu  Cu6       1.0  0.23250  0.20750  0.27676  1.0000
-  Cu  Cu7       1.0  0.79250  0.23250  0.27676  1.0000
-  Cu  Cu8       1.0  0.20750  0.76750  0.27676  1.0000
-  Cu  Cu9       1.0  0.26750  0.70750  0.77676  1.0000
-  Cu  Cu10      1.0  0.73249  0.29251  0.77678  1.0000
-  Cu  Cu11      1.0  0.29251  0.26749  0.77678  1.0000
-  Cu  Cu12      1.0  0.70750  0.73249  0.77676  1.0000
-  Cu  Cu13      1.0  0.23249  0.20750  0.72324  1.0000
-  Cu  Cu14      1.0  0.76749  0.79252  0.72322  1.0000
-  Cu  Cu15      1.0  0.20750  0.76750  0.72324  1.0000
-  Cu  Cu16      1.0  0.79252  0.23249  0.72322  1.0000
-  H   H1        1.0  0.01520  0.45173  0.06202  1.0000
-  H   H2        1.0  0.96906  0.35933  0.09267  1.0000
-  H   H3        1.0  0.90202  0.32039  0.14556  1.0000
-  H   H4        1.0  0.01255  0.24349  0.24520  1.0000
-  H   H5        1.0  0.12878  0.29649  0.14259  1.0000
-  H   H6        1.0  0.98480  0.54827  0.06202  1.0000
-  H   H7        1.0  0.03094  0.64067  0.09267  1.0000
-  H   H8        1.0  0.09798  0.67961  0.14556  1.0000
-  H   H9        1.0  0.98745  0.75651  0.24520  1.0000
-  H   H10       1.0  0.87122  0.70351  0.14259  1.0000
-  H   H11       1.0  0.54827  0.01520  0.06202  1.0000
-  H   H12       1.0  0.64067  0.96906  0.09267  1.0000
-  H   H13       1.0  0.67961  0.90202  0.14556  1.0000
-  H   H14       1.0  0.75651  0.01255  0.24520  1.0000
-  H   H15       1.0  0.70351  0.12879  0.14259  1.0000
-  H   H16       1.0  0.45173  0.98480  0.06202  1.0000
-  H   H17       1.0  0.35933  0.03094  0.09267  1.0000
-  H   H18       1.0  0.32039  0.09798  0.14556  1.0000
-  H   H19       1.0  0.24349  0.98745  0.24520  1.0000
-  H   H20       1.0  0.29649  0.87121  0.14259  1.0000
-  H   H21       1.0  0.48480  0.95173  0.43798  1.0000
-  H   H22       1.0  0.53094  0.85933  0.40733  1.0000
-  H   H23       1.0  0.59798  0.82039  0.35444  1.0000
-  H   H24       1.0  0.48745  0.74349  0.25479  1.0000
-  H   H25       1.0  0.37121  0.79649  0.35741  1.0000
-  H   H26       1.0  0.51520  0.04827  0.43798  1.0000
-  H   H27       1.0  0.46906  0.14067  0.40733  1.0000
-  H   H28       1.0  0.40202  0.17961  0.35444  1.0000
-  H   H29       1.0  0.51255  0.25651  0.25480  1.0000
-  H   H30       1.0  0.62879  0.20351  0.35741  1.0000
-  H   H31       1.0  0.95173  0.51520  0.43798  1.0000
-  H   H32       1.0  0.85933  0.46906  0.40733  1.0000
-  H   H33       1.0  0.82039  0.40202  0.35444  1.0000
-  H   H34       1.0  0.74349  0.51255  0.25480  1.0000
-  H   H35       1.0  0.79649  0.62878  0.35741  1.0000
-  H   H36       1.0  0.04827  0.48480  0.43798  1.0000
-  H   H37       1.0  0.14067  0.53094  0.40733  1.0000
-  H   H38       1.0  0.17961  0.59798  0.35444  1.0000
-  H   H39       1.0  0.25651  0.48745  0.25480  1.0000
-  H   H40       1.0  0.20351  0.37122  0.35741  1.0000
-  H   H41       1.0  0.98480  0.54827  0.93795  1.0000
-  H   H42       1.0  0.03095  0.64067  0.90731  1.0000
-  H   H43       1.0  0.09799  0.67961  0.85442  1.0000
-  H   H44       1.0  0.98745  0.75652  0.75478  1.0000
-  H   H45       1.0  0.87122  0.70351  0.85739  1.0000
-  H   H46       1.0  0.01520  0.45173  0.93795  1.0000
-  H   H47       1.0  0.96905  0.35933  0.90731  1.0000
-  H   H48       1.0  0.90201  0.32039  0.85442  1.0000
-  H   H49       1.0  0.01255  0.24348  0.75478  1.0000
-  H   H50       1.0  0.12878  0.29649  0.85739  1.0000
-  H   H51       1.0  0.45173  0.98480  0.93795  1.0000
-  H   H52       1.0  0.35935  0.03095  0.90731  1.0000
-  H   H53       1.0  0.32041  0.09798  0.85442  1.0000
-  H   H54       1.0  0.24348  0.98745  0.75478  1.0000
-  H   H55       1.0  0.29649  0.87122  0.85739  1.0000
-  H   H56       1.0  0.54826  0.01521  0.93795  1.0000
-  H   H57       1.0  0.64066  0.96906  0.90730  1.0000
-  H   H58       1.0  0.67961  0.90203  0.85441  1.0000
-  H   H59       1.0  0.75653  0.01253  0.75476  1.0000
-  H   H60       1.0  0.70345  0.12880  0.85738  1.0000
-  H   H61       1.0  0.51521  0.04826  0.56205  1.0000
-  H   H62       1.0  0.46906  0.14066  0.59269  1.0000
-  H   H63       1.0  0.40203  0.17961  0.64559  1.0000
-  H   H64       1.0  0.51255  0.25648  0.74525  1.0000
-  H   H65       1.0  0.62880  0.20345  0.64262  1.0000
-  H   H66       1.0  0.48480  0.95173  0.56205  1.0000
-  H   H67       1.0  0.53095  0.85935  0.59269  1.0000
-  H   H68       1.0  0.59798  0.82041  0.64558  1.0000
-  H   H69       1.0  0.48745  0.74347  0.74522  1.0000
-  H   H70       1.0  0.37122  0.79649  0.64261  1.0000
-  H   H71       1.0  0.04827  0.48480  0.56205  1.0000
-  H   H72       1.0  0.14067  0.53095  0.59269  1.0000
-  H   H73       1.0  0.17961  0.59799  0.64558  1.0000
-  H   H74       1.0  0.25652  0.48745  0.74522  1.0000
-  H   H75       1.0  0.20351  0.37122  0.64261  1.0000
-  H   H76       1.0  0.95173  0.51520  0.56205  1.0000
-  H   H77       1.0  0.85933  0.46905  0.59269  1.0000
-  H   H78       1.0  0.82039  0.40201  0.64558  1.0000
-  H   H79       1.0  0.74348  0.51255  0.74522  1.0000
-  H   H80       1.0  0.79649  0.62878  0.64261  1.0000
-  H   H81       1.0  0.08231  0.26766  0.99999  1.0000
-  H   H82       1.0  0.91769  0.73234  0.99999  1.0000
-  H   H83       1.0  0.73234  0.08231  0.99999  1.0000
-  H   H84       1.0  0.26766  0.91769  0.99999  1.0000
-  H   H85       1.0  0.41769  0.76766  0.50001  1.0000
-  H   H86       1.0  0.58231  0.23234  0.50001  1.0000
-  H   H87       1.0  0.76766  0.58231  0.50001  1.0000
-  H   H88       1.0  0.23234  0.41769  0.50001  1.0000
-  C   C1        1.0  0.02268  0.42546  0.03444  1.0000
-  C   C2        1.0  0.04692  0.35574  0.03464  1.0000
-  C   C3        1.0  0.06127  0.31811  0.07185  1.0000
-  C   C4        1.0  0.01555  0.31019  0.13907  1.0000
-  C   C5        1.0  0.95177  0.30591  0.15919  1.0000
-  C   C6        1.0  0.95068  0.28183  0.19722  1.0000
-  C   C7        1.0  0.01337  0.26264  0.21569  1.0000
-  C   C8        1.0  0.07714  0.26950  0.19585  1.0000
-  C   C9        1.0  0.07871  0.29250  0.15757  1.0000
-  C   C10       1.0  0.88158  0.27570  0.21757  1.0000
-  C   C11       1.0  0.14553  0.25531  0.21584  1.0000
-  C   C12       1.0  0.97732  0.57454  0.03444  1.0000
-  C   C13       1.0  0.95308  0.64426  0.03464  1.0000
-  C   C14       1.0  0.93873  0.68189  0.07185  1.0000
-  C   C15       1.0  0.98445  0.68981  0.13907  1.0000
-  C   C16       1.0  0.04823  0.69409  0.15919  1.0000
-  C   C17       1.0  0.04932  0.71817  0.19722  1.0000
-  C   C18       1.0  0.98663  0.73736  0.21569  1.0000
-  C   C19       1.0  0.92286  0.73050  0.19585  1.0000
-  C   C20       1.0  0.92129  0.70750  0.15757  1.0000
-  C   C21       1.0  0.11842  0.72430  0.21757  1.0000
-  C   C22       1.0  0.85447  0.74469  0.21584  1.0000
-  C   C23       1.0  0.57454  0.02268  0.03444  1.0000
-  C   C24       1.0  0.64426  0.04693  0.03464  1.0000
-  C   C25       1.0  0.68189  0.06127  0.07185  1.0000
-  C   C26       1.0  0.68981  0.01555  0.13907  1.0000
-  C   C27       1.0  0.69409  0.95177  0.15919  1.0000
-  C   C28       1.0  0.71817  0.95069  0.19722  1.0000
-  C   C29       1.0  0.73736  0.01337  0.21569  1.0000
-  C   C30       1.0  0.73050  0.07715  0.19585  1.0000
-  C   C31       1.0  0.70750  0.07871  0.15757  1.0000
-  C   C32       1.0  0.72430  0.88158  0.21757  1.0000
-  C   C33       1.0  0.74469  0.14553  0.21584  1.0000
-  C   C34       1.0  0.42546  0.97732  0.03444  1.0000
-  C   C35       1.0  0.35574  0.95307  0.03464  1.0000
-  C   C36       1.0  0.31811  0.93873  0.07185  1.0000
-  C   C37       1.0  0.31019  0.98445  0.13907  1.0000
-  C   C38       1.0  0.30591  0.04823  0.15919  1.0000
-  C   C39       1.0  0.28183  0.04931  0.19722  1.0000
-  C   C40       1.0  0.26264  0.98663  0.21569  1.0000
-  C   C41       1.0  0.26950  0.92285  0.19585  1.0000
-  C   C42       1.0  0.29250  0.92129  0.15757  1.0000
-  C   C43       1.0  0.27570  0.11842  0.21757  1.0000
-  C   C44       1.0  0.25531  0.85447  0.21584  1.0000
-  C   C45       1.0  0.47732  0.92546  0.46556  1.0000
-  C   C46       1.0  0.45307  0.85574  0.46536  1.0000
-  C   C47       1.0  0.43873  0.81811  0.42815  1.0000
-  C   C48       1.0  0.48445  0.81019  0.36093  1.0000
-  C   C49       1.0  0.54823  0.80591  0.34081  1.0000
-  C   C50       1.0  0.54931  0.78183  0.30278  1.0000
-  C   C51       1.0  0.48663  0.76264  0.28431  1.0000
-  C   C52       1.0  0.42286  0.76950  0.30415  1.0000
-  C   C53       1.0  0.42129  0.79250  0.34243  1.0000
-  C   C54       1.0  0.61842  0.77570  0.28243  1.0000
-  C   C55       1.0  0.35447  0.75531  0.28416  1.0000
-  C   C56       1.0  0.52268  0.07454  0.46556  1.0000
-  C   C57       1.0  0.54693  0.14426  0.46536  1.0000
-  C   C58       1.0  0.56127  0.18189  0.42815  1.0000
-  C   C59       1.0  0.51555  0.18981  0.36093  1.0000
-  C   C60       1.0  0.45177  0.19409  0.34081  1.0000
-  C   C61       1.0  0.45069  0.21817  0.30278  1.0000
-  C   C62       1.0  0.51337  0.23736  0.28431  1.0000
-  C   C63       1.0  0.57715  0.23050  0.30415  1.0000
-  C   C64       1.0  0.57871  0.20750  0.34243  1.0000
-  C   C65       1.0  0.38158  0.22430  0.28243  1.0000
-  C   C66       1.0  0.64553  0.24469  0.28416  1.0000
-  C   C67       1.0  0.92546  0.52268  0.46556  1.0000
-  C   C68       1.0  0.85574  0.54692  0.46536  1.0000
-  C   C69       1.0  0.81811  0.56127  0.42815  1.0000
-  C   C70       1.0  0.81019  0.51555  0.36093  1.0000
-  C   C71       1.0  0.80591  0.45177  0.34081  1.0000
-  C   C72       1.0  0.78183  0.45068  0.30278  1.0000
-  C   C73       1.0  0.76264  0.51337  0.28431  1.0000
-  C   C74       1.0  0.76950  0.57714  0.30415  1.0000
-  C   C75       1.0  0.79250  0.57871  0.34243  1.0000
-  C   C76       1.0  0.77570  0.38158  0.28243  1.0000
-  C   C77       1.0  0.75531  0.64553  0.28416  1.0000
-  C   C78       1.0  0.07454  0.47732  0.46556  1.0000
-  C   C79       1.0  0.14426  0.45308  0.46536  1.0000
-  C   C80       1.0  0.18189  0.43873  0.42815  1.0000
-  C   C81       1.0  0.18981  0.48445  0.36093  1.0000
-  C   C82       1.0  0.19409  0.54823  0.34081  1.0000
-  C   C83       1.0  0.21817  0.54932  0.30278  1.0000
-  C   C84       1.0  0.23736  0.48663  0.28431  1.0000
-  C   C85       1.0  0.23050  0.42286  0.30415  1.0000
-  C   C86       1.0  0.20750  0.42129  0.34243  1.0000
-  C   C87       1.0  0.22430  0.61842  0.28243  1.0000
-  C   C88       1.0  0.24469  0.35447  0.28416  1.0000
-  C   C89       1.0  0.97731  0.57453  0.96554  1.0000
-  C   C90       1.0  0.95307  0.64426  0.96533  1.0000
-  C   C91       1.0  0.93873  0.68188  0.92812  1.0000
-  C   C92       1.0  0.98445  0.68981  0.86091  1.0000
-  C   C93       1.0  0.04823  0.69409  0.84079  1.0000
-  C   C94       1.0  0.04932  0.71817  0.80276  1.0000
-  C   C95       1.0  0.98663  0.73736  0.78429  1.0000
-  C   C96       1.0  0.92286  0.73050  0.80414  1.0000
-  C   C97       1.0  0.92129  0.70750  0.84241  1.0000
-  C   C98       1.0  0.11842  0.72431  0.78241  1.0000
-  C   C99       1.0  0.85448  0.74470  0.78415  1.0000
-  C   C100      1.0  0.02268  0.42547  0.96554  1.0000
-  C   C101      1.0  0.04693  0.35574  0.96533  1.0000
-  C   C102      1.0  0.06127  0.31812  0.92812  1.0000
-  C   C103      1.0  0.01555  0.31020  0.86091  1.0000
-  C   C104      1.0  0.95177  0.30591  0.84079  1.0000
-  C   C105      1.0  0.95068  0.28182  0.80276  1.0000
-  C   C106      1.0  0.01337  0.26263  0.78429  1.0000
-  C   C107      1.0  0.07714  0.26950  0.80414  1.0000
-  C   C108      1.0  0.07870  0.29250  0.84241  1.0000
-  C   C109      1.0  0.88158  0.27569  0.78241  1.0000
-  C   C110      1.0  0.14552  0.25530  0.78415  1.0000
-  C   C111      1.0  0.42547  0.97731  0.96554  1.0000
-  C   C112      1.0  0.35574  0.95307  0.96533  1.0000
-  C   C113      1.0  0.31812  0.93873  0.92812  1.0000
-  C   C114      1.0  0.31019  0.98445  0.86091  1.0000
-  C   C115      1.0  0.30591  0.04823  0.84079  1.0000
-  C   C116      1.0  0.28184  0.04932  0.80276  1.0000
-  C   C117      1.0  0.26264  0.98663  0.78429  1.0000
-  C   C118      1.0  0.26950  0.92286  0.80414  1.0000
-  C   C119      1.0  0.29250  0.92129  0.84241  1.0000
-  C   C120      1.0  0.27570  0.11842  0.78241  1.0000
-  C   C121      1.0  0.25530  0.85448  0.78415  1.0000
-  C   C122      1.0  0.57453  0.02268  0.96553  1.0000
-  C   C123      1.0  0.64426  0.04693  0.96533  1.0000
-  C   C124      1.0  0.68187  0.06129  0.92812  1.0000
-  C   C125      1.0  0.68980  0.01557  0.86092  1.0000
-  C   C126      1.0  0.69405  0.95179  0.84077  1.0000
-  C   C127      1.0  0.71811  0.95069  0.80275  1.0000
-  C   C128      1.0  0.73747  0.01338  0.78429  1.0000
-  C   C129      1.0  0.73070  0.07713  0.80420  1.0000
-  C   C130      1.0  0.70757  0.07871  0.84244  1.0000
-  C   C131      1.0  0.72430  0.88157  0.78240  1.0000
-  C   C132      1.0  0.74486  0.14556  0.78422  1.0000
-  C   C133      1.0  0.52268  0.07453  0.53447  1.0000
-  C   C134      1.0  0.54693  0.14426  0.53467  1.0000
-  C   C135      1.0  0.56129  0.18187  0.57188  1.0000
-  C   C136      1.0  0.51557  0.18979  0.63908  1.0000
-  C   C137      1.0  0.45179  0.19406  0.65922  1.0000
-  C   C138      1.0  0.45069  0.21813  0.69725  1.0000
-  C   C139      1.0  0.51337  0.23739  0.71573  1.0000
-  C   C140      1.0  0.57713  0.23058  0.69583  1.0000
-  C   C141      1.0  0.57871  0.20752  0.65757  1.0000
-  C   C142      1.0  0.38157  0.22430  0.71760  1.0000
-  C   C143      1.0  0.64554  0.24485  0.71581  1.0000
-  C   C144      1.0  0.47731  0.92547  0.53446  1.0000
-  C   C145      1.0  0.45307  0.85574  0.53467  1.0000
-  C   C146      1.0  0.43873  0.81812  0.57188  1.0000
-  C   C147      1.0  0.48445  0.81019  0.63909  1.0000
-  C   C148      1.0  0.54824  0.80591  0.65921  1.0000
-  C   C149      1.0  0.54932  0.78184  0.69724  1.0000
-  C   C150      1.0  0.48663  0.76264  0.71571  1.0000
-  C   C151      1.0  0.42286  0.76950  0.69586  1.0000
-  C   C152      1.0  0.42129  0.79250  0.65759  1.0000
-  C   C153      1.0  0.61842  0.77570  0.71759  1.0000
-  C   C154      1.0  0.35448  0.75530  0.71585  1.0000
-  C   C155      1.0  0.07453  0.47731  0.53446  1.0000
-  C   C156      1.0  0.14426  0.45307  0.53467  1.0000
-  C   C157      1.0  0.18188  0.43873  0.57188  1.0000
-  C   C158      1.0  0.18981  0.48445  0.63909  1.0000
-  C   C159      1.0  0.19409  0.54823  0.65921  1.0000
-  C   C160      1.0  0.21817  0.54932  0.69724  1.0000
-  C   C161      1.0  0.23736  0.48663  0.71571  1.0000
-  C   C162      1.0  0.23050  0.42286  0.69586  1.0000
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+ _atom_site_label
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+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
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+  O  O380  1  0.21964000  0.29940000  0.69949000  1.0
+  O  O381  1  0.27892000  0.35647000  0.74749000  1.0
+  O  O382  1  0.61088000  0.22312000  0.57574000  1.0
+  O  O383  1  0.32727000  0.20133000  0.69969000  1.0
+  O  O384  1  0.38252000  0.25249000  0.75101000  1.0
+  O  O385  1  0.70060000  0.21965000  0.69949000  1.0
+  O  O386  1  0.64353000  0.27892000  0.74749000  1.0
+  O  O387  1  0.38912000  0.77688000  0.57574000  1.0
+  O  O388  1  0.67273000  0.79866000  0.69969000  1.0
+  O  O389  1  0.61749000  0.74751000  0.75101000  1.0
+  O  O390  1  0.29941000  0.78035000  0.69949000  1.0
+  O  O391  1  0.35648000  0.72108000  0.74749000  1.0

From 2912003e80f44b2ddc0c8d9d4885c45d74e0bb0f Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Sun, 17 Dec 2023 18:45:15 -0500
Subject: [PATCH 13/19] Add references for the MOF csv files

---
 tests/informatics/test_MOF_descriptors.py     |  44 +++---
 .../odac-21383/lc_descriptors.csv             | 125 ++++++++++++++++++
 .../{ => odac-21383}/odac-21383.json          |   0
 .../odac-21383/sbu_descriptors.csv            |  17 +++
 .../odac-21433/lc_descriptors.csv             |  97 ++++++++++++++
 .../{ => odac-21433}/odac-21433.json          |   0
 .../odac-21433/sbu_descriptors.csv            |  25 ++++
 .../odac-21478/lc_descriptors.csv             |  97 ++++++++++++++
 .../{ => odac-21478}/odac-21478.json          |   0
 .../odac-21478/sbu_descriptors.csv            |  25 ++++
 .../odac-21735/lc_descriptors.csv             |   7 +
 .../{ => odac-21735}/odac-21735.json          |   0
 .../odac-21735/sbu_descriptors.csv            |   2 +
 .../odac-21816/lc_descriptors.csv             |  33 +++++
 .../{ => odac-21816}/odac-21816.json          |   0
 .../odac-21816/sbu_descriptors.csv            |   9 ++
 16 files changed, 466 insertions(+), 15 deletions(-)
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21383/lc_descriptors.csv
 rename tests/testresources/refs/MOF_descriptors/{ => odac-21383}/odac-21383.json (100%)
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21383/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21433/lc_descriptors.csv
 rename tests/testresources/refs/MOF_descriptors/{ => odac-21433}/odac-21433.json (100%)
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21433/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21478/lc_descriptors.csv
 rename tests/testresources/refs/MOF_descriptors/{ => odac-21478}/odac-21478.json (100%)
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21478/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21735/lc_descriptors.csv
 rename tests/testresources/refs/MOF_descriptors/{ => odac-21735}/odac-21735.json (100%)
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21735/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21816/lc_descriptors.csv
 rename tests/testresources/refs/MOF_descriptors/{ => odac-21816}/odac-21816.json (100%)
 create mode 100644 tests/testresources/refs/MOF_descriptors/odac-21816/sbu_descriptors.csv

diff --git a/tests/informatics/test_MOF_descriptors.py b/tests/informatics/test_MOF_descriptors.py
index 510012b7..94364c0e 100644
--- a/tests/informatics/test_MOF_descriptors.py
+++ b/tests/informatics/test_MOF_descriptors.py
@@ -1,14 +1,15 @@
 import pytest
 import json
 import numpy as np
+import pandas as pd
 from molSimplify.Informatics.MOF.MOF_descriptors import get_MOF_descriptors
 from molSimplify.utils.timer import DebugTimer
 
 
 @pytest.fixture
-def ref_names(depth=3):
+def RACs_names(depth=3):
 
-    def RACs_names(starts, properties, depth, scope="all"):
+    def generate_names(starts, properties, depth, scope="all"):
         names = []
         for start in starts:
             for prop in properties:
@@ -21,28 +22,33 @@ def RACs_names(starts, properties, depth, scope="all"):
 
     properties = ["chi", "Z", "I", "T", "S", "Gval"]
 
-    names = RACs_names(["f", "mc", "D_mc"], properties, depth)
+    names = generate_names(["f", "mc", "D_mc"], properties, depth)
     # f-lig does not include the "scope"
-    names.extend(RACs_names(["f-lig"], properties, depth, scope=None))
+    names.extend(generate_names(["f-lig"], properties, depth, scope=None))
 
     # Same for the starts that include the additional property alpha
     properties.append("alpha")
     names.extend(
-        RACs_names(["lc", "D_lc", "func", "D_func"], properties, depth))
+        generate_names(["lc", "D_lc", "func", "D_func"], properties, depth))
     return names
 
 
 @pytest.mark.parametrize(
-    "cif_file",
-    ["odac-21383.cif",
-     "odac-21433.cif",
-     "odac-21478.cif",
-     "odac-21735.cif",
-     "odac-21816.cif"])
-def test_get_MOF_descriptors(resource_path_root, tmpdir, cif_file, ref_names):
+    "name",
+    [
+        "odac-21383",
+        "odac-21433",
+        "odac-21478",
+        "odac-21735",
+        "odac-21816",
+    ])
+def test_get_MOF_descriptors(resource_path_root, tmpdir, name, RACs_names):
+    # NOTE All the .cif files were converted to primitive unit cell using the
+    # MOF_descriptors.get_primitive() function
+
     with DebugTimer("get_MOF_descriptors()"):
         full_names, full_descriptors = get_MOF_descriptors(
-            str(resource_path_root / "inputs" / "cif_files" / cif_file),
+            str(resource_path_root / "inputs" / "cif_files" / f"{name}.cif"),
             depth=3,
             path=str(tmpdir),
             xyzpath=str(tmpdir / "test.xyz"),
@@ -50,8 +56,16 @@ def test_get_MOF_descriptors(resource_path_root, tmpdir, cif_file, ref_names):
         )
 
     with open(resource_path_root / "refs" / "MOF_descriptors"
-              / cif_file.replace("cif", "json"), "r") as fin:
+              / name / f"{name}.json", "r") as fin:
         ref = json.load(fin)
 
-    assert full_names == ref_names
+    assert full_names == RACs_names
     np.testing.assert_allclose(full_descriptors, ref["descriptors"], atol=1e-6)
+
+    lc_descriptors = pd.read_csv(tmpdir / "lc_descriptors.csv")
+    lc_ref = pd.read_csv(resource_path_root / "refs" / "MOF_descriptors" / name / "lc_descriptors.csv")
+    assert all(lc_descriptors == lc_ref)
+
+    sbu_descriptors = pd.read_csv(tmpdir / "sbu_descriptors.csv")
+    sbu_ref = pd.read_csv(resource_path_root / "refs" / "MOF_descriptors" / name / "sbu_descriptors.csv")
+    assert all(sbu_descriptors == sbu_ref)
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21383/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21383/lc_descriptors.csv
new file mode 100644
index 00000000..fa6968cc
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21383/lc_descriptors.csv
@@ -0,0 +1,125 @@
+lc-chi-0-all,lc-chi-1-all,lc-chi-2-all,lc-chi-3-all,lc-Z-0-all,lc-Z-1-all,lc-Z-2-all,lc-Z-3-all,lc-I-0-all,lc-I-1-all,lc-I-2-all,lc-I-3-all,lc-T-0-all,lc-T-1-all,lc-T-2-all,lc-T-3-all,lc-S-0-all,lc-S-1-all,lc-S-2-all,lc-S-3-all,lc-Gval-0-all,lc-Gval-1-all,lc-Gval-2-all,lc-Gval-3-all,lc-alpha-0-all,lc-alpha-1-all,lc-alpha-2-all,lc-alpha-3-all,D_lc-chi-0-all,D_lc-chi-1-all,D_lc-chi-2-all,D_lc-chi-3-all,D_lc-Z-0-all,D_lc-Z-1-all,D_lc-Z-2-all,D_lc-Z-3-all,D_lc-I-0-all,D_lc-I-1-all,D_lc-I-2-all,D_lc-I-3-all,D_lc-T-0-all,D_lc-T-1-all,D_lc-T-2-all,D_lc-T-3-all,D_lc-S-0-all,D_lc-S-1-all,D_lc-S-2-all,D_lc-S-3-all,D_lc-Gval-0-all,D_lc-Gval-1-all,D_lc-Gval-2-all,D_lc-Gval-3-all,D_lc-alpha-0-all,D_lc-alpha-1-all,D_lc-alpha-2-all,D_lc-alpha-3-all,func-chi-0-all,func-chi-1-all,func-chi-2-all,func-chi-3-all,func-Z-0-all,func-Z-1-all,func-Z-2-all,func-Z-3-all,func-I-0-all,func-I-1-all,func-I-2-all,func-I-3-all,func-T-0-all,func-T-1-all,func-T-2-all,func-T-3-all,func-S-0-all,func-S-1-all,func-S-2-all,func-S-3-all,func-Gval-0-all,func-Gval-1-all,func-Gval-2-all,func-Gval-3-all,func-alpha-0-all,func-alpha-1-all,func-alpha-2-all,func-alpha-3-all,D_func-chi-0-all,D_func-chi-1-all,D_func-chi-2-all,D_func-chi-3-all,D_func-Z-0-all,D_func-Z-1-all,D_func-Z-2-all,D_func-Z-3-all,D_func-I-0-all,D_func-I-1-all,D_func-I-2-all,D_func-I-3-all,D_func-T-0-all,D_func-T-1-all,D_func-T-2-all,D_func-T-3-all,D_func-S-0-all,D_func-S-1-all,D_func-S-2-all,D_func-S-3-all,D_func-Gval-0-all,D_func-Gval-1-all,D_func-Gval-2-all,D_func-Gval-3-all,D_func-alpha-0-all,D_func-alpha-1-all,D_func-alpha-2-all,D_func-alpha-3-all,name
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21383.json b/tests/testresources/refs/MOF_descriptors/odac-21383/odac-21383.json
similarity index 100%
rename from tests/testresources/refs/MOF_descriptors/odac-21383.json
rename to tests/testresources/refs/MOF_descriptors/odac-21383/odac-21383.json
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21383/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21383/sbu_descriptors.csv
new file mode 100644
index 00000000..979b9bd3
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21383/sbu_descriptors.csv
@@ -0,0 +1,17 @@
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21433/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21433/lc_descriptors.csv
new file mode 100644
index 00000000..a18bee78
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21433/lc_descriptors.csv
@@ -0,0 +1,97 @@
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21433.json b/tests/testresources/refs/MOF_descriptors/odac-21433/odac-21433.json
similarity index 100%
rename from tests/testresources/refs/MOF_descriptors/odac-21433.json
rename to tests/testresources/refs/MOF_descriptors/odac-21433/odac-21433.json
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21433/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21433/sbu_descriptors.csv
new file mode 100644
index 00000000..35dfca23
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21433/sbu_descriptors.csv
@@ -0,0 +1,25 @@
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21478/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21478/lc_descriptors.csv
new file mode 100644
index 00000000..a5b44108
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21478/lc_descriptors.csv
@@ -0,0 +1,97 @@
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21478.json b/tests/testresources/refs/MOF_descriptors/odac-21478/odac-21478.json
similarity index 100%
rename from tests/testresources/refs/MOF_descriptors/odac-21478.json
rename to tests/testresources/refs/MOF_descriptors/odac-21478/odac-21478.json
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21478/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21478/sbu_descriptors.csv
new file mode 100644
index 00000000..427d0dc5
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21478/sbu_descriptors.csv
@@ -0,0 +1,25 @@
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21735/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21735/lc_descriptors.csv
new file mode 100644
index 00000000..33b08664
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21735/lc_descriptors.csv
@@ -0,0 +1,7 @@
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21735.json b/tests/testresources/refs/MOF_descriptors/odac-21735/odac-21735.json
similarity index 100%
rename from tests/testresources/refs/MOF_descriptors/odac-21735.json
rename to tests/testresources/refs/MOF_descriptors/odac-21735/odac-21735.json
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21735/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21735/sbu_descriptors.csv
new file mode 100644
index 00000000..4a5846c5
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21735/sbu_descriptors.csv
@@ -0,0 +1,2 @@
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21816/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21816/lc_descriptors.csv
new file mode 100644
index 00000000..378ccf7c
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21816/lc_descriptors.csv
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diff --git a/tests/testresources/refs/MOF_descriptors/odac-21816.json b/tests/testresources/refs/MOF_descriptors/odac-21816/odac-21816.json
similarity index 100%
rename from tests/testresources/refs/MOF_descriptors/odac-21816.json
rename to tests/testresources/refs/MOF_descriptors/odac-21816/odac-21816.json
diff --git a/tests/testresources/refs/MOF_descriptors/odac-21816/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/odac-21816/sbu_descriptors.csv
new file mode 100644
index 00000000..74e5ccea
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/odac-21816/sbu_descriptors.csv
@@ -0,0 +1,9 @@
+f-chi-0-all,f-chi-1-all,f-chi-2-all,f-chi-3-all,f-Z-0-all,f-Z-1-all,f-Z-2-all,f-Z-3-all,f-I-0-all,f-I-1-all,f-I-2-all,f-I-3-all,f-T-0-all,f-T-1-all,f-T-2-all,f-T-3-all,f-S-0-all,f-S-1-all,f-S-2-all,f-S-3-all,f-Gval-0-all,f-Gval-1-all,f-Gval-2-all,f-Gval-3-all,mc-chi-0-all,mc-chi-1-all,mc-chi-2-all,mc-chi-3-all,mc-Z-0-all,mc-Z-1-all,mc-Z-2-all,mc-Z-3-all,mc-I-0-all,mc-I-1-all,mc-I-2-all,mc-I-3-all,mc-T-0-all,mc-T-1-all,mc-T-2-all,mc-T-3-all,mc-S-0-all,mc-S-1-all,mc-S-2-all,mc-S-3-all,mc-Gval-0-all,mc-Gval-1-all,mc-Gval-2-all,mc-Gval-3-all,D_mc-chi-0-all,D_mc-chi-1-all,D_mc-chi-2-all,D_mc-chi-3-all,D_mc-Z-0-all,D_mc-Z-1-all,D_mc-Z-2-all,D_mc-Z-3-all,D_mc-I-0-all,D_mc-I-1-all,D_mc-I-2-all,D_mc-I-3-all,D_mc-T-0-all,D_mc-T-1-all,D_mc-T-2-all,D_mc-T-3-all,D_mc-S-0-all,D_mc-S-1-all,D_mc-S-2-all,D_mc-S-3-all,D_mc-Gval-0-all,D_mc-Gval-1-all,D_mc-Gval-2-all,D_mc-Gval-3-all,name
+127.8988,244.9279999999999,456.19520000000006,525.6319999999998,2338.0,4480.0,4832.0,6016.0,14.0,32.0,48.0,64.0,80.0,192.0,256.0,320.0,10.443599999999998,25.112000000000005,34.054399999999994,43.09919999999999,594.0,1440.0,1856.0,2208.0,3.61,26.144,19.38,45.524,841.0,928.0,696.0,1624.0,1.0,4.0,4.0,8.0,16.0,32.0,48.0,80.0,1.9043999999999992,4.0296,4.2504,8.28,121.0,264.0,176.0,440.0,0.0,-6.159999999999998,-2.6000000000000005,-8.76,0.0,84.0,92.0,176.0,0.0,0.0,0.0,0.0,0.0,8.0,4.0,12.0,0.0,2.6000000000000005,2.4399999999999986,5.039999999999997,0.0,20.0,28.0,48.0,odac-21816
+127.8988,244.92799999999988,456.19520000000006,525.632,2338.0,4480.0,4832.0,6016.0,14.0,32.0,48.0,64.0,80.0,192.0,256.0,320.0,10.443599999999998,25.11200000000001,34.054399999999994,43.0992,594.0,1440.0,1856.0,2208.0,3.61,26.144,19.38,45.524,841.0,928.0,696.0,1624.0,1.0,4.0,4.0,8.0,16.0,32.0,48.0,80.0,1.9043999999999992,4.0296,4.2504,8.28,121.0,264.0,176.0,440.0,0.0,-6.159999999999998,-2.6000000000000005,-8.76,0.0,84.0,92.0,176.0,0.0,0.0,0.0,0.0,0.0,8.0,4.0,12.0,0.0,2.6000000000000005,2.4399999999999986,5.039999999999997,0.0,20.0,28.0,48.0,odac-21816
+127.8988,244.9279999999999,456.19520000000006,525.632,2338.0,4480.0,4832.0,6016.0,14.0,32.0,48.0,64.0,80.0,192.0,256.0,320.0,10.4436,25.112,34.054399999999994,43.09919999999999,594.0,1440.0,1856.0,2208.0,3.61,26.144,19.38,45.524,841.0,928.0,696.0,1624.0,1.0,4.0,4.0,8.0,16.0,32.0,48.0,80.0,1.9043999999999992,4.0296,4.2504,8.28,121.0,264.0,176.0,440.0,0.0,-6.159999999999998,-2.6000000000000005,-8.76,0.0,84.0,92.0,176.0,0.0,0.0,0.0,0.0,0.0,8.0,4.0,12.0,0.0,2.6000000000000005,2.4399999999999986,5.039999999999997,0.0,20.0,28.0,48.0,odac-21816
+127.8988,244.92799999999997,456.19520000000006,525.632,2338.0,4480.0,4832.0,6016.0,14.0,32.0,48.0,64.0,80.0,192.0,256.0,320.0,10.443599999999998,25.112000000000005,34.054399999999994,43.0992,594.0,1440.0,1856.0,2208.0,3.61,26.144,19.38,45.524,841.0,928.0,696.0,1624.0,1.0,4.0,4.0,8.0,16.0,32.0,48.0,80.0,1.9043999999999992,4.0296,4.2504,8.28,121.0,264.0,176.0,440.0,0.0,-6.159999999999998,-2.6000000000000005,-8.76,0.0,84.0,92.0,176.0,0.0,0.0,0.0,0.0,0.0,8.0,4.0,12.0,0.0,2.6000000000000005,2.4399999999999986,5.039999999999997,0.0,20.0,28.0,48.0,odac-21816
+127.8988,244.92799999999988,456.1952,525.6319999999998,2338.0,4480.0,4832.0,6016.0,14.0,32.0,48.0,64.0,80.0,192.0,256.0,320.0,10.443599999999998,25.11200000000001,34.054399999999994,43.09919999999999,594.0,1440.0,1856.0,2208.0,3.61,26.144,19.38,45.524,841.0,928.0,696.0,1624.0,1.0,4.0,4.0,8.0,16.0,32.0,48.0,80.0,1.9043999999999992,4.0296,4.2504,8.28,121.0,264.0,176.0,440.0,0.0,-6.159999999999998,-2.6000000000000005,-8.76,0.0,84.0,92.0,176.0,0.0,0.0,0.0,0.0,0.0,8.0,4.0,12.0,0.0,2.6000000000000005,2.4399999999999986,5.039999999999997,0.0,20.0,28.0,48.0,odac-21816
+127.8988,244.92799999999988,456.1952,525.632,2338.0,4480.0,4832.0,6016.0,14.0,32.0,48.0,64.0,80.0,192.0,256.0,320.0,10.4436,25.11200000000001,34.054399999999994,43.09919999999999,594.0,1440.0,1856.0,2208.0,3.61,26.144,19.38,45.524,841.0,928.0,696.0,1624.0,1.0,4.0,4.0,8.0,16.0,32.0,48.0,80.0,1.9043999999999992,4.0296,4.2504,8.28,121.0,264.0,176.0,440.0,0.0,-6.159999999999998,-2.6000000000000005,-8.76,0.0,84.0,92.0,176.0,0.0,0.0,0.0,0.0,0.0,8.0,4.0,12.0,0.0,2.6000000000000005,2.4399999999999986,5.039999999999997,0.0,20.0,28.0,48.0,odac-21816
+127.8988,244.9279999999999,456.19520000000006,525.6319999999998,2338.0,4480.0,4832.0,6016.0,14.0,32.0,48.0,64.0,80.0,192.0,256.0,320.0,10.443599999999998,25.112000000000005,34.054399999999994,43.0992,594.0,1440.0,1856.0,2208.0,3.61,26.144,19.38,45.524,841.0,928.0,696.0,1624.0,1.0,4.0,4.0,8.0,16.0,32.0,48.0,80.0,1.9043999999999992,4.0296,4.2504,8.28,121.0,264.0,176.0,440.0,0.0,-6.159999999999998,-2.6000000000000005,-8.76,0.0,84.0,92.0,176.0,0.0,0.0,0.0,0.0,0.0,8.0,4.0,12.0,0.0,2.6000000000000005,2.4399999999999986,5.039999999999997,0.0,20.0,28.0,48.0,odac-21816
+127.8988,244.9279999999999,456.1952,525.6319999999998,2338.0,4480.0,4832.0,6016.0,14.0,32.0,48.0,64.0,80.0,192.0,256.0,320.0,10.443599999999998,25.11200000000001,34.054399999999994,43.0992,594.0,1440.0,1856.0,2208.0,3.61,26.144,19.38,45.524,841.0,928.0,696.0,1624.0,1.0,4.0,4.0,8.0,16.0,32.0,48.0,80.0,1.9043999999999992,4.0296,4.2504,8.28,121.0,264.0,176.0,440.0,0.0,-6.159999999999998,-2.6000000000000005,-8.76,0.0,84.0,92.0,176.0,0.0,0.0,0.0,0.0,0.0,8.0,4.0,12.0,0.0,2.6000000000000005,2.4399999999999986,5.039999999999997,0.0,20.0,28.0,48.0,odac-21816

From 22ff3573d4345124c10786a91447f8a974de1786 Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Sun, 17 Dec 2023 18:45:53 -0500
Subject: [PATCH 14/19] Remove unnecessay code

---
 molSimplify/Informatics/MOF/MOF_descriptors.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/molSimplify/Informatics/MOF/MOF_descriptors.py b/molSimplify/Informatics/MOF/MOF_descriptors.py
index 83027ce2..c214618e 100644
--- a/molSimplify/Informatics/MOF/MOF_descriptors.py
+++ b/molSimplify/Informatics/MOF/MOF_descriptors.py
@@ -355,7 +355,6 @@ def make_MOF_SBU_RACs(
         # Some formatting
         descriptor_names += ['name']
         descriptors += [name]
-        descriptors == list(descriptors)
         desc_dict = {key: descriptors[ii] for ii, key in enumerate(descriptor_names)}
         descriptors.remove(name)
         descriptor_names.remove('name')

From 65ee867cf545bedbb739eafc2269c97e181cb1b0 Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Sun, 17 Dec 2023 19:43:53 -0500
Subject: [PATCH 15/19] Replace df.append with pd.concat

---
 .../Informatics/MOF/MOF_descriptors.py        | 45 ++++++++-----------
 1 file changed, 19 insertions(+), 26 deletions(-)

diff --git a/molSimplify/Informatics/MOF/MOF_descriptors.py b/molSimplify/Informatics/MOF/MOF_descriptors.py
index c214618e..8e922c7c 100644
--- a/molSimplify/Informatics/MOF/MOF_descriptors.py
+++ b/molSimplify/Informatics/MOF/MOF_descriptors.py
@@ -220,7 +220,7 @@ def make_MOF_SBU_RACs(
 
     """
     descriptor_list = []
-    lc_descriptor_list = []
+    lc_descriptor_list: List[List[float]] = []
     lc_names = []
     names = []
     descriptor_names = []
@@ -247,10 +247,12 @@ def make_MOF_SBU_RACs(
         For each linker connected to the SBU, find the lc atoms for the lc-RACs.
         lc atoms are those bonded to a metal.
         """""""""
+        # lc_descriptors for SBU i
+        lc_descriptors_i: List[List[float]] = []
         for j, linker in enumerate(connections_list):  # Iterating over the different linkers
-            descriptor_names = []
-            descriptors = []
             if len(set(SBU).intersection(linker)) > 0:
+                descriptor_names = []
+                descriptors = []
                 # This means that the SBU and the current linker are connected.
                 temp_mol = mol3D()
                 link_list = []  # Will hold the lc atoms for the current linker.
@@ -301,19 +303,16 @@ def make_MOF_SBU_RACs(
                         print('Mixed typing. Please convert to python float, and avoid np float')
                         raise AssertionError('Mixed typing creates issues. Please convert your typing.')
 
-                # Some formatting
-                descriptor_names += ['name']
-                descriptors += [name]
-                desc_dict = {key2: descriptors[kk] for kk, key2 in enumerate(descriptor_names)}
-                descriptors.remove(name)
-                descriptor_names.remove('name')
-                lc_descriptors = lc_descriptors.append(desc_dict, ignore_index=True)
-                lc_descriptor_list.append(descriptors)
+                lc_descriptors_i.append(descriptors)
                 if j == 0:
                     lc_names = descriptor_names
 
+        lc_descriptor_list.extend(lc_descriptors_i)
         averaged_lc_descriptors = np.mean(np.array(lc_descriptor_list), axis=0)  # Average the lc RACs over all of the linkers in the MOF.
-        # This CSV will be overwritten until the last SBU, but information on all linkers is being kept thanks to the append function
+        lc_descriptor_df = pd.DataFrame(lc_descriptors_i, columns=lc_names)
+        lc_descriptor_df['name'] = name
+        # This CSV will be overwritten until the last SBU, but information on all linkers is being kept thanks to the concat function
+        lc_descriptors = pd.concat([lc_descriptors, lc_descriptor_df], ignore_index=True)
         lc_descriptors.to_csv(sbu_descriptor_path+'/lc_descriptors.csv', index=False)
         descriptors = []
         descriptor_names = []
@@ -344,7 +343,7 @@ def make_MOF_SBU_RACs(
             SBU_mol, depth=depth, loud=False, flag_name=False, Gval=Gval)
         descriptor_names, descriptors = append_descriptors(
             descriptor_names, descriptors, results_dictionary['colnames'], results_dictionary['results'], 'f', 'all')
-        #### Now starts at every metal on the graph and autocorrelates
+        # Now starts at every metal on the graph and autocorrelates
         results_dictionary = generate_multimetal_autocorrelations(molcif, depth=depth, loud=False, Gval=Gval)
         descriptor_names, descriptors = append_descriptors(
             descriptor_names, descriptors, results_dictionary['colnames'], results_dictionary['results'], 'mc', 'all')
@@ -352,13 +351,10 @@ def make_MOF_SBU_RACs(
         descriptor_names, descriptors = append_descriptors(
             descriptor_names, descriptors, results_dictionary['colnames'], results_dictionary['results'], 'D_mc', 'all')
 
-        # Some formatting
-        descriptor_names += ['name']
-        descriptors += [name]
-        desc_dict = {key: descriptors[ii] for ii, key in enumerate(descriptor_names)}
-        descriptors.remove(name)
-        descriptor_names.remove('name')
-        sbu_descriptors = sbu_descriptors.append(desc_dict, ignore_index=True)
+        # Add to DataFrame
+        sbu_descriptors_df = pd.DataFrame([descriptors], columns=descriptor_names)
+        sbu_descriptors_df["name"] = name
+        sbu_descriptors = pd.concat([sbu_descriptors, sbu_descriptors_df], ignore_index=True)
         descriptor_list.append(descriptors)
         if i == 0:
             names = descriptor_names
@@ -470,12 +466,9 @@ def make_MOF_linker_RACs(
         # Some formatting
         lig_full = [item for sublist in lig_full for item in sublist]  # flatten lists
         colnames = [item for sublist in colnames for item in sublist]
-        colnames += ['name']
-        lig_full += [name]
-        desc_dict = {key: lig_full[i] for i, key in enumerate(colnames)}
-        linker_descriptors = linker_descriptors.append(desc_dict, ignore_index=True)
-        lig_full.remove(name)
-        colnames.remove('name')
+        linker_descriptors_df = pd.DataFrame([lig_full], columns=colnames)
+        linker_descriptors_df['name'] = name
+        linker_descriptors = pd.concat([linker_descriptors, linker_descriptors_df], ignore_index=True)
         descriptor_list.append(lig_full)
 
     # We dump the standard lc descriptors without averaging or summing so that the user

From 93fbfe228e253342b34ea8b4a12ceaffebee768d Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Tue, 19 Dec 2023 11:18:08 -0500
Subject: [PATCH 16/19] Remove dead code

---
 molSimplify/Informatics/MOF/MOF_descriptors.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/molSimplify/Informatics/MOF/MOF_descriptors.py b/molSimplify/Informatics/MOF/MOF_descriptors.py
index 8e922c7c..2602d67f 100644
--- a/molSimplify/Informatics/MOF/MOF_descriptors.py
+++ b/molSimplify/Informatics/MOF/MOF_descriptors.py
@@ -742,7 +742,6 @@ def surrounded_sbu_gen(SBU_list, linker_list, sbupath, molcif, adj_matrix, cell_
             for starting_atom_idx in connection_atoms[linker_idx]:
                 atom3D_dict_copy = atom3D_dict.copy()
                 added_idx = [starting_atom_idx]
-                starting_atom3D = atom3D_dict_copy[starting_atom_idx]  # Position of the starting atom in the SBU, which has been built by this point in the code.
 
                 atoms_connected_to_start = list(np.nonzero(dense_adj_mat[starting_atom_idx])[0])
                 atoms_connected_to_start = [i for i in atoms_connected_to_start if i in linker_indices]
@@ -1086,7 +1085,6 @@ def get_MOF_descriptors(
     linker_list, linker_subgraphlist = get_closed_subgraph(linkers.copy(), removelist.copy(), adj_matrix)
     connections_list = copy.deepcopy(linker_list)
     connections_subgraphlist = copy.deepcopy(linker_subgraphlist)
-    linker_length_list = [len(linker_val) for linker_val in linker_list]  # The number of atoms in each linker.
     """""""""
     find all anchoring atoms on linkers and ligands (lc identification)
         The atoms that are bonded to a metal.

From c33449cf8b84d9710d8ccf0032d0d818b4d74b95 Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Tue, 19 Dec 2023 19:52:18 -0500
Subject: [PATCH 17/19] Add test case for MOFs from Aditya's JACS paper

---
 tests/informatics/test_MOF_descriptors.py     | 105 ++++-
 .../inputs/cif_files/FOKYIP_clean.cif         | 142 ++++++
 .../inputs/cif_files/NEXXIZ_clean.cif         | 278 +++++++++++
 .../inputs/cif_files/SETDUS_clean.cif         |  76 +++
 .../inputs/cif_files/UXUPEK_clean.cif         |  42 ++
 .../inputs/cif_files/VONBIK_clean.cif         | 434 ++++++++++++++++++
 .../inputs/cif_files/YICDAR_clean.cif         | 104 +++++
 .../FOKYIP_clean/FOKYIP_clean.json            |   1 +
 .../FOKYIP_clean/lc_descriptors.csv           |   9 +
 .../FOKYIP_clean/sbu_descriptors.csv          |   3 +
 .../NEXXIZ_clean/NEXXIZ_clean.json            |   1 +
 .../NEXXIZ_clean/lc_descriptors.csv           |  17 +
 .../NEXXIZ_clean/sbu_descriptors.csv          |   3 +
 .../SETDUS_clean/SETDUS_clean.json            |   1 +
 .../SETDUS_clean/lc_descriptors.csv           |   3 +
 .../SETDUS_clean/sbu_descriptors.csv          |   2 +
 .../UXUPEK_clean/UXUPEK_clean.json            |   1 +
 .../UXUPEK_clean/lc_descriptors.csv           |   2 +
 .../UXUPEK_clean/sbu_descriptors.csv          |   2 +
 .../VONBIK_clean/VONBIK_clean.json            |   1 +
 .../VONBIK_clean/lc_descriptors.csv           |  25 +
 .../VONBIK_clean/sbu_descriptors.csv          |   9 +
 .../YICDAR_clean/YICDAR_clean.json            |   1 +
 .../YICDAR_clean/lc_descriptors.csv           |  10 +
 .../YICDAR_clean/sbu_descriptors.csv          |   2 +
 25 files changed, 1250 insertions(+), 24 deletions(-)
 create mode 100644 tests/testresources/inputs/cif_files/FOKYIP_clean.cif
 create mode 100644 tests/testresources/inputs/cif_files/NEXXIZ_clean.cif
 create mode 100644 tests/testresources/inputs/cif_files/SETDUS_clean.cif
 create mode 100644 tests/testresources/inputs/cif_files/UXUPEK_clean.cif
 create mode 100644 tests/testresources/inputs/cif_files/VONBIK_clean.cif
 create mode 100644 tests/testresources/inputs/cif_files/YICDAR_clean.cif
 create mode 100644 tests/testresources/refs/MOF_descriptors/FOKYIP_clean/FOKYIP_clean.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/FOKYIP_clean/lc_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/FOKYIP_clean/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/NEXXIZ_clean.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/lc_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/SETDUS_clean/SETDUS_clean.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/SETDUS_clean/lc_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/SETDUS_clean/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/UXUPEK_clean/UXUPEK_clean.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/UXUPEK_clean/lc_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/UXUPEK_clean/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/VONBIK_clean/VONBIK_clean.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/VONBIK_clean/lc_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/VONBIK_clean/sbu_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/YICDAR_clean/YICDAR_clean.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/YICDAR_clean/lc_descriptors.csv
 create mode 100644 tests/testresources/refs/MOF_descriptors/YICDAR_clean/sbu_descriptors.csv

diff --git a/tests/informatics/test_MOF_descriptors.py b/tests/informatics/test_MOF_descriptors.py
index 94364c0e..6a6c9992 100644
--- a/tests/informatics/test_MOF_descriptors.py
+++ b/tests/informatics/test_MOF_descriptors.py
@@ -2,35 +2,40 @@
 import json
 import numpy as np
 import pandas as pd
-from molSimplify.Informatics.MOF.MOF_descriptors import get_MOF_descriptors
+from molSimplify.Informatics.MOF.MOF_descriptors import get_MOF_descriptors, get_primitive
 from molSimplify.utils.timer import DebugTimer
 
 
 @pytest.fixture
-def RACs_names(depth=3):
-
-    def generate_names(starts, properties, depth, scope="all"):
-        names = []
-        for start in starts:
-            for prop in properties:
-                for d in range(depth + 1):
-                    if scope is None:
-                        names.append(f"{start}-{prop}-{d}")
-                    else:
-                        names.append(f"{start}-{prop}-{d}-{scope}")
-        return names
+def ref_names():
+    def RACs_names(depth=3, Gval=True, alpha=True):
+
+        def generate_names(starts, properties, depth, scope="all"):
+            names = []
+            for start in starts:
+                for prop in properties:
+                    for d in range(depth + 1):
+                        if scope is None:
+                            names.append(f"{start}-{prop}-{d}")
+                        else:
+                            names.append(f"{start}-{prop}-{d}-{scope}")
+            return names
 
-    properties = ["chi", "Z", "I", "T", "S", "Gval"]
+        properties = ["chi", "Z", "I", "T", "S"]
+        if Gval:
+            properties.append("Gval")
 
-    names = generate_names(["f", "mc", "D_mc"], properties, depth)
-    # f-lig does not include the "scope"
-    names.extend(generate_names(["f-lig"], properties, depth, scope=None))
+        names = generate_names(["f", "mc", "D_mc"], properties, depth)
+        # f-lig does not include the "scope"
+        names.extend(generate_names(["f-lig"], properties, depth, scope=None))
 
-    # Same for the starts that include the additional property alpha
-    properties.append("alpha")
-    names.extend(
-        generate_names(["lc", "D_lc", "func", "D_func"], properties, depth))
-    return names
+        # Same for the starts that include the additional property alpha
+        if alpha:
+            properties.append("alpha")
+        names.extend(
+            generate_names(["lc", "D_lc", "func", "D_func"], properties, depth))
+        return names
+    return RACs_names
 
 
 @pytest.mark.parametrize(
@@ -42,7 +47,7 @@ def generate_names(starts, properties, depth, scope="all"):
         "odac-21735",
         "odac-21816",
     ])
-def test_get_MOF_descriptors(resource_path_root, tmpdir, name, RACs_names):
+def test_get_MOF_descriptors_ODAC(resource_path_root, tmpdir, name, ref_names):
     # NOTE All the .cif files were converted to primitive unit cell using the
     # MOF_descriptors.get_primitive() function
 
@@ -59,7 +64,7 @@ def test_get_MOF_descriptors(resource_path_root, tmpdir, name, RACs_names):
               / name / f"{name}.json", "r") as fin:
         ref = json.load(fin)
 
-    assert full_names == RACs_names
+    assert full_names == ref_names()
     np.testing.assert_allclose(full_descriptors, ref["descriptors"], atol=1e-6)
 
     lc_descriptors = pd.read_csv(tmpdir / "lc_descriptors.csv")
@@ -69,3 +74,55 @@ def test_get_MOF_descriptors(resource_path_root, tmpdir, name, RACs_names):
     sbu_descriptors = pd.read_csv(tmpdir / "sbu_descriptors.csv")
     sbu_ref = pd.read_csv(resource_path_root / "refs" / "MOF_descriptors" / name / "sbu_descriptors.csv")
     assert all(sbu_descriptors == sbu_ref)
+
+
+@pytest.mark.parametrize(
+    "name",
+    [
+        "FOKYIP_clean",
+        "SETDUS_clean",
+        "UXUPEK_clean",
+        "NEXXIZ_clean",
+        # "ETECIR_clean",
+        # "FAVGUH_clean", Disagreement on all ligand center RACs
+        "YICDAR_clean",
+        "VONBIK_clean",
+    ])
+def test_get_MOF_descriptors_JACS(resource_path_root, tmpdir, name, ref_names):
+    """
+    Tests a handful of the MOFs used in
+    Nandy et al., J. Am. Chem. Soc. 2021, 143, 42, 17535-17547
+    https://doi.org/10.1021/jacs.1c07217
+    """
+    # NOTE All the .cif files were converted to primitive unit cell using the
+    # MOF_descriptors.get_primitive() function
+
+    with DebugTimer("get_MOF_descriptors()"):
+        full_names, full_descriptors = get_MOF_descriptors(
+            str(resource_path_root / "inputs" / "cif_files" / f"{name}.cif"),
+            depth=3,
+            path=str(tmpdir),
+            xyzpath=str(tmpdir / "test.xyz"),
+            Gval=False,
+        )
+
+    with open(resource_path_root / "refs" / "MOF_descriptors"
+              / name / f"{name}.json", "r") as fin:
+        ref = json.load(fin)
+
+    # For now we are using a workaround because polarization descriptors
+    # are now added by default.
+    # Here they should be compared to ref_names(Gval=False, alpha=False)
+    assert full_names == ref_names(Gval=False, alpha=True)
+    np.testing.assert_allclose(
+        # Get only the subset of descriptors without the property alpha
+        [d for d, n in zip(full_descriptors, full_names) if "alpha" not in n],
+        ref["descriptors"], atol=1e-6)
+
+    lc_descriptors = pd.read_csv(tmpdir / "lc_descriptors.csv")
+    lc_ref = pd.read_csv(resource_path_root / "refs" / "MOF_descriptors" / name / "lc_descriptors.csv")
+    assert all(lc_descriptors == lc_ref)
+
+    sbu_descriptors = pd.read_csv(tmpdir / "sbu_descriptors.csv")
+    sbu_ref = pd.read_csv(resource_path_root / "refs" / "MOF_descriptors" / name / "sbu_descriptors.csv")
+    assert all(sbu_descriptors == sbu_ref)
diff --git a/tests/testresources/inputs/cif_files/FOKYIP_clean.cif b/tests/testresources/inputs/cif_files/FOKYIP_clean.cif
new file mode 100644
index 00000000..38f1f2ec
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/FOKYIP_clean.cif
@@ -0,0 +1,142 @@
+# generated using pymatgen
+data_NdH7(C5O2)3
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   13.68320000
+_cell_length_b   13.75910000
+_cell_length_c   14.21196035
+_cell_angle_alpha   118.95140427
+_cell_angle_beta   97.82313437
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   NdH7(C5O2)3
+_chemical_formula_sum   'Nd4 H28 C60 O24'
+_cell_volume   2312.78840258
+_cell_formula_units_Z   4
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Nd  Nd0  1  0.53886000  0.61409000  0.66014000  1.0
+  Nd  Nd1  1  0.96114000  0.95395000  0.33986000  1.0
+  Nd  Nd2  1  0.46114000  0.38591000  0.33986000  1.0
+  Nd  Nd3  1  0.03886000  0.04605000  0.66014000  1.0
+  H  H4  1  0.41200000  0.82990000  0.01580000  1.0
+  H  H5  1  0.37210000  0.86050000  0.18020000  1.0
+  H  H6  1  0.38310000  0.53660000  0.08760000  1.0
+  H  H7  1  0.42170000  0.50620000  0.92320000  1.0
+  H  H8  1  0.24470000  0.83310000  0.26440000  1.0
+  H  H9  1  0.31480000  0.83410000  0.54860000  1.0
+  H  H10  1  0.44190000  0.62950000  0.29080000  1.0
+  H  H11  1  0.08800000  0.81410000  0.98420000  1.0
+  H  H12  1  0.12790000  0.68030000  0.81980000  1.0
+  H  H13  1  0.11690000  0.44900000  0.91240000  1.0
+  H  H14  1  0.07830000  0.58300000  0.07680000  1.0
+  H  H15  1  0.25530000  0.56870000  0.73560000  1.0
+  H  H16  1  0.18520000  0.28550000  0.45140000  1.0
+  H  H17  1  0.05810000  0.33870000  0.70920000  1.0
+  H  H18  1  0.58800000  0.17010000  0.98420000  1.0
+  H  H19  1  0.62790000  0.13950000  0.81980000  1.0
+  H  H20  1  0.61690000  0.46340000  0.91240000  1.0
+  H  H21  1  0.57830000  0.49380000  0.07680000  1.0
+  H  H22  1  0.75530000  0.16690000  0.73560000  1.0
+  H  H23  1  0.68520000  0.16590000  0.45140000  1.0
+  H  H24  1  0.55810000  0.37050000  0.70920000  1.0
+  H  H25  1  0.91200000  0.18590000  0.01580000  1.0
+  H  H26  1  0.87210000  0.31970000  0.18020000  1.0
+  H  H27  1  0.88310000  0.55100000  0.08760000  1.0
+  H  H28  1  0.92170000  0.41700000  0.92320000  1.0
+  H  H29  1  0.74470000  0.43130000  0.26440000  1.0
+  H  H30  1  0.81480000  0.71450000  0.54860000  1.0
+  H  H31  1  0.94190000  0.66130000  0.29080000  1.0
+  C  C32  1  0.46206000  0.64384000  0.85110000  1.0
+  C  C33  1  0.42455000  0.66336000  0.95322000  1.0
+  C  C34  1  0.40720000  0.77099000  0.03018000  1.0
+  C  C35  1  0.38260000  0.78861000  0.12842000  1.0
+  C  C36  1  0.37304000  0.70268000  0.15222000  1.0
+  C  C37  1  0.38877000  0.59593000  0.07406000  1.0
+  C  C38  1  0.41298000  0.57838000  0.97580000  1.0
+  C  C39  1  0.35106000  0.73052000  0.26256000  1.0
+  C  C40  1  0.28095000  0.80681000  0.30654000  1.0
+  C  C41  1  0.26459000  0.84423000  0.41370000  1.0
+  C  C42  1  0.32109000  0.80561000  0.47576000  1.0
+  C  C43  1  0.38686000  0.72494000  0.43014000  1.0
+  C  C44  1  0.40002000  0.68586000  0.32234000  1.0
+  C  C45  1  0.18486000  0.92266000  0.45704000  1.0
+  C  C46  1  0.44081000  0.68159000  0.49910000  1.0
+  C  C47  1  0.03794000  0.79274000  0.14890000  1.0
+  C  C48  1  0.07545000  0.71014000  0.04678000  1.0
+  C  C49  1  0.09280000  0.74081000  0.96982000  1.0
+  C  C50  1  0.11740000  0.66019000  0.87158000  1.0
+  C  C51  1  0.12696000  0.55046000  0.84778000  1.0
+  C  C52  1  0.11123000  0.52187000  0.92594000  1.0
+  C  C53  1  0.08702000  0.60258000  0.02420000  1.0
+  C  C54  1  0.14894000  0.46796000  0.73744000  1.0
+  C  C55  1  0.21905000  0.50027000  0.69346000  1.0
+  C  C56  1  0.23541000  0.43053000  0.58630000  1.0
+  C  C57  1  0.17891000  0.32985000  0.52424000  1.0
+  C  C58  1  0.11314000  0.29480000  0.56986000  1.0
+  C  C59  1  0.09998000  0.36352000  0.67766000  1.0
+  C  C60  1  0.31514000  0.46562000  0.54296000  1.0
+  C  C61  1  0.05919000  0.18249000  0.50090000  1.0
+  C  C62  1  0.53794000  0.35616000  0.14890000  1.0
+  C  C63  1  0.57545000  0.33664000  0.04678000  1.0
+  C  C64  1  0.59280000  0.22901000  0.96982000  1.0
+  C  C65  1  0.61740000  0.21139000  0.87158000  1.0
+  C  C66  1  0.62696000  0.29732000  0.84778000  1.0
+  C  C67  1  0.61123000  0.40407000  0.92594000  1.0
+  C  C68  1  0.58702000  0.42162000  0.02420000  1.0
+  C  C69  1  0.64894000  0.26948000  0.73744000  1.0
+  C  C70  1  0.71905000  0.19319000  0.69346000  1.0
+  C  C71  1  0.73541000  0.15577000  0.58630000  1.0
+  C  C72  1  0.67891000  0.19439000  0.52424000  1.0
+  C  C73  1  0.61314000  0.27506000  0.56986000  1.0
+  C  C74  1  0.59998000  0.31414000  0.67766000  1.0
+  C  C75  1  0.81514000  0.07734000  0.54296000  1.0
+  C  C76  1  0.55919000  0.31841000  0.50090000  1.0
+  C  C77  1  0.96206000  0.20726000  0.85110000  1.0
+  C  C78  1  0.92455000  0.28986000  0.95322000  1.0
+  C  C79  1  0.90720000  0.25919000  0.03018000  1.0
+  C  C80  1  0.88260000  0.33981000  0.12842000  1.0
+  C  C81  1  0.87304000  0.44954000  0.15222000  1.0
+  C  C82  1  0.88877000  0.47813000  0.07406000  1.0
+  C  C83  1  0.91298000  0.39742000  0.97580000  1.0
+  C  C84  1  0.85106000  0.53204000  0.26256000  1.0
+  C  C85  1  0.78095000  0.49973000  0.30654000  1.0
+  C  C86  1  0.76459000  0.56947000  0.41370000  1.0
+  C  C87  1  0.82109000  0.67015000  0.47576000  1.0
+  C  C88  1  0.88686000  0.70520000  0.43014000  1.0
+  C  C89  1  0.90002000  0.63648000  0.32234000  1.0
+  C  C90  1  0.68486000  0.53438000  0.45704000  1.0
+  C  C91  1  0.94081000  0.81751000  0.49910000  1.0
+  O  O92  1  0.48420000  0.54884000  0.78706000  1.0
+  O  O93  1  0.47199000  0.72510000  0.83360000  1.0
+  O  O94  1  0.47098000  0.58491000  0.45558000  1.0
+  O  O95  1  0.45544000  0.74311000  0.60114000  1.0
+  O  O96  1  0.17232000  0.95149000  0.55446000  1.0
+  O  O97  1  0.13841000  0.95222000  0.39698000  1.0
+  O  O98  1  0.01580000  0.76178000  0.21294000  1.0
+  O  O99  1  0.02801000  0.89150000  0.16640000  1.0
+  O  O100  1  0.02902000  0.12933000  0.54442000  1.0
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+  O  O115  1  0.63841000  0.44476000  0.39698000  1.0
diff --git a/tests/testresources/inputs/cif_files/NEXXIZ_clean.cif b/tests/testresources/inputs/cif_files/NEXXIZ_clean.cif
new file mode 100644
index 00000000..0afee98f
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/NEXXIZ_clean.cif
@@ -0,0 +1,278 @@
+# generated using pymatgen
+data_Li4H19C30(NO4)2
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   12.96000000
+_cell_length_b   21.18930000
+_cell_length_c   21.18931864
+_cell_angle_alpha   84.86581798
+_cell_angle_beta   72.19274308
+_cell_angle_gamma   72.19280000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Li4H19C30(NO4)2
+_chemical_formula_sum   'Li16 H76 C120 N8 O32'
+_cell_volume   5274.61852353
+_cell_formula_units_Z   4
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
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+  Li  Li1  1  0.28441000  0.04596000  0.52242000  1.0
+  Li  Li2  1  0.63873000  0.99363000  0.56331000  1.0
+  Li  Li3  1  0.07440000  0.69510000  0.97870000  1.0
+  Li  Li4  1  0.53275000  0.51415000  0.95115000  1.0
+  Li  Li5  1  0.85279000  0.95404000  0.47758000  1.0
+  Li  Li6  1  0.19567000  0.00637000  0.43669000  1.0
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+  O  O222  1  0.38271000  0.05813000  0.57101000  1.0
+  O  O223  1  0.49939000  0.03691000  0.63385000  1.0
+  O  O224  1  0.28111000  0.96089000  0.49935000  1.0
+  O  O225  1  0.17241000  0.89274000  0.52514000  1.0
+  O  O226  1  0.21862000  0.62321000  0.93835000  1.0
+  O  O227  1  0.39397000  0.55986000  0.92906000  1.0
+  O  O228  1  0.55096000  0.50739000  0.03877000  1.0
+  O  O229  1  0.63064000  0.54535000  0.10069000  1.0
+  O  O230  1  0.01185000  0.94187000  0.42899000  1.0
+  O  O231  1  0.17015000  0.96309000  0.36615000  1.0
+  O  O232  1  0.74135000  0.03911000  0.50065000  1.0
+  O  O233  1  0.59029000  0.10726000  0.47486000  1.0
+  O  O234  1  0.78018000  0.37679000  0.06165000  1.0
+  O  O235  1  0.88289000  0.44014000  0.07094000  1.0
+  O  O236  1  0.59712000  0.96123000  0.49261000  1.0
+  O  O237  1  0.77668000  0.89931000  0.45465000  1.0
+  O  O238  1  0.88271000  0.57101000  0.05813000  1.0
+  O  O239  1  0.99939000  0.63385000  0.03691000  1.0
+  O  O240  1  0.78111000  0.49935000  0.96089000  1.0
+  O  O241  1  0.67241000  0.52514000  0.89274000  1.0
+  O  O242  1  0.71862000  0.93835000  0.62321000  1.0
+  O  O243  1  0.89397000  0.92906000  0.55986000  1.0
+  O  O244  1  0.05096000  0.03877000  0.50739000  1.0
+  O  O245  1  0.13064000  0.10069000  0.54535000  1.0
+  O  O246  1  0.51185000  0.42899000  0.94187000  1.0
+  O  O247  1  0.67015000  0.36615000  0.96309000  1.0
+  O  O248  1  0.24135000  0.50065000  0.03911000  1.0
+  O  O249  1  0.09029000  0.47486000  0.10726000  1.0
+  O  O250  1  0.28018000  0.06165000  0.37679000  1.0
+  O  O251  1  0.38289000  0.07094000  0.44014000  1.0
diff --git a/tests/testresources/inputs/cif_files/SETDUS_clean.cif b/tests/testresources/inputs/cif_files/SETDUS_clean.cif
new file mode 100644
index 00000000..0b774bb9
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/SETDUS_clean.cif
@@ -0,0 +1,76 @@
+# generated using pymatgen
+data_CuH10(C4N3)2
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   7.25900000
+_cell_length_b   11.27536272
+_cell_length_c   11.27536272
+_cell_angle_alpha   110.75238677
+_cell_angle_beta   102.27463566
+_cell_angle_gamma   102.27463566
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   CuH10(C4N3)2
+_chemical_formula_sum   'Cu2 H20 C16 N12'
+_cell_volume   800.30196914
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Cu  Cu0  1  0.00000000  0.00000000  0.00000000  1.0
+  Cu  Cu1  1  0.50000000  0.00000000  0.00000000  1.0
+  H  H2  1  0.86750000  0.68370000  0.88390000  1.0
+  H  H3  1  0.32410000  0.68120000  0.86500000  1.0
+  H  H4  1  0.44190000  0.37170000  0.92670000  1.0
+  H  H5  1  0.36270000  0.44120000  0.75640000  1.0
+  H  H6  1  0.58560000  0.43520000  0.78640000  1.0
+  H  H7  1  0.63250000  0.11610000  0.31630000  1.0
+  H  H8  1  0.17590000  0.13500000  0.31880000  1.0
+  H  H9  1  0.05810000  0.07330000  0.62830000  1.0
+  H  H10  1  0.13730000  0.24360000  0.55880000  1.0
+  H  H11  1  0.91440000  0.21360000  0.56480000  1.0
+  H  H12  1  0.13250000  0.31630000  0.11610000  1.0
+  H  H13  1  0.67590000  0.31880000  0.13500000  1.0
+  H  H14  1  0.55810000  0.62830000  0.07330000  1.0
+  H  H15  1  0.63730000  0.55880000  0.24360000  1.0
+  H  H16  1  0.41440000  0.56480000  0.21360000  1.0
+  H  H17  1  0.36750000  0.88390000  0.68370000  1.0
+  H  H18  1  0.82410000  0.86500000  0.68120000  1.0
+  H  H19  1  0.94190000  0.92670000  0.37170000  1.0
+  H  H20  1  0.86270000  0.75640000  0.44120000  1.0
+  H  H21  1  0.08560000  0.78640000  0.43520000  1.0
+  C  C22  1  0.75500000  0.71340000  0.89060000  1.0
+  C  C23  1  0.46300000  0.71030000  0.87970000  1.0
+  C  C24  1  0.48400000  0.46320000  0.94280000  1.0
+  C  C25  1  0.49600000  0.48170000  0.82430000  1.0
+  C  C26  1  0.74500000  0.10940000  0.28660000  1.0
+  C  C27  1  0.03700000  0.12030000  0.28970000  1.0
+  C  C28  1  0.01600000  0.05720000  0.53680000  1.0
+  C  C29  1  0.00400000  0.17570000  0.51830000  1.0
+  C  C30  1  0.24500000  0.28660000  0.10940000  1.0
+  C  C31  1  0.53700000  0.28970000  0.12030000  1.0
+  C  C32  1  0.51600000  0.53680000  0.05720000  1.0
+  C  C33  1  0.50400000  0.51830000  0.17570000  1.0
+  C  C34  1  0.25500000  0.89060000  0.71340000  1.0
+  C  C35  1  0.96300000  0.87970000  0.71030000  1.0
+  C  C36  1  0.98400000  0.94280000  0.46320000  1.0
+  C  C37  1  0.99600000  0.82430000  0.48170000  1.0
+  N  N38  1  0.76500000  0.83700000  0.93380000  1.0
+  N  N39  1  0.57700000  0.83720000  0.92680000  1.0
+  N  N40  1  0.57400000  0.62930000  0.85470000  1.0
+  N  N41  1  0.73500000  0.06620000  0.16300000  1.0
+  N  N42  1  0.92300000  0.07320000  0.16280000  1.0
+  N  N43  1  0.92600000  0.14530000  0.37070000  1.0
+  N  N44  1  0.23500000  0.16300000  0.06620000  1.0
+  N  N45  1  0.42300000  0.16280000  0.07320000  1.0
+  N  N46  1  0.42600000  0.37070000  0.14530000  1.0
+  N  N47  1  0.26500000  0.93380000  0.83700000  1.0
+  N  N48  1  0.07700000  0.92680000  0.83720000  1.0
+  N  N49  1  0.07400000  0.85470000  0.62930000  1.0
diff --git a/tests/testresources/inputs/cif_files/UXUPEK_clean.cif b/tests/testresources/inputs/cif_files/UXUPEK_clean.cif
new file mode 100644
index 00000000..98f1eb7e
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/UXUPEK_clean.cif
@@ -0,0 +1,42 @@
+# generated using pymatgen
+data_CuPH2CO3
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.36300000
+_cell_length_b   6.68440000
+_cell_length_c   8.13615541
+_cell_angle_alpha   114.25407495
+_cell_angle_beta   92.99020777
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   CuPH2CO3
+_chemical_formula_sum   'Cu2 P2 H4 C2 O6'
+_cell_volume   215.98443241
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Cu  Cu0  1  0.50000000  0.50000000  0.50000000  1.0
+  Cu  Cu1  1  0.50000000  0.00000000  0.50000000  1.0
+  P  P2  1  0.02830000  0.85070000  0.70140000  1.0
+  P  P3  1  0.97170000  0.14930000  0.29860000  1.0
+  H  H4  1  0.77200000  0.84300000  0.93140000  1.0
+  H  H5  1  0.22800000  0.91160000  0.06860000  1.0
+  H  H6  1  0.22800000  0.15700000  0.06860000  1.0
+  H  H7  1  0.77200000  0.08840000  0.93140000  1.0
+  C  C8  1  0.87950000  0.96130000  0.92260000  1.0
+  C  C9  1  0.12050000  0.03870000  0.07740000  1.0
+  O  O10  1  0.21480000  0.65150000  0.68240000  1.0
+  O  O11  1  0.78520000  0.96910000  0.31760000  1.0
+  O  O12  1  0.78520000  0.34850000  0.31760000  1.0
+  O  O13  1  0.21480000  0.03090000  0.68240000  1.0
+  O  O14  1  0.74330000  0.78260000  0.56520000  1.0
+  O  O15  1  0.25670000  0.21740000  0.43480000  1.0
diff --git a/tests/testresources/inputs/cif_files/VONBIK_clean.cif b/tests/testresources/inputs/cif_files/VONBIK_clean.cif
new file mode 100644
index 00000000..aba73ba7
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/VONBIK_clean.cif
@@ -0,0 +1,434 @@
+# generated using pymatgen
+data_ZnH18C24N3O5
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   16.44100000
+_cell_length_b   17.30900000
+_cell_length_c   18.12800000
+_cell_angle_alpha   92.43900000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   ZnH18C24N3O5
+_chemical_formula_sum   'Zn8 H144 C192 N24 O40'
+_cell_volume   5154.14333347
+_cell_formula_units_Z   8
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Zn  Zn0  1  0.49907000  0.72403000  0.22756000  1.0
+  Zn  Zn1  1  0.00625000  0.70831000  0.79086000  1.0
+  Zn  Zn2  1  0.00093000  0.22403000  0.72756000  1.0
+  Zn  Zn3  1  0.49375000  0.20831000  0.29086000  1.0
+  Zn  Zn4  1  0.99907000  0.77597000  0.27244000  1.0
+  Zn  Zn5  1  0.50625000  0.79169000  0.70914000  1.0
+  Zn  Zn6  1  0.50093000  0.27597000  0.77244000  1.0
+  Zn  Zn7  1  0.99375000  0.29169000  0.20914000  1.0
+  H  H8  1  0.82750000  0.69360000  0.52470000  1.0
+  H  H9  1  0.82120000  0.78350000  0.53860000  1.0
+  H  H10  1  0.69890000  0.75570000  0.61070000  1.0
+  H  H11  1  0.73120000  0.67040000  0.61000000  1.0
+  H  H12  1  0.77150000  0.84770000  0.30420000  1.0
+  H  H13  1  0.81900000  0.75520000  0.39610000  1.0
+  H  H14  1  0.78270000  0.67130000  0.39140000  1.0
+  H  H15  1  0.82360000  0.58650000  0.60250000  1.0
+  H  H16  1  0.24870000  0.02180000  0.75420000  1.0
+  H  H17  1  0.52190000  0.14500000  0.53890000  1.0
+  H  H18  1  0.68680000  0.70170000  0.47880000  1.0
+  H  H19  1  0.70370000  0.79060000  0.47420000  1.0
+  H  H20  1  0.86310000  0.85870000  0.79450000  1.0
+  H  H21  1  0.14740000  0.93720000  0.78490000  1.0
+  H  H22  1  0.48430000  0.08450000  0.64500000  1.0
+  H  H23  1  0.15680000  0.44100000  0.72040000  1.0
+  H  H24  1  0.26400000  0.52410000  0.74410000  1.0
+  H  H25  1  0.31740000  0.50110000  0.96270000  1.0
+  H  H26  1  0.29620000  0.98690000  0.53650000  1.0
+  H  H27  1  0.99830000  0.44150000  0.66200000  1.0
+  H  H28  1  0.68360000  0.59500000  0.40090000  1.0
+  H  H29  1  0.22590000  0.78410000  0.62900000  1.0
+  H  H30  1  0.23620000  0.30230000  0.87560000  1.0
+  H  H31  1  0.04560000  0.53640000  0.74460000  1.0
+  H  H32  1  0.75060000  0.85020000  0.70530000  1.0
+  H  H33  1  0.33100000  0.86730000  0.60070000  1.0
+  H  H34  1  0.60900000  0.48250000  0.41480000  1.0
+  H  H35  1  0.34750000  0.38220000  0.89700000  1.0
+  H  H36  1  0.49450000  0.60400000  0.85310000  1.0
+  H  H37  1  0.33470000  0.04840000  0.43120000  1.0
+  H  H38  1  0.88670000  0.46700000  0.59030000  1.0
+  H  H39  1  0.65400000  0.86060000  0.22120000  1.0
+  H  H40  1  0.35960000  0.56440000  0.07100000  1.0
+  H  H41  1  0.44520000  0.56020000  0.27500000  1.0
+  H  H42  1  0.48830000  0.46540000  0.35000000  1.0
+  H  H43  1  0.53460000  0.66900000  0.96020000  1.0
+  H  H44  1  0.67250000  0.19360000  0.02470000  1.0
+  H  H45  1  0.67880000  0.28350000  0.03860000  1.0
+  H  H46  1  0.80110000  0.25570000  0.11070000  1.0
+  H  H47  1  0.76880000  0.17040000  0.11000000  1.0
+  H  H48  1  0.72850000  0.34770000  0.80420000  1.0
+  H  H49  1  0.68100000  0.25520000  0.89610000  1.0
+  H  H50  1  0.71730000  0.17130000  0.89140000  1.0
+  H  H51  1  0.67640000  0.08650000  0.10250000  1.0
+  H  H52  1  0.25130000  0.52180000  0.25420000  1.0
+  H  H53  1  0.97810000  0.64500000  0.03890000  1.0
+  H  H54  1  0.81320000  0.20170000  0.97880000  1.0
+  H  H55  1  0.79630000  0.29060000  0.97420000  1.0
+  H  H56  1  0.63690000  0.35870000  0.29450000  1.0
+  H  H57  1  0.35260000  0.43720000  0.28490000  1.0
+  H  H58  1  0.01570000  0.58450000  0.14500000  1.0
+  H  H59  1  0.34320000  0.94100000  0.22040000  1.0
+  H  H60  1  0.23600000  0.02410000  0.24410000  1.0
+  H  H61  1  0.18260000  0.00110000  0.46270000  1.0
+  H  H62  1  0.20380000  0.48690000  0.03650000  1.0
+  H  H63  1  0.50170000  0.94150000  0.16200000  1.0
+  H  H64  1  0.81640000  0.09500000  0.90090000  1.0
+  H  H65  1  0.27410000  0.28410000  0.12900000  1.0
+  H  H66  1  0.26380000  0.80230000  0.37560000  1.0
+  H  H67  1  0.45440000  0.03640000  0.24460000  1.0
+  H  H68  1  0.74940000  0.35020000  0.20530000  1.0
+  H  H69  1  0.16900000  0.36730000  0.10070000  1.0
+  H  H70  1  0.89100000  0.98250000  0.91480000  1.0
+  H  H71  1  0.15250000  0.88220000  0.39700000  1.0
+  H  H72  1  0.00550000  0.10400000  0.35310000  1.0
+  H  H73  1  0.16530000  0.54840000  0.93120000  1.0
+  H  H74  1  0.61330000  0.96700000  0.09030000  1.0
+  H  H75  1  0.84600000  0.36060000  0.72120000  1.0
+  H  H76  1  0.14040000  0.06440000  0.57100000  1.0
+  H  H77  1  0.05480000  0.06020000  0.77500000  1.0
+  H  H78  1  0.01170000  0.96540000  0.85000000  1.0
+  H  H79  1  0.96540000  0.16900000  0.46020000  1.0
+  H  H80  1  0.32750000  0.80640000  0.97530000  1.0
+  H  H81  1  0.32120000  0.71650000  0.96140000  1.0
+  H  H82  1  0.19890000  0.74430000  0.88930000  1.0
+  H  H83  1  0.23120000  0.82960000  0.89000000  1.0
+  H  H84  1  0.27150000  0.65230000  0.19580000  1.0
+  H  H85  1  0.31900000  0.74480000  0.10390000  1.0
+  H  H86  1  0.28270000  0.82870000  0.10860000  1.0
+  H  H87  1  0.32360000  0.91350000  0.89750000  1.0
+  H  H88  1  0.74870000  0.47820000  0.74580000  1.0
+  H  H89  1  0.02190000  0.35500000  0.96110000  1.0
+  H  H90  1  0.18680000  0.79830000  0.02120000  1.0
+  H  H91  1  0.20370000  0.70940000  0.02580000  1.0
+  H  H92  1  0.36310000  0.64130000  0.70550000  1.0
+  H  H93  1  0.64740000  0.56280000  0.71510000  1.0
+  H  H94  1  0.98430000  0.41550000  0.85500000  1.0
+  H  H95  1  0.65680000  0.05900000  0.77960000  1.0
+  H  H96  1  0.76400000  0.97590000  0.75590000  1.0
+  H  H97  1  0.81740000  0.99890000  0.53730000  1.0
+  H  H98  1  0.79620000  0.51310000  0.96350000  1.0
+  H  H99  1  0.49830000  0.05850000  0.83800000  1.0
+  H  H100  1  0.18360000  0.90500000  0.09910000  1.0
+  H  H101  1  0.72590000  0.71590000  0.87100000  1.0
+  H  H102  1  0.73620000  0.19770000  0.62440000  1.0
+  H  H103  1  0.54560000  0.96360000  0.75540000  1.0
+  H  H104  1  0.25060000  0.64980000  0.79470000  1.0
+  H  H105  1  0.83100000  0.63270000  0.89930000  1.0
+  H  H106  1  0.10900000  0.01750000  0.08520000  1.0
+  H  H107  1  0.84750000  0.11780000  0.60300000  1.0
+  H  H108  1  0.99450000  0.89600000  0.64690000  1.0
+  H  H109  1  0.83470000  0.45160000  0.06880000  1.0
+  H  H110  1  0.38670000  0.03300000  0.90970000  1.0
+  H  H111  1  0.15400000  0.63940000  0.27880000  1.0
+  H  H112  1  0.85960000  0.93560000  0.42900000  1.0
+  H  H113  1  0.94520000  0.93980000  0.22500000  1.0
+  H  H114  1  0.98830000  0.03460000  0.15000000  1.0
+  H  H115  1  0.03460000  0.83100000  0.53980000  1.0
+  H  H116  1  0.17250000  0.30640000  0.47530000  1.0
+  H  H117  1  0.17880000  0.21650000  0.46140000  1.0
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+  O  O376  1  0.06827000  0.32400000  0.72590000  1.0
+  O  O377  1  0.10700000  0.24900000  0.81210000  1.0
+  O  O378  1  0.98370000  0.68637000  0.90457000  1.0
+  O  O379  1  0.13356000  0.50044000  0.16821000  1.0
+  O  O380  1  0.09139000  0.63614000  0.84937000  1.0
+  O  O381  1  0.42603000  0.31035000  0.29354000  1.0
+  O  O382  1  0.11755000  0.00975000  0.33038000  1.0
+  O  O383  1  0.40090000  0.23530000  0.19737000  1.0
+  O  O384  1  0.97280000  0.21810000  0.59891000  1.0
+  O  O385  1  0.06500000  0.15171000  0.65544000  1.0
+  O  O386  1  0.43173000  0.82400000  0.22590000  1.0
+  O  O387  1  0.39300000  0.74900000  0.31210000  1.0
+  O  O388  1  0.01630000  0.31363000  0.09543000  1.0
+  O  O389  1  0.86644000  0.49956000  0.83179000  1.0
+  O  O390  1  0.90861000  0.36386000  0.15063000  1.0
+  O  O391  1  0.57397000  0.68965000  0.70646000  1.0
+  O  O392  1  0.88245000  0.99025000  0.66962000  1.0
+  O  O393  1  0.59910000  0.76470000  0.80263000  1.0
+  O  O394  1  0.02720000  0.78190000  0.40109000  1.0
+  O  O395  1  0.93500000  0.84829000  0.34456000  1.0
+  O  O396  1  0.56827000  0.17600000  0.77410000  1.0
+  O  O397  1  0.60700000  0.25100000  0.68790000  1.0
+  O  O398  1  0.48370000  0.81363000  0.59543000  1.0
+  O  O399  1  0.63356000  0.99956000  0.33179000  1.0
+  O  O400  1  0.59139000  0.86386000  0.65063000  1.0
+  O  O401  1  0.92603000  0.18965000  0.20646000  1.0
+  O  O402  1  0.61755000  0.49025000  0.16962000  1.0
+  O  O403  1  0.90090000  0.26470000  0.30263000  1.0
+  O  O404  1  0.47280000  0.28190000  0.90109000  1.0
+  O  O405  1  0.56500000  0.34829000  0.84456000  1.0
+  O  O406  1  0.93173000  0.67600000  0.27410000  1.0
+  O  O407  1  0.89300000  0.75100000  0.18790000  1.0
diff --git a/tests/testresources/inputs/cif_files/YICDAR_clean.cif b/tests/testresources/inputs/cif_files/YICDAR_clean.cif
new file mode 100644
index 00000000..b82be21f
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/YICDAR_clean.cif
@@ -0,0 +1,104 @@
+# generated using pymatgen
+data_MgHC5(NO2)2
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   9.11400000
+_cell_length_b   16.09939738
+_cell_length_c   16.09939738
+_cell_angle_alpha   116.52491473
+_cell_angle_beta   100.87708582
+_cell_angle_gamma   100.87708582
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   MgHC5(NO2)2
+_chemical_formula_sum   'Mg6 H6 C30 N12 O24'
+_cell_volume   1972.93225717
+_cell_formula_units_Z   6
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Mg  Mg0  1  0.19586000  0.09839000  0.23299000  1.0
+  Mg  Mg1  1  0.96287000  0.76701000  0.86540000  1.0
+  Mg  Mg2  1  0.09747000  0.13460000  0.90161000  1.0
+  Mg  Mg3  1  0.80414000  0.90161000  0.76701000  1.0
+  Mg  Mg4  1  0.03713000  0.23299000  0.13460000  1.0
+  Mg  Mg5  1  0.90253000  0.86540000  0.09839000  1.0
+  H  H6  1  0.37050000  0.14570000  0.05110000  1.0
+  H  H7  1  0.31940000  0.94890000  0.09460000  1.0
+  H  H8  1  0.22480000  0.90540000  0.85430000  1.0
+  H  H9  1  0.62950000  0.85430000  0.94890000  1.0
+  H  H10  1  0.68060000  0.05110000  0.90540000  1.0
+  H  H11  1  0.77520000  0.09460000  0.14570000  1.0
+  C  C12  1  0.28826000  0.31773000  0.33405000  1.0
+  C  C13  1  0.39488000  0.41194000  0.41930000  1.0
+  C  C14  1  0.47967000  0.41408000  0.50173000  1.0
+  C  C15  1  0.41599000  0.49968000  0.41709000  1.0
+  C  C16  1  0.29386000  0.14946000  0.08232000  1.0
+  C  C17  1  0.95421000  0.66595000  0.98368000  1.0
+  C  C18  1  0.97558000  0.58070000  0.99264000  1.0
+  C  C19  1  0.97794000  0.49827000  0.91235000  1.0
+  C  C20  1  0.99890000  0.58291000  0.08259000  1.0
+  C  C21  1  0.21154000  0.91768000  0.06714000  1.0
+  C  C22  1  0.97053000  0.01632000  0.68227000  1.0
+  C  C23  1  0.98294000  0.00736000  0.58806000  1.0
+  C  C24  1  0.06559000  0.08765000  0.58592000  1.0
+  C  C25  1  0.91631000  0.91741000  0.50032000  1.0
+  C  C26  1  0.14440000  0.93286000  0.85054000  1.0
+  C  C27  1  0.71174000  0.68227000  0.66595000  1.0
+  C  C28  1  0.60512000  0.58806000  0.58070000  1.0
+  C  C29  1  0.52033000  0.58592000  0.49827000  1.0
+  C  C30  1  0.58401000  0.50032000  0.58291000  1.0
+  C  C31  1  0.70614000  0.85054000  0.91768000  1.0
+  C  C32  1  0.04579000  0.33405000  0.01632000  1.0
+  C  C33  1  0.02442000  0.41930000  0.00736000  1.0
+  C  C34  1  0.02206000  0.50173000  0.08765000  1.0
+  C  C35  1  0.00110000  0.41709000  0.91741000  1.0
+  C  C36  1  0.78846000  0.08232000  0.93286000  1.0
+  C  C37  1  0.02947000  0.98368000  0.31773000  1.0
+  C  C38  1  0.01706000  0.99264000  0.41194000  1.0
+  C  C39  1  0.93441000  0.91235000  0.41408000  1.0
+  C  C40  1  0.08369000  0.08259000  0.49968000  1.0
+  C  C41  1  0.85560000  0.06714000  0.14946000  1.0
+  N  N42  1  0.33460000  0.50950000  0.33950000  1.0
+  N  N43  1  0.47900000  0.33680000  0.50920000  1.0
+  N  N44  1  0.99510000  0.66050000  0.17000000  1.0
+  N  N45  1  0.96980000  0.49080000  0.82760000  1.0
+  N  N46  1  0.82510000  0.83000000  0.49050000  1.0
+  N  N47  1  0.14220000  0.17240000  0.66320000  1.0
+  N  N48  1  0.66540000  0.49050000  0.66050000  1.0
+  N  N49  1  0.52100000  0.66320000  0.49080000  1.0
+  N  N50  1  0.00490000  0.33950000  0.83000000  1.0
+  N  N51  1  0.03020000  0.50920000  0.17240000  1.0
+  N  N52  1  0.17490000  0.17000000  0.50950000  1.0
+  N  N53  1  0.85780000  0.82760000  0.33680000  1.0
+  O  O54  1  0.27347000  0.24213000  0.34128000  1.0
+  O  O55  1  0.22095000  0.31950000  0.25905000  1.0
+  O  O56  1  0.31799000  0.13556000  0.15241000  1.0
+  O  O57  1  0.17626000  0.16806000  0.04902000  1.0
+  O  O58  1  0.93219000  0.65872000  0.90085000  1.0
+  O  O59  1  0.96190000  0.74095000  0.06045000  1.0
+  O  O60  1  0.16558000  0.84759000  0.98315000  1.0
+  O  O61  1  0.12724000  0.95098000  0.11904000  1.0
+  O  O62  1  0.03134000  0.09915000  0.75787000  1.0
+  O  O63  1  0.90145000  0.93955000  0.68050000  1.0
+  O  O64  1  0.18243000  0.01685000  0.86444000  1.0
+  O  O65  1  0.00820000  0.88096000  0.83194000  1.0
+  O  O66  1  0.72653000  0.75787000  0.65872000  1.0
+  O  O67  1  0.77905000  0.68050000  0.74095000  1.0
+  O  O68  1  0.68201000  0.86444000  0.84759000  1.0
+  O  O69  1  0.82374000  0.83194000  0.95098000  1.0
+  O  O70  1  0.06781000  0.34128000  0.09915000  1.0
+  O  O71  1  0.03810000  0.25905000  0.93955000  1.0
+  O  O72  1  0.83442000  0.15241000  0.01685000  1.0
+  O  O73  1  0.87276000  0.04902000  0.88096000  1.0
+  O  O74  1  0.96866000  0.90085000  0.24213000  1.0
+  O  O75  1  0.09855000  0.06045000  0.31950000  1.0
+  O  O76  1  0.81757000  0.98315000  0.13556000  1.0
+  O  O77  1  0.99180000  0.11904000  0.16806000  1.0
diff --git a/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/FOKYIP_clean.json b/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/FOKYIP_clean.json
new file mode 100644
index 00000000..a5847e76
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/FOKYIP_clean.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all"], "descriptors": [196.6224, 357.9708, 1324.0448, 1071.29999999999, 8256.0, 16176.0, 21248.0, 16416.0, 22.0, 60.0, 136.0, 140.0, 236.0, 792.0, 1058.0, 968.0, 17.1932, 56.7868, 94.4194, 96.4596, 1.2996, 30.3582, 15.8345999999999, 39.957, 3600.0, 3720.0, 5400.0, 4920.0, 1.0, 8.0, 6.0, 12.0, 64.0, 160.0, 184.0, 256.0, 3.0276, 10.2312, 9.7266, 15.7296, 0.0, -17.51, -7.05, -21.37, 0.0, 418.0, 270.0, 638.0, 0.0, 0.0, 0.0, 0.0, 0.0, 44.0, 25.0, 64.0, 0.0, 8.04, 4.85, 11.84, 202.4191, 391.884, 619.455599999999, 759.267999999999, 931.0, 1812.0, 2712.0, 2884.0, 28.0, 58.0, 90.0, 116.0, 148.0, 366.0, 522.0, 580.0, 13.0492, 29.7066, 44.0074, 51.4292, 11.0720142857142, 10.9540714285714, 19.5198, 18.4984285714285, 60.0, 60.0, 106.285714285714, 94.2857142857143, 1.0, 1.28571428571428, 2.0, 2.28571428571428, 2.14285714285714, 4.71428571428571, 6.0, 8.57142857142857, 0.541471428571428, 0.7271, 1.10797142857142, 1.2144, 0.0, 0.508571428571428, 0.762857142857143, 1.62571428571428, 0.0, 1.14285714285714, 1.71428571428571, 4.85714285714285, 0.0, 0.0, 0.0, 0.0, 0.0, -1.14285714285714, -1.71428571428571, -2.85714285714285, 0.0, -0.0228571428571428, -0.0342857142857143, 0.0457142857142856, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]}
diff --git a/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/lc_descriptors.csv
new file mode 100644
index 00000000..aa6c8f31
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/lc_descriptors.csv
@@ -0,0 +1,9 @@
+lc-chi-0-all,lc-chi-1-all,lc-chi-2-all,lc-chi-3-all,lc-Z-0-all,lc-Z-1-all,lc-Z-2-all,lc-Z-3-all,lc-I-0-all,lc-I-1-all,lc-I-2-all,lc-I-3-all,lc-T-0-all,lc-T-1-all,lc-T-2-all,lc-T-3-all,lc-S-0-all,lc-S-1-all,lc-S-2-all,lc-S-3-all,lc-alpha-0-all,lc-alpha-1-all,lc-alpha-2-all,lc-alpha-3-all,D_lc-chi-0-all,D_lc-chi-1-all,D_lc-chi-2-all,D_lc-chi-3-all,D_lc-Z-0-all,D_lc-Z-1-all,D_lc-Z-2-all,D_lc-Z-3-all,D_lc-I-0-all,D_lc-I-1-all,D_lc-I-2-all,D_lc-I-3-all,D_lc-T-0-all,D_lc-T-1-all,D_lc-T-2-all,D_lc-T-3-all,D_lc-S-0-all,D_lc-S-1-all,D_lc-S-2-all,D_lc-S-3-all,D_lc-alpha-0-all,D_lc-alpha-1-all,D_lc-alpha-2-all,D_lc-alpha-3-all,func-chi-0-all,func-chi-1-all,func-chi-2-all,func-chi-3-all,func-Z-0-all,func-Z-1-all,func-Z-2-all,func-Z-3-all,func-I-0-all,func-I-1-all,func-I-2-all,func-I-3-all,func-T-0-all,func-T-1-all,func-T-2-all,func-T-3-all,func-S-0-all,func-S-1-all,func-S-2-all,func-S-3-all,func-alpha-0-all,func-alpha-1-all,func-alpha-2-all,func-alpha-3-all,D_func-chi-0-all,D_func-chi-1-all,D_func-chi-2-all,D_func-chi-3-all,D_func-Z-0-all,D_func-Z-1-all,D_func-Z-2-all,D_func-Z-3-all,D_func-I-0-all,D_func-I-1-all,D_func-I-2-all,D_func-I-3-all,D_func-T-0-all,D_func-T-1-all,D_func-T-2-all,D_func-T-3-all,D_func-S-0-all,D_func-S-1-all,D_func-S-2-all,D_func-S-3-all,D_func-alpha-0-all,D_func-alpha-1-all,D_func-alpha-2-all,D_func-alpha-3-all,name
+11.072014285714284,10.954071428571426,19.519799999999996,18.49842857142857,60.0,60.0,106.28571428571428,94.28571428571428,1.0,1.2857142857142858,2.0,2.2857142857142856,2.142857142857143,4.714285714285714,6.0,8.571428571428571,0.5414714285714285,0.7271000000000001,1.1079714285714284,1.2144,42.318571428571424,86.68714285714286,111.89428571428572,153.70295514285712,0.0,0.5085714285714287,0.7628571428571431,1.625714285714286,0.0,1.1428571428571428,1.7142857142857142,4.857142857142857,0.0,0.0,0.0,0.0,0.0,-1.1428571428571428,-1.7142857142857142,-2.857142857142857,0.0,-0.0228571428571428,-0.0342857142857143,0.0457142857142856,0.0,-3.4285714285714293,-5.142857142857144,-8.344888571428573,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,FOKYIP_clean
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diff --git a/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/sbu_descriptors.csv
new file mode 100644
index 00000000..5082eeab
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/FOKYIP_clean/sbu_descriptors.csv
@@ -0,0 +1,3 @@
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diff --git a/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/NEXXIZ_clean.json b/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/NEXXIZ_clean.json
new file mode 100644
index 00000000..cf4ec56b
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/NEXXIZ_clean.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all"], "descriptors": [249.0408, 469.4912, 1149.33279999999, 1376.2752, 1384.0, 2880.0, 6528.0, 8064.0, 32.0, 88.0, 156.0, 216.0, 260.0, 768.0, 1300.0, 1632.0, 27.4208, 72.3576, 130.4156, 160.6584, 0.9604, 11.7992, 10.6672999999999, 28.9737, 9.0, 84.0, 81.0, 207.0, 1.0, 3.5, 5.5, 9.5, 13.0, 37.0, 67.0, 99.0, 1.76889999999999, 3.39815, 7.12214999999999, 9.40975, 0.0, -8.61, -5.495, -20.255, 0.0, -17.5, -10.5, -40.5, 0.0, 0.0, 0.0, 0.0, 0.0, 3.0, 2.5, 8.0, 0.0, 2.1, 1.96, 5.55999999999999, 200.093499999999, 405.348, 640.7254, 786.742, 854.5, 1758.0, 2560.0, 2740.0, 29.5, 61.0, 96.0, 122.0, 157.0, 387.0, 544.0, 602.0, 12.88815, 29.9761, 44.1386, 51.3786, 11.8335999999999, 8.77199999999999, 20.6055999999999, 17.5439999999999, 64.0, 48.0, 112.0, 96.0, 1.0, 1.0, 2.0, 2.0, 1.0, 3.0, 4.0, 6.0, 0.532899999999999, 0.5621, 1.095, 1.1242, 0.0, 0.89, 0.89, 1.78, 0.0, 2.0, 2.0, 4.0, 0.0, 0.0, 0.0, 0.0, 0.0, -2.0, -2.0, -4.0, 0.0, -0.04, -0.04, -0.08, 9.2416, 23.256, 41.04, 57.76, 49.0, 126.0, 178.5, 196.0, 1.0, 3.0, 5.5, 8.0, 9.0, 25.5, 40.5, 48.0, 0.5625, 1.7325, 2.72625, 3.42, 0.0, 1.47, 3.22, 5.31999999999999, 0.0, 3.0, 13.0, 28.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 3.0, 8.0, 0.0, -0.06, 0.49, 1.44]}
diff --git a/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/lc_descriptors.csv
new file mode 100644
index 00000000..73f37f56
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/lc_descriptors.csv
@@ -0,0 +1,17 @@
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+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,23.256,51.07200000000001,57.76000000000001,49.0,126.0,189.0,196.0,1.0,3.0,7.0,8.0,9.0,30.0,45.0,48.0,0.5625,1.7325,3.1425,3.4199999999999995,54.760000000000005,250.86,434.53784200000007,467.8904560000001,0.0,1.4700000000000006,4.48,5.32,0.0,3.0,22.0,28.0,0.0,0.0,0.0,0.0,0.0,-1.0,6.0,8.0,0.0,-0.06,1.06,1.44,0.0,-11.7,-6.92133,-4.028440000000001,NEXXIZ_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,23.256,31.008,57.760000000000005,49.0,126.0,168.0,196.0,1.0,3.0,4.0,8.0,9.0,21.0,36.0,48.0,0.5625,1.7325,2.31,3.4199999999999995,54.760000000000005,250.86,334.48,467.8904560000001,0.0,1.4700000000000006,1.9600000000000009,5.32,0.0,3.0,4.0,28.0,0.0,0.0,0.0,0.0,0.0,2.0,0.0,8.0,0.0,-0.06,-0.08,1.44,0.0,-11.7,-15.6,-4.028439999999998,NEXXIZ_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,23.256,51.072,57.760000000000005,49.0,126.0,189.0,196.0,1.0,3.0,7.0,8.0,9.0,30.0,45.0,48.0,0.5625,1.7325,3.1424999999999996,3.4199999999999995,54.760000000000005,250.86,434.53784200000007,467.8904560000001,0.0,1.4700000000000006,4.48,5.32,0.0,3.0,22.0,28.0,0.0,0.0,0.0,0.0,0.0,-1.0,6.0,8.0,0.0,-0.06,1.06,1.44,0.0,-11.7,-6.921329999999998,-4.028439999999998,NEXXIZ_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,23.256,31.008,57.760000000000005,49.0,126.0,168.0,196.0,1.0,3.0,4.0,8.0,9.0,21.0,36.0,48.0,0.5625,1.7325,2.31,3.4199999999999995,54.760000000000005,250.86,334.48,467.8904560000001,0.0,1.4700000000000006,1.9600000000000009,5.32,0.0,3.0,4.0,28.0,0.0,0.0,0.0,0.0,0.0,2.0,0.0,8.0,0.0,-0.06,-0.08,1.44,0.0,-11.7,-15.6,-4.028439999999998,NEXXIZ_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,23.256,31.008,57.760000000000005,49.0,126.0,168.0,196.0,1.0,3.0,4.0,8.0,9.0,21.0,36.0,48.0,0.5625,1.7325,2.31,3.4199999999999995,54.760000000000005,250.86,334.48,467.8904560000001,0.0,1.4700000000000006,1.9600000000000009,5.32,0.0,3.0,4.0,28.0,0.0,0.0,0.0,0.0,0.0,2.0,0.0,8.0,0.0,-0.06,-0.08,1.44,0.0,-11.7,-15.6,-4.028439999999998,NEXXIZ_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,23.256,51.072,57.760000000000005,49.0,126.0,189.0,196.0,1.0,3.0,7.0,8.0,9.0,30.0,45.0,48.0,0.5625,1.7325,3.1424999999999996,3.4199999999999995,54.760000000000005,250.86,434.53784200000007,467.8904560000001,0.0,1.4700000000000006,4.48,5.32,0.0,3.0,22.0,28.0,0.0,0.0,0.0,0.0,0.0,-1.0,6.0,8.0,0.0,-0.06,1.06,1.44,0.0,-11.7,-6.921329999999998,-4.028439999999998,NEXXIZ_clean
diff --git a/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/sbu_descriptors.csv
new file mode 100644
index 00000000..23b1f97a
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/NEXXIZ_clean/sbu_descriptors.csv
@@ -0,0 +1,3 @@
+f-chi-0-all,f-chi-1-all,f-chi-2-all,f-chi-3-all,f-Z-0-all,f-Z-1-all,f-Z-2-all,f-Z-3-all,f-I-0-all,f-I-1-all,f-I-2-all,f-I-3-all,f-T-0-all,f-T-1-all,f-T-2-all,f-T-3-all,f-S-0-all,f-S-1-all,f-S-2-all,f-S-3-all,mc-chi-0-all,mc-chi-1-all,mc-chi-2-all,mc-chi-3-all,mc-Z-0-all,mc-Z-1-all,mc-Z-2-all,mc-Z-3-all,mc-I-0-all,mc-I-1-all,mc-I-2-all,mc-I-3-all,mc-T-0-all,mc-T-1-all,mc-T-2-all,mc-T-3-all,mc-S-0-all,mc-S-1-all,mc-S-2-all,mc-S-3-all,D_mc-chi-0-all,D_mc-chi-1-all,D_mc-chi-2-all,D_mc-chi-3-all,D_mc-Z-0-all,D_mc-Z-1-all,D_mc-Z-2-all,D_mc-Z-3-all,D_mc-I-0-all,D_mc-I-1-all,D_mc-I-2-all,D_mc-I-3-all,D_mc-T-0-all,D_mc-T-1-all,D_mc-T-2-all,D_mc-T-3-all,D_mc-S-0-all,D_mc-S-1-all,D_mc-S-2-all,D_mc-S-3-all,name
+249.0407999999999,469.4912000000001,1149.3327999999997,1376.2752,1384.0,2880.0,6528.0,8064.0,32.0,88.0,156.0,216.0,260.0,768.0,1300.0,1632.0,27.420800000000025,72.35760000000003,130.41560000000007,160.65840000000003,0.9604,11.799200000000004,10.667299999999996,28.9737,9.0,84.0,81.0,207.0,1.0,3.5,5.5,9.5,13.0,37.0,67.0,99.0,1.7688999999999997,3.3981500000000007,7.122149999999999,9.40975,0.0,-8.610000000000001,-5.495,-20.255000000000003,0.0,-17.5,-10.5,-40.5,0.0,0.0,0.0,0.0,0.0,3.0,2.5,8.0,0.0,2.1,1.9600000000000009,5.559999999999999,NEXXIZ_clean
+249.0407999999999,469.4912000000001,1149.3327999999997,1376.2752,1384.0,2880.0,6528.0,8064.0,32.0,88.0,156.0,216.0,260.0,768.0,1300.0,1632.0,27.420800000000025,72.35760000000003,130.41560000000007,160.6584,0.9604,11.799200000000004,10.667299999999996,28.9737,9.0,84.0,81.0,207.0,1.0,3.5,5.5,9.5,13.0,37.0,67.0,99.0,1.7688999999999997,3.3981500000000007,7.122149999999999,9.40975,0.0,-8.610000000000001,-5.495,-20.255000000000003,0.0,-17.5,-10.5,-40.5,0.0,0.0,0.0,0.0,0.0,3.0,2.5,8.0,0.0,2.1,1.9600000000000009,5.559999999999999,NEXXIZ_clean
diff --git a/tests/testresources/refs/MOF_descriptors/SETDUS_clean/SETDUS_clean.json b/tests/testresources/refs/MOF_descriptors/SETDUS_clean/SETDUS_clean.json
new file mode 100644
index 00000000..0b3b8af9
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/SETDUS_clean/SETDUS_clean.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all"], "descriptors": [133.1728, 290.3808, 515.766399999999, 730.654399999999, 2362.0, 4312.0, 7880.0, 7946.0, 18.0, 40.0, 72.0, 98.0, 112.0, 312.0, 520.0, 464.0, 13.052, 30.3, 56.3015999999999, 66.7736, 3.61, 23.104, 42.4839999999999, 62.8139999999999, 841.0, 812.0, 1508.0, 2465.0, 1.0, 4.0, 8.0, 13.0, 16.0, 48.0, 96.0, 128.0, 1.9044, 4.14, 8.3904, 12.3372, 0.0, -4.56, -7.16, -8.36, 0.0, 88.0, 180.0, 292.0, 0.0, 0.0, 0.0, 0.0, 0.0, 4.0, 8.0, 20.0, 0.0, 2.52, 4.95999999999999, 8.99999999999999, 155.8696, 343.2214, 540.6288, 533.545, 592.0, 1372.0, 1740.0, 1222.0, 24.0, 50.0, 80.0, 88.0, 130.0, 318.0, 432.0, 386.0, 9.48719999999999, 23.0554, 32.6824, 30.0936, 9.2416, 16.9936, 23.6816, 14.44, 49.0, 91.0, 98.0, 49.0, 1.0, 2.0, 3.0, 2.0, 4.0, 10.0, 14.0, 10.0, 0.5625, 1.14, 1.4175, 0.855, 0.0, 0.49, 1.33, 1.33, 0.0, 1.0, 7.0, 7.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -0.02, 0.36, 0.36, 9.2416, 23.256, 52.9872, 14.44, 49.0, 126.0, 168.0, 49.0, 1.0, 3.0, 7.0, 2.0, 9.0, 30.0, 33.0, 12.0, 0.5625, 1.7325, 2.8125, 0.855, 0.0, 1.47, 3.85, 1.33, 0.0, 3.0, 25.0, 7.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, 10.0, 2.0, 0.0, -0.06, 1.5, 0.36]}
diff --git a/tests/testresources/refs/MOF_descriptors/SETDUS_clean/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/SETDUS_clean/lc_descriptors.csv
new file mode 100644
index 00000000..a86b1980
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/SETDUS_clean/lc_descriptors.csv
@@ -0,0 +1,3 @@
+lc-chi-0-all,lc-chi-1-all,lc-chi-2-all,lc-chi-3-all,lc-Z-0-all,lc-Z-1-all,lc-Z-2-all,lc-Z-3-all,lc-I-0-all,lc-I-1-all,lc-I-2-all,lc-I-3-all,lc-T-0-all,lc-T-1-all,lc-T-2-all,lc-T-3-all,lc-S-0-all,lc-S-1-all,lc-S-2-all,lc-S-3-all,lc-alpha-0-all,lc-alpha-1-all,lc-alpha-2-all,lc-alpha-3-all,D_lc-chi-0-all,D_lc-chi-1-all,D_lc-chi-2-all,D_lc-chi-3-all,D_lc-Z-0-all,D_lc-Z-1-all,D_lc-Z-2-all,D_lc-Z-3-all,D_lc-I-0-all,D_lc-I-1-all,D_lc-I-2-all,D_lc-I-3-all,D_lc-T-0-all,D_lc-T-1-all,D_lc-T-2-all,D_lc-T-3-all,D_lc-S-0-all,D_lc-S-1-all,D_lc-S-2-all,D_lc-S-3-all,D_lc-alpha-0-all,D_lc-alpha-1-all,D_lc-alpha-2-all,D_lc-alpha-3-all,func-chi-0-all,func-chi-1-all,func-chi-2-all,func-chi-3-all,func-Z-0-all,func-Z-1-all,func-Z-2-all,func-Z-3-all,func-I-0-all,func-I-1-all,func-I-2-all,func-I-3-all,func-T-0-all,func-T-1-all,func-T-2-all,func-T-3-all,func-S-0-all,func-S-1-all,func-S-2-all,func-S-3-all,func-alpha-0-all,func-alpha-1-all,func-alpha-2-all,func-alpha-3-all,D_func-chi-0-all,D_func-chi-1-all,D_func-chi-2-all,D_func-chi-3-all,D_func-Z-0-all,D_func-Z-1-all,D_func-Z-2-all,D_func-Z-3-all,D_func-I-0-all,D_func-I-1-all,D_func-I-2-all,D_func-I-3-all,D_func-T-0-all,D_func-T-1-all,D_func-T-2-all,D_func-T-3-all,D_func-S-0-all,D_func-S-1-all,D_func-S-2-all,D_func-S-3-all,D_func-alpha-0-all,D_func-alpha-1-all,D_func-alpha-2-all,D_func-alpha-3-all,name
+9.2416,16.9936,23.681600000000003,14.44,49.0,91.0,98.0,49.0,1.0,2.0,3.0,2.0,4.0,10.0,14.0,10.0,0.5625,1.14,1.4175,0.855,54.760000000000005,138.38,171.732614,116.972614,0.0,0.4900000000000002,1.33,1.33,0.0,1.0,7.0,7.0,0.0,0.0,0.0,0.0,0.0,-1.0,-1.0,-1.0,0.0,-0.02,0.36,0.36,0.0,-3.9,-1.00711,-1.00711,9.2416,23.256,52.9872,14.44,49.0,126.0,168.0,49.0,1.0,3.0,7.0,2.0,9.0,30.0,33.0,12.0,0.5625,1.7325,2.8125,0.855,54.760000000000005,250.86,326.550456,116.972614,0.0,1.4700000000000006,3.85,1.33,0.0,3.0,25.0,7.0,0.0,0.0,0.0,0.0,0.0,-1.0,10.0,2.0,0.0,-0.06,1.5,0.36,0.0,-11.7,7.671560000000001,-1.00711,SETDUS_clean
+9.2416,16.9936,23.681600000000003,14.44,49.0,91.0,98.0,49.0,1.0,2.0,3.0,2.0,4.0,10.0,14.0,10.0,0.5625,1.14,1.4175,0.855,54.760000000000005,138.38,171.732614,116.972614,0.0,0.4900000000000002,1.33,1.33,0.0,1.0,7.0,7.0,0.0,0.0,0.0,0.0,0.0,-1.0,-1.0,-1.0,0.0,-0.02,0.36,0.36,0.0,-3.9,-1.00711,-1.00711,9.2416,23.256,52.9872,14.44,49.0,126.0,168.0,49.0,1.0,3.0,7.0,2.0,9.0,30.0,33.0,12.0,0.5625,1.7325,2.8125,0.855,54.760000000000005,250.86,326.550456,116.972614,0.0,1.4700000000000006,3.85,1.33,0.0,3.0,25.0,7.0,0.0,0.0,0.0,0.0,0.0,-1.0,10.0,2.0,0.0,-0.06,1.5,0.36,0.0,-11.7,7.671560000000001,-1.00711,SETDUS_clean
diff --git a/tests/testresources/refs/MOF_descriptors/SETDUS_clean/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/SETDUS_clean/sbu_descriptors.csv
new file mode 100644
index 00000000..b92e0ab7
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/SETDUS_clean/sbu_descriptors.csv
@@ -0,0 +1,2 @@
+f-chi-0-all,f-chi-1-all,f-chi-2-all,f-chi-3-all,f-Z-0-all,f-Z-1-all,f-Z-2-all,f-Z-3-all,f-I-0-all,f-I-1-all,f-I-2-all,f-I-3-all,f-T-0-all,f-T-1-all,f-T-2-all,f-T-3-all,f-S-0-all,f-S-1-all,f-S-2-all,f-S-3-all,mc-chi-0-all,mc-chi-1-all,mc-chi-2-all,mc-chi-3-all,mc-Z-0-all,mc-Z-1-all,mc-Z-2-all,mc-Z-3-all,mc-I-0-all,mc-I-1-all,mc-I-2-all,mc-I-3-all,mc-T-0-all,mc-T-1-all,mc-T-2-all,mc-T-3-all,mc-S-0-all,mc-S-1-all,mc-S-2-all,mc-S-3-all,D_mc-chi-0-all,D_mc-chi-1-all,D_mc-chi-2-all,D_mc-chi-3-all,D_mc-Z-0-all,D_mc-Z-1-all,D_mc-Z-2-all,D_mc-Z-3-all,D_mc-I-0-all,D_mc-I-1-all,D_mc-I-2-all,D_mc-I-3-all,D_mc-T-0-all,D_mc-T-1-all,D_mc-T-2-all,D_mc-T-3-all,D_mc-S-0-all,D_mc-S-1-all,D_mc-S-2-all,D_mc-S-3-all,name
+133.1728,290.3808,515.7663999999999,730.6543999999997,2362.0,4312.0,7880.0,7946.0,18.0,40.0,72.0,98.0,112.0,312.0,520.0,464.0,13.052,30.300000000000008,56.30159999999997,66.7736,3.61,23.104,42.483999999999995,62.81399999999999,841.0,812.0,1508.0,2465.0,1.0,4.0,8.0,13.0,16.0,48.0,96.0,128.0,1.9043999999999996,4.14,8.3904,12.3372,0.0,-4.5600000000000005,-7.160000000000002,-8.360000000000003,0.0,88.0,180.0,292.0,0.0,0.0,0.0,0.0,0.0,4.0,8.0,20.0,0.0,2.5199999999999996,4.959999999999999,8.999999999999996,SETDUS_clean
diff --git a/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/UXUPEK_clean.json b/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/UXUPEK_clean.json
new file mode 100644
index 00000000..caef286f
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/UXUPEK_clean.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all"], "descriptors": [87.8137999999999, 194.9792, 348.181599999999, 142.691199999999, 2516.0, 5152.0, 6826.0, 3296.0, 10.0, 28.0, 36.0, 20.0, 84.0, 244.0, 274.0, 148.0, 9.25339999999999, 25.404, 29.3665999999999, 17.3448, 3.61, 26.144, 11.932, 22.762, 841.0, 928.0, 1711.0, 812.0, 1.0, 4.0, 3.0, 4.0, 16.0, 40.0, 48.0, 48.0, 1.9044, 4.02959999999999, 4.82999999999999, 4.14, 0.0, -6.16, -0.58, -4.38, 0.0, 84.0, 28.0, 88.0, 0.0, 0.0, 0.0, 0.0, 0.0, 6.0, 0.0, 4.0, 0.0, 2.6, 0.639999999999999, 2.52, 112.9588, 170.6262, 372.3892, 373.7522, 910.0, 1920.0, 1876.0, 1346.0, 14.0, 26.0, 48.0, 54.0, 74.0, 176.0, 192.0, 144.0, 7.17799999999999, 16.0154, 22.3692, 19.7076, 11.8336, 7.5336, 32.4391999999999, 23.908, 64.0, 120.0, 176.0, 64.0, 1.0, 1.0, 3.0, 3.0, 1.0, 4.0, 6.0, 6.0, 0.532899999999999, 0.7738, 1.6279, 1.10229999999999, 0.0, 1.25, 0.89, 3.37, 0.0, -7.0, 2.0, 16.0, 0.0, 0.0, 0.0, 0.0, 0.0, -3.0, -3.0, -3.0, 0.0, -0.33, -0.04, 0.679999999999999, 4.7961, 28.1853, 15.2205, 14.4321, 225.0, 450.0, 120.0, 255.0, 1.0, 4.0, 3.0, 3.0, 16.0, 28.0, 24.0, 24.0, 1.1236, 3.1376, 1.6006, 1.908, 0.0, -4.10999999999999, -0.38, -0.0200000000000004, 0.0, 30.0, 37.0, 28.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.0, 6.0, 6.0, 0.0, 1.28, 1.67, 1.38]}
diff --git a/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/lc_descriptors.csv
new file mode 100644
index 00000000..f42f68e8
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/lc_descriptors.csv
@@ -0,0 +1,2 @@
+lc-chi-0-all,lc-chi-1-all,lc-chi-2-all,lc-chi-3-all,lc-Z-0-all,lc-Z-1-all,lc-Z-2-all,lc-Z-3-all,lc-I-0-all,lc-I-1-all,lc-I-2-all,lc-I-3-all,lc-T-0-all,lc-T-1-all,lc-T-2-all,lc-T-3-all,lc-S-0-all,lc-S-1-all,lc-S-2-all,lc-S-3-all,lc-alpha-0-all,lc-alpha-1-all,lc-alpha-2-all,lc-alpha-3-all,D_lc-chi-0-all,D_lc-chi-1-all,D_lc-chi-2-all,D_lc-chi-3-all,D_lc-Z-0-all,D_lc-Z-1-all,D_lc-Z-2-all,D_lc-Z-3-all,D_lc-I-0-all,D_lc-I-1-all,D_lc-I-2-all,D_lc-I-3-all,D_lc-T-0-all,D_lc-T-1-all,D_lc-T-2-all,D_lc-T-3-all,D_lc-S-0-all,D_lc-S-1-all,D_lc-S-2-all,D_lc-S-3-all,D_lc-alpha-0-all,D_lc-alpha-1-all,D_lc-alpha-2-all,D_lc-alpha-3-all,func-chi-0-all,func-chi-1-all,func-chi-2-all,func-chi-3-all,func-Z-0-all,func-Z-1-all,func-Z-2-all,func-Z-3-all,func-I-0-all,func-I-1-all,func-I-2-all,func-I-3-all,func-T-0-all,func-T-1-all,func-T-2-all,func-T-3-all,func-S-0-all,func-S-1-all,func-S-2-all,func-S-3-all,func-alpha-0-all,func-alpha-1-all,func-alpha-2-all,func-alpha-3-all,D_func-chi-0-all,D_func-chi-1-all,D_func-chi-2-all,D_func-chi-3-all,D_func-Z-0-all,D_func-Z-1-all,D_func-Z-2-all,D_func-Z-3-all,D_func-I-0-all,D_func-I-1-all,D_func-I-2-all,D_func-I-3-all,D_func-T-0-all,D_func-T-1-all,D_func-T-2-all,D_func-T-3-all,D_func-S-0-all,D_func-S-1-all,D_func-S-2-all,D_func-S-3-all,D_func-alpha-0-all,D_func-alpha-1-all,D_func-alpha-2-all,D_func-alpha-3-all,name
+11.8336,7.5336,32.4392,23.908,64.0,120.0,176.0,64.0,1.0,1.0,3.0,3.0,1.0,4.0,6.0,6.0,0.5328999999999998,0.7738,1.6279,1.1022999999999998,28.09,132.5,116.06999999999998,107.665366,0.0,1.25,0.8900000000000002,3.3699999999999997,0.0,-7.0,2.0,16.0,0.0,0.0,0.0,0.0,0.0,-3.0,-3.0,-3.0,0.0,-0.33,-0.04,0.6799999999999998,0.0,-19.7,-6.000000000000001,-4.414220000000001,4.7961,28.1853,15.2205,14.432100000000002,225.0,450.0,120.0,255.0,1.0,4.0,3.0,3.0,16.0,28.0,24.0,24.0,1.1236000000000002,3.1376,1.6006,1.908,625.0,680.0,507.8555,850.3555000000001,0.0,-4.109999999999999,-0.3800000000000003,-0.0200000000000004,0.0,30.0,37.0,28.0,0.0,0.0,0.0,0.0,0.0,9.0,6.0,6.0,0.0,1.2800000000000002,1.6700000000000002,1.38,0.0,72.8,54.685779999999994,40.98578,UXUPEK_clean
diff --git a/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/sbu_descriptors.csv
new file mode 100644
index 00000000..f0d87117
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/UXUPEK_clean/sbu_descriptors.csv
@@ -0,0 +1,2 @@
+f-chi-0-all,f-chi-1-all,f-chi-2-all,f-chi-3-all,f-Z-0-all,f-Z-1-all,f-Z-2-all,f-Z-3-all,f-I-0-all,f-I-1-all,f-I-2-all,f-I-3-all,f-T-0-all,f-T-1-all,f-T-2-all,f-T-3-all,f-S-0-all,f-S-1-all,f-S-2-all,f-S-3-all,mc-chi-0-all,mc-chi-1-all,mc-chi-2-all,mc-chi-3-all,mc-Z-0-all,mc-Z-1-all,mc-Z-2-all,mc-Z-3-all,mc-I-0-all,mc-I-1-all,mc-I-2-all,mc-I-3-all,mc-T-0-all,mc-T-1-all,mc-T-2-all,mc-T-3-all,mc-S-0-all,mc-S-1-all,mc-S-2-all,mc-S-3-all,D_mc-chi-0-all,D_mc-chi-1-all,D_mc-chi-2-all,D_mc-chi-3-all,D_mc-Z-0-all,D_mc-Z-1-all,D_mc-Z-2-all,D_mc-Z-3-all,D_mc-I-0-all,D_mc-I-1-all,D_mc-I-2-all,D_mc-I-3-all,D_mc-T-0-all,D_mc-T-1-all,D_mc-T-2-all,D_mc-T-3-all,D_mc-S-0-all,D_mc-S-1-all,D_mc-S-2-all,D_mc-S-3-all,name
+87.8138,194.9792,348.18159999999995,142.69119999999998,2516.0,5152.0,6826.0,3296.0,10.0,28.0,36.0,20.0,84.0,244.0,274.0,148.0,9.253399999999996,25.403999999999993,29.366599999999995,17.344800000000003,3.61,26.144,11.932,22.762,841.0,928.0,1711.0,812.0,1.0,4.0,3.0,4.0,16.0,40.0,48.0,48.0,1.9043999999999996,4.029599999999999,4.829999999999999,4.14,0.0,-6.16,-0.5800000000000001,-4.38,0.0,84.0,28.0,88.0,0.0,0.0,0.0,0.0,0.0,6.0,0.0,4.0,0.0,2.5999999999999996,0.6399999999999997,2.5199999999999996,UXUPEK_clean
diff --git a/tests/testresources/refs/MOF_descriptors/VONBIK_clean/VONBIK_clean.json b/tests/testresources/refs/MOF_descriptors/VONBIK_clean/VONBIK_clean.json
new file mode 100644
index 00000000..c8b10920
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/VONBIK_clean/VONBIK_clean.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all"], "descriptors": [89.8046999999999, 167.325, 277.9016, 338.333999999999, 1374.0, 2688.0, 3386.0, 1848.0, 11.5, 24.0, 36.0, 41.0, 62.0, 158.0, 203.0, 122.0, 7.73075, 17.3278, 25.5176, 23.3541, 2.7225, 24.222, 25.245, 41.8274999999999, 900.0, 1020.0, 1080.0, 1530.0, 1.0, 4.5, 6.0, 9.5, 20.5, 50.0, 81.0, 96.5, 1.7161, 4.35575, 6.0522, 8.42985, 0.0, -7.255, -5.4, -9.675, 0.0, 101.0, 144.0, 234.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.5, 9.0, 21.0, 0.0, 2.57, 3.24, 6.00999999999999, 220.048533333333, 463.573, 743.597733333333, 897.5446, 899.333333333333, 1952.0, 2789.33333333333, 2776.0, 33.3333333333333, 70.0, 112.0, 140.666666666666, 182.0, 453.333333333333, 632.0, 654.666666666666, 14.0305333333333, 33.7208666666666, 49.6621333333333, 54.3626, 10.9696, 11.0159999999999, 23.9666666666666, 23.5368, 59.0, 60.0, 120.166666666666, 113.0, 1.0, 1.33333333333333, 2.66666666666666, 2.83333333333333, 2.0, 6.0, 9.33333333333333, 10.6666666666666, 0.542766666666666, 0.759733333333333, 1.39749999999999, 1.45821666666666, 0.0, 0.92, 1.28166666666666, 1.85166666666666, 0.0, 2.0, 4.16666666666666, 6.16666666666666, 0.0, 0.0, 0.0, 0.0, 0.0, -2.0, -2.0, -3.0, 0.0, -0.04, 0.0833333333333333, 0.126666666666666, 10.9696, 16.0366666666666, 35.2804888888889, 39.9147555555555, 59.0, 87.3333333333333, 162.222222222222, 150.888888888888, 1.0, 1.94444444444444, 4.22222222222222, 5.0, 4.5, 14.5, 23.2222222222222, 23.2222222222222, 0.542766666666666, 1.10837222222222, 2.09288888888888, 2.21185555555555, 0.0, 1.33055555555555, 2.665, 4.22555555555555, 0.0, 2.88888888888888, 10.0, 18.2222222222222, 0.0, 0.0, 0.0, 0.0, 0.0, -1.66666666666666, 0.111111111111111, 0.444444444444444, 0.0, -0.0577777777777778, 0.3, 0.69111111111111]}
diff --git a/tests/testresources/refs/MOF_descriptors/VONBIK_clean/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/VONBIK_clean/lc_descriptors.csv
new file mode 100644
index 00000000..fed030d2
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/VONBIK_clean/lc_descriptors.csv
@@ -0,0 +1,25 @@
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+9.2416,15.504,30.688799999999997,35.522400000000005,49.0,84.0,136.5,147.0,1.0,2.0,4.0,4.5,4.0,12.0,20.0,20.0,0.5625,1.155,2.0025000000000004,2.12625,54.760000000000005,167.24,269.782614,257.598921,0.0,0.9800000000000004,2.0650000000000004,1.995,0.0,2.0,8.5,10.5,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-1.0,0.0,-0.04,0.3299999999999999,0.5399999999999999,0.0,-7.800000000000001,-6.8571100000000005,-1.510665,9.2416,23.256,52.56160000000001,44.8096,49.0,126.0,196.0,154.0,1.0,3.0,7.0,6.0,9.0,30.0,45.0,36.0,0.5625,1.7325,3.1275000000000004,2.55,54.760000000000005,250.86,405.67784200000006,322.05784200000005,0.0,1.4700000000000006,3.99,3.5,0.0,3.0,21.0,20.0,0.0,0.0,0.0,0.0,0.0,-1.0,6.0,6.0,0.0,-0.06,1.08,1.1,0.0,-11.7,-3.0213300000000007,0.8786700000000001,VONBIK_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,11.8336,11.695999999999998,25.43306666666666,33.48266666666666,64.0,64.0,138.66666666666666,138.66666666666666,1.0,1.3333333333333333,2.6666666666666665,4.0,2.0,6.0,10.666666666666666,14.666666666666666,0.5328999999999999,0.7494666666666667,1.4794666666666665,1.8590666666666669,28.09,79.85333333333334,138.5066666666667,191.55691066666665,0.0,1.1866666666666668,1.7800000000000005,4.026666666666667,0.0,2.6666666666666665,4.0,14.666666666666666,0.0,0.0,0.0,0.0,0.0,-2.0,-2.6666666666666665,-2.6666666666666665,0.0,-0.0533333333333333,-0.08,0.3733333333333332,0.0,-8.000000000000002,-12.000000000000002,-14.942813333333335,VONBIK_clean
diff --git a/tests/testresources/refs/MOF_descriptors/VONBIK_clean/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/VONBIK_clean/sbu_descriptors.csv
new file mode 100644
index 00000000..0bd88ecf
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/VONBIK_clean/sbu_descriptors.csv
@@ -0,0 +1,9 @@
+f-chi-0-all,f-chi-1-all,f-chi-2-all,f-chi-3-all,f-Z-0-all,f-Z-1-all,f-Z-2-all,f-Z-3-all,f-I-0-all,f-I-1-all,f-I-2-all,f-I-3-all,f-T-0-all,f-T-1-all,f-T-2-all,f-T-3-all,f-S-0-all,f-S-1-all,f-S-2-all,f-S-3-all,mc-chi-0-all,mc-chi-1-all,mc-chi-2-all,mc-chi-3-all,mc-Z-0-all,mc-Z-1-all,mc-Z-2-all,mc-Z-3-all,mc-I-0-all,mc-I-1-all,mc-I-2-all,mc-I-3-all,mc-T-0-all,mc-T-1-all,mc-T-2-all,mc-T-3-all,mc-S-0-all,mc-S-1-all,mc-S-2-all,mc-S-3-all,D_mc-chi-0-all,D_mc-chi-1-all,D_mc-chi-2-all,D_mc-chi-3-all,D_mc-Z-0-all,D_mc-Z-1-all,D_mc-Z-2-all,D_mc-Z-3-all,D_mc-I-0-all,D_mc-I-1-all,D_mc-I-2-all,D_mc-I-3-all,D_mc-T-0-all,D_mc-T-1-all,D_mc-T-2-all,D_mc-T-3-all,D_mc-S-0-all,D_mc-S-1-all,D_mc-S-2-all,D_mc-S-3-all,name
+83.88789999999999,152.87699999999998,233.3191999999999,294.474,1342.0,2400.0,3146.0,1608.0,11.0,22.0,32.0,36.0,54.0,132.0,170.0,100.0,7.464300000000001,15.8094,23.356800000000003,20.5436,2.7224999999999997,24.222,25.245,41.827499999999986,900.0,1020.0,1080.0,1530.0,1.0,4.5,6.0,9.5,20.5,50.0,81.0,96.5,1.7161000000000004,4.3557500000000005,6.0522,8.429850000000002,0.0,-7.255000000000001,-5.3999999999999995,-9.675,0.0,101.0,144.0,234.0,0.0,0.0,0.0,0.0,0.0,9.5,9.0,21.0,0.0,2.5700000000000003,3.240000000000001,6.01,VONBIK_clean
+95.7215,181.773,322.484,382.194,1406.0,2976.0,3626.0,2088.0,12.0,26.0,40.0,46.0,70.0,184.0,236.0,144.0,7.9972,18.8462,27.678399999999996,26.164600000000004,2.7224999999999997,24.222,25.245,41.827499999999986,900.0,1020.0,1080.0,1530.0,1.0,4.5,6.0,9.5,20.5,50.0,81.0,96.5,1.7161000000000004,4.3557500000000005,6.0522,8.429850000000002,0.0,-7.255000000000001,-5.3999999999999995,-9.675,0.0,101.0,144.0,234.0,0.0,0.0,0.0,0.0,0.0,9.5,9.0,21.0,0.0,2.5700000000000003,3.240000000000001,6.01,VONBIK_clean
+95.7215,181.773,322.484,382.19399999999985,1406.0,2976.0,3626.0,2088.0,12.0,26.0,40.0,46.0,70.0,184.0,236.0,144.0,7.9972,18.8462,27.678400000000003,26.1646,2.7224999999999997,24.222,25.245,41.827499999999986,900.0,1020.0,1080.0,1530.0,1.0,4.5,6.0,9.5,20.5,50.0,81.0,96.5,1.7161000000000004,4.3557500000000005,6.0522,8.429850000000002,0.0,-7.255000000000001,-5.3999999999999995,-9.675,0.0,101.0,144.0,234.0,0.0,0.0,0.0,0.0,0.0,9.5,9.0,21.0,0.0,2.5700000000000003,3.240000000000001,6.01,VONBIK_clean
+83.88789999999999,152.87699999999998,233.3192,294.47399999999993,1342.0,2400.0,3146.0,1608.0,11.0,22.0,32.0,36.0,54.0,132.0,170.0,100.0,7.464300000000001,15.809400000000004,23.3568,20.5436,2.7224999999999997,24.222,25.245,41.827499999999986,900.0,1020.0,1080.0,1530.0,1.0,4.5,6.0,9.5,20.5,50.0,81.0,96.5,1.7161000000000004,4.3557500000000005,6.0522,8.429850000000002,0.0,-7.255000000000001,-5.3999999999999995,-9.675,0.0,101.0,144.0,234.0,0.0,0.0,0.0,0.0,0.0,9.5,9.0,21.0,0.0,2.5700000000000003,3.240000000000001,6.01,VONBIK_clean
+95.7215,181.773,322.4839999999999,382.194,1406.0,2976.0,3626.0,2088.0,12.0,26.0,40.0,46.0,70.0,184.0,236.0,144.0,7.9972,18.846200000000003,27.678400000000003,26.1646,2.7224999999999997,24.222,25.245,41.827499999999986,900.0,1020.0,1080.0,1530.0,1.0,4.5,6.0,9.5,20.5,50.0,81.0,96.5,1.7161000000000004,4.3557500000000005,6.0522,8.429850000000002,0.0,-7.255000000000001,-5.3999999999999995,-9.675,0.0,101.0,144.0,234.0,0.0,0.0,0.0,0.0,0.0,9.5,9.0,21.0,0.0,2.5700000000000003,3.240000000000001,6.01,VONBIK_clean
+95.7215,181.77299999999997,322.4839999999999,382.194,1406.0,2976.0,3626.0,2088.0,12.0,26.0,40.0,46.0,70.0,184.0,236.0,144.0,7.997200000000001,18.846200000000003,27.678399999999996,26.164600000000004,2.7224999999999997,24.222,25.245,41.827499999999986,900.0,1020.0,1080.0,1530.0,1.0,4.5,6.0,9.5,20.5,50.0,81.0,96.5,1.7161000000000004,4.3557500000000005,6.0522,8.429850000000002,0.0,-7.255000000000001,-5.3999999999999995,-9.675,0.0,101.0,144.0,234.0,0.0,0.0,0.0,0.0,0.0,9.5,9.0,21.0,0.0,2.5700000000000003,3.240000000000001,6.01,VONBIK_clean
+83.88789999999999,152.877,233.31919999999997,294.47399999999993,1342.0,2400.0,3146.0,1608.0,11.0,22.0,32.0,36.0,54.0,132.0,170.0,100.0,7.464300000000001,15.8094,23.3568,20.5436,2.7224999999999997,24.222,25.245,41.827499999999986,900.0,1020.0,1080.0,1530.0,1.0,4.5,6.0,9.5,20.5,50.0,81.0,96.5,1.7161000000000004,4.3557500000000005,6.0522,8.429850000000002,0.0,-7.255000000000001,-5.3999999999999995,-9.675,0.0,101.0,144.0,234.0,0.0,0.0,0.0,0.0,0.0,9.5,9.0,21.0,0.0,2.5700000000000003,3.240000000000001,6.01,VONBIK_clean
+83.88789999999999,152.87699999999998,233.3192,294.47399999999993,1342.0,2400.0,3146.0,1608.0,11.0,22.0,32.0,36.0,54.0,132.0,170.0,100.0,7.464300000000001,15.809400000000004,23.356800000000007,20.5436,2.7224999999999997,24.222,25.245,41.827499999999986,900.0,1020.0,1080.0,1530.0,1.0,4.5,6.0,9.5,20.5,50.0,81.0,96.5,1.7161000000000004,4.3557500000000005,6.0522,8.429850000000002,0.0,-7.255000000000001,-5.3999999999999995,-9.675,0.0,101.0,144.0,234.0,0.0,0.0,0.0,0.0,0.0,9.5,9.0,21.0,0.0,2.5700000000000003,3.240000000000001,6.01,VONBIK_clean
diff --git a/tests/testresources/refs/MOF_descriptors/YICDAR_clean/YICDAR_clean.json b/tests/testresources/refs/MOF_descriptors/YICDAR_clean/YICDAR_clean.json
new file mode 100644
index 00000000..0b2ccaa3
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/YICDAR_clean/YICDAR_clean.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all"], "descriptors": [372.332999999999, 691.44, 1925.06159999999, 2381.4432, 2832.0, 8064.0, 15264.0, 20736.0, 42.0, 108.0, 216.0, 324.0, 324.0, 936.0, 1704.0, 2208.0, 31.497, 87.8628, 164.1408, 231.0012, 1.7161, 22.532, 20.1347, 55.8846, 144.0, 480.0, 648.0, 1044.0, 1.0, 5.0, 7.0, 14.0, 25.0, 60.0, 125.0, 145.0, 1.9321, 5.07349999999999, 9.21569999999999, 12.8157999999999, 0.0, -10.65, -6.19999999999999, -24.32, 0.0, 20.0, 30.0, 81.0, 0.0, 0.0, 0.0, 0.0, 0.0, 13.0, 10.0, 41.0, 0.0, 3.3, 3.1, 10.24, 68.7800666666666, 109.616, 159.823599999999, 151.467133333333, 356.666666666666, 568.0, 784.0, 825.333333333333, 8.0, 14.6666666666666, 20.0, 19.3333333333333, 34.6666666666666, 76.0, 89.3333333333333, 83.3333333333333, 4.23866666666666, 8.07986666666667, 10.6729333333333, 11.1347333333333, 11.8336, 8.77199999999999, 19.8029333333333, 5.84799999999999, 64.0, 48.0, 85.3333333333333, 32.0, 1.0, 1.0, 2.0, 0.666666666666666, 1.0, 3.0, 2.66666666666666, 2.0, 0.532899999999999, 0.5621, 0.900333333333333, 0.374733333333333, 0.0, 0.89, 1.12333333333333, 0.593333333333333, 0.0, 2.0, 5.33333333333333, 1.33333333333333, 0.0, 0.0, 0.0, 0.0, 0.0, -2.0, -0.666666666666666, -1.33333333333333, 0.0, -0.04, 0.226666666666666, -0.0266666666666666, 3.08053333333333, 2.584, 5.16799999999999, 10.8325333333333, 16.3333333333333, 14.0, 28.0, 58.3333333333333, 0.333333333333333, 0.333333333333333, 0.666666666666666, 1.33333333333333, 0.333333333333333, 1.0, 2.0, 3.33333333333333, 0.1875, 0.1925, 0.385, 0.765, 0.0, 0.163333333333333, 0.326666666666666, 0.49, 0.0, 0.333333333333333, 0.666666666666666, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.666666666666666, -1.33333333333333, -2.0, 0.0, -0.00666666666666667, -0.0133333333333333, -0.02]}
diff --git a/tests/testresources/refs/MOF_descriptors/YICDAR_clean/lc_descriptors.csv b/tests/testresources/refs/MOF_descriptors/YICDAR_clean/lc_descriptors.csv
new file mode 100644
index 00000000..8946fccd
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/YICDAR_clean/lc_descriptors.csv
@@ -0,0 +1,10 @@
+lc-chi-0-all,lc-chi-1-all,lc-chi-2-all,lc-chi-3-all,lc-Z-0-all,lc-Z-1-all,lc-Z-2-all,lc-Z-3-all,lc-I-0-all,lc-I-1-all,lc-I-2-all,lc-I-3-all,lc-T-0-all,lc-T-1-all,lc-T-2-all,lc-T-3-all,lc-S-0-all,lc-S-1-all,lc-S-2-all,lc-S-3-all,lc-alpha-0-all,lc-alpha-1-all,lc-alpha-2-all,lc-alpha-3-all,D_lc-chi-0-all,D_lc-chi-1-all,D_lc-chi-2-all,D_lc-chi-3-all,D_lc-Z-0-all,D_lc-Z-1-all,D_lc-Z-2-all,D_lc-Z-3-all,D_lc-I-0-all,D_lc-I-1-all,D_lc-I-2-all,D_lc-I-3-all,D_lc-T-0-all,D_lc-T-1-all,D_lc-T-2-all,D_lc-T-3-all,D_lc-S-0-all,D_lc-S-1-all,D_lc-S-2-all,D_lc-S-3-all,D_lc-alpha-0-all,D_lc-alpha-1-all,D_lc-alpha-2-all,D_lc-alpha-3-all,func-chi-0-all,func-chi-1-all,func-chi-2-all,func-chi-3-all,func-Z-0-all,func-Z-1-all,func-Z-2-all,func-Z-3-all,func-I-0-all,func-I-1-all,func-I-2-all,func-I-3-all,func-T-0-all,func-T-1-all,func-T-2-all,func-T-3-all,func-S-0-all,func-S-1-all,func-S-2-all,func-S-3-all,func-alpha-0-all,func-alpha-1-all,func-alpha-2-all,func-alpha-3-all,D_func-chi-0-all,D_func-chi-1-all,D_func-chi-2-all,D_func-chi-3-all,D_func-Z-0-all,D_func-Z-1-all,D_func-Z-2-all,D_func-Z-3-all,D_func-I-0-all,D_func-I-1-all,D_func-I-2-all,D_func-I-3-all,D_func-T-0-all,D_func-T-1-all,D_func-T-2-all,D_func-T-3-all,D_func-S-0-all,D_func-S-1-all,D_func-S-2-all,D_func-S-3-all,D_func-alpha-0-all,D_func-alpha-1-all,D_func-alpha-2-all,D_func-alpha-3-all,name
+11.8336,8.771999999999998,19.4016,0.0,64.0,48.0,72.0,0.0,1.0,1.0,2.0,0.0,1.0,3.0,2.0,0.0,0.5328999999999999,0.5621,0.8029999999999999,0.0,28.09,59.89,51.977683,0.0,0.0,0.8900000000000001,1.2399999999999998,0.0,0.0,2.0,7.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.0,0.0,0.0,0.0,-0.04,0.36,0.0,0.0,-6.000000000000001,0.7928899999999999,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,YICDAR_clean
+11.8336,8.771999999999998,19.4016,0.0,64.0,48.0,72.0,0.0,1.0,1.0,2.0,0.0,1.0,3.0,2.0,0.0,0.5328999999999999,0.5621,0.8029999999999999,0.0,28.09,59.89,51.977683,0.0,0.0,0.8900000000000001,1.2399999999999998,0.0,0.0,2.0,7.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.0,0.0,0.0,0.0,-0.04,0.36,0.0,0.0,-6.000000000000001,0.7928899999999999,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,YICDAR_clean
+11.8336,8.771999999999998,19.4016,0.0,64.0,48.0,72.0,0.0,1.0,1.0,2.0,0.0,1.0,3.0,2.0,0.0,0.5328999999999999,0.5621,0.8029999999999999,0.0,28.09,59.89,51.977683,0.0,0.0,0.8900000000000001,1.2399999999999998,0.0,0.0,2.0,7.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.0,0.0,0.0,0.0,-0.04,0.36,0.0,0.0,-6.000000000000001,0.7928899999999999,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,YICDAR_clean
+11.8336,8.771999999999998,19.4016,0.0,64.0,48.0,72.0,0.0,1.0,1.0,2.0,0.0,1.0,3.0,2.0,0.0,0.5328999999999999,0.5621,0.8029999999999999,0.0,28.09,59.89,51.977683,0.0,0.0,0.8900000000000001,1.2399999999999998,0.0,0.0,2.0,7.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.0,0.0,0.0,0.0,-0.04,0.36,0.0,0.0,-6.000000000000001,0.7928899999999999,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,YICDAR_clean
+11.8336,8.771999999999998,19.4016,0.0,64.0,48.0,72.0,0.0,1.0,1.0,2.0,0.0,1.0,3.0,2.0,0.0,0.5328999999999999,0.5621,0.8029999999999999,0.0,28.09,59.89,51.977683,0.0,0.0,0.8900000000000001,1.2399999999999998,0.0,0.0,2.0,7.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.0,0.0,0.0,0.0,-0.04,0.36,0.0,0.0,-6.000000000000001,0.7928899999999999,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,YICDAR_clean
+11.8336,8.771999999999998,19.4016,0.0,64.0,48.0,72.0,0.0,1.0,1.0,2.0,0.0,1.0,3.0,2.0,0.0,0.5328999999999999,0.5621,0.8029999999999999,0.0,28.09,59.89,51.977683,0.0,0.0,0.8900000000000001,1.2399999999999998,0.0,0.0,2.0,7.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.0,0.0,0.0,0.0,-0.04,0.36,0.0,0.0,-6.000000000000001,0.7928899999999999,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,YICDAR_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,7.752,15.504,32.4976,49.0,42.0,84.0,175.0,1.0,1.0,2.0,4.0,1.0,3.0,6.0,10.0,0.5625,0.5775,1.155,2.2950000000000004,54.760000000000005,83.62,167.24,305.62,0.0,0.4900000000000002,0.9800000000000004,1.4700000000000006,0.0,1.0,2.0,3.0,0.0,0.0,0.0,0.0,0.0,-2.0,-4.0,-6.0,0.0,-0.02,-0.04,-0.06,0.0,-3.9,-7.800000000000001,-11.7,YICDAR_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,7.752,15.504,32.4976,49.0,42.0,84.0,175.0,1.0,1.0,2.0,4.0,1.0,3.0,6.0,10.0,0.5625,0.5775,1.155,2.295,54.760000000000005,83.62,167.24,305.62,0.0,0.4900000000000002,0.9800000000000004,1.4700000000000006,0.0,1.0,2.0,3.0,0.0,0.0,0.0,0.0,0.0,-2.0,-4.0,-6.0,0.0,-0.02,-0.04,-0.06,0.0,-3.9,-7.800000000000001,-11.7,YICDAR_clean
+11.8336,8.771999999999998,20.605599999999995,17.543999999999997,64.0,48.0,112.0,96.0,1.0,1.0,2.0,2.0,1.0,3.0,4.0,6.0,0.5328999999999999,0.5621,1.095,1.1242,28.09,59.89,87.98,119.78,0.0,0.8900000000000001,0.8900000000000001,1.7800000000000002,0.0,2.0,2.0,4.0,0.0,0.0,0.0,0.0,0.0,-2.0,-2.0,-4.0,0.0,-0.04,-0.04,-0.08,0.0,-6.000000000000001,-6.000000000000001,-12.000000000000002,9.2416,7.752,15.504,32.4976,49.0,42.0,84.0,175.0,1.0,1.0,2.0,4.0,1.0,3.0,6.0,10.0,0.5625,0.5775,1.155,2.295,54.760000000000005,83.62,167.24,305.62,0.0,0.4900000000000002,0.9800000000000004,1.4700000000000006,0.0,1.0,2.0,3.0,0.0,0.0,0.0,0.0,0.0,-2.0,-4.0,-6.0,0.0,-0.02,-0.04,-0.06,0.0,-3.9,-7.800000000000001,-11.7,YICDAR_clean
diff --git a/tests/testresources/refs/MOF_descriptors/YICDAR_clean/sbu_descriptors.csv b/tests/testresources/refs/MOF_descriptors/YICDAR_clean/sbu_descriptors.csv
new file mode 100644
index 00000000..093579d2
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/YICDAR_clean/sbu_descriptors.csv
@@ -0,0 +1,2 @@
+f-chi-0-all,f-chi-1-all,f-chi-2-all,f-chi-3-all,f-Z-0-all,f-Z-1-all,f-Z-2-all,f-Z-3-all,f-I-0-all,f-I-1-all,f-I-2-all,f-I-3-all,f-T-0-all,f-T-1-all,f-T-2-all,f-T-3-all,f-S-0-all,f-S-1-all,f-S-2-all,f-S-3-all,mc-chi-0-all,mc-chi-1-all,mc-chi-2-all,mc-chi-3-all,mc-Z-0-all,mc-Z-1-all,mc-Z-2-all,mc-Z-3-all,mc-I-0-all,mc-I-1-all,mc-I-2-all,mc-I-3-all,mc-T-0-all,mc-T-1-all,mc-T-2-all,mc-T-3-all,mc-S-0-all,mc-S-1-all,mc-S-2-all,mc-S-3-all,D_mc-chi-0-all,D_mc-chi-1-all,D_mc-chi-2-all,D_mc-chi-3-all,D_mc-Z-0-all,D_mc-Z-1-all,D_mc-Z-2-all,D_mc-Z-3-all,D_mc-I-0-all,D_mc-I-1-all,D_mc-I-2-all,D_mc-I-3-all,D_mc-T-0-all,D_mc-T-1-all,D_mc-T-2-all,D_mc-T-3-all,D_mc-S-0-all,D_mc-S-1-all,D_mc-S-2-all,D_mc-S-3-all,name
+372.3329999999998,691.4399999999999,1925.061599999999,2381.4431999999993,2832.0,8064.0,15264.0,20736.0,42.0,108.0,216.0,324.0,324.0,936.0,1704.0,2208.0,31.497000000000035,87.86280000000005,164.14080000000004,231.0012,1.7161000000000002,22.532,20.1347,55.8846,144.0,480.0,648.0,1044.0,1.0,5.0,7.0,14.0,25.0,60.0,125.0,145.0,1.9321,5.073499999999999,9.215699999999998,12.815799999999996,0.0,-10.65,-6.199999999999999,-24.319999999999993,0.0,20.0,30.0,81.0,0.0,0.0,0.0,0.0,0.0,13.0,10.0,41.0,0.0,3.3000000000000003,3.0999999999999996,10.24,YICDAR_clean

From d0e8443c24a431f9eb81c2542d455c6f2c41bbdd Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Mon, 26 Feb 2024 16:18:22 -0500
Subject: [PATCH 18/19] Add failing test cases as commented lines

---
 tests/informatics/test_MOF_descriptors.py     |   6 +-
 .../inputs/cif_files/ETECIR_clean.cif         | 154 ++++++++++++++++
 .../inputs/cif_files/FAVGUH_clean.cif         | 164 ++++++++++++++++++
 .../ETECIR_clean/ETECIR_clean.json            |   1 +
 .../FAVGUH_clean/FAVGUH_clean.json            |   1 +
 5 files changed, 323 insertions(+), 3 deletions(-)
 create mode 100644 tests/testresources/inputs/cif_files/ETECIR_clean.cif
 create mode 100644 tests/testresources/inputs/cif_files/FAVGUH_clean.cif
 create mode 100644 tests/testresources/refs/MOF_descriptors/ETECIR_clean/ETECIR_clean.json
 create mode 100644 tests/testresources/refs/MOF_descriptors/FAVGUH_clean/FAVGUH_clean.json

diff --git a/tests/informatics/test_MOF_descriptors.py b/tests/informatics/test_MOF_descriptors.py
index 6a6c9992..5487866a 100644
--- a/tests/informatics/test_MOF_descriptors.py
+++ b/tests/informatics/test_MOF_descriptors.py
@@ -2,7 +2,7 @@
 import json
 import numpy as np
 import pandas as pd
-from molSimplify.Informatics.MOF.MOF_descriptors import get_MOF_descriptors, get_primitive
+from molSimplify.Informatics.MOF.MOF_descriptors import get_MOF_descriptors
 from molSimplify.utils.timer import DebugTimer
 
 
@@ -83,8 +83,8 @@ def test_get_MOF_descriptors_ODAC(resource_path_root, tmpdir, name, ref_names):
         "SETDUS_clean",
         "UXUPEK_clean",
         "NEXXIZ_clean",
-        # "ETECIR_clean",
-        # "FAVGUH_clean", Disagreement on all ligand center RACs
+        # "ETECIR_clean",  TODO: Figure out why these two example do not work!
+        # "FAVGUH_clean",  Disagreement on all ligand center RACs
         "YICDAR_clean",
         "VONBIK_clean",
     ])
diff --git a/tests/testresources/inputs/cif_files/ETECIR_clean.cif b/tests/testresources/inputs/cif_files/ETECIR_clean.cif
new file mode 100644
index 00000000..c9de4aac
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/ETECIR_clean.cif
@@ -0,0 +1,154 @@
+# generated using pymatgen
+data_In(CO2)5
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   9.74540000
+_cell_length_b   18.42795747
+_cell_length_c   18.42795747
+_cell_angle_alpha   85.99076004
+_cell_angle_beta   74.66757418
+_cell_angle_gamma   74.66757417
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   In(CO2)5
+_chemical_formula_sum   'In8 C40 O80'
+_cell_volume   3078.04961579
+_cell_formula_units_Z   8
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  In  In0  1  0.34065000  0.05923000  0.65291000  1.0
+  In  In1  1  0.55279000  0.44077000  0.84709000  1.0
+  In  In2  1  0.99356000  0.34709000  0.55923000  1.0
+  In  In3  1  0.39988000  0.15291000  0.94077000  1.0
+  In  In4  1  0.65935000  0.94077000  0.34709000  1.0
+  In  In5  1  0.44721000  0.55923000  0.15291000  1.0
+  In  In6  1  0.00644000  0.65291000  0.44077000  1.0
+  In  In7  1  0.60012000  0.84709000  0.05923000  1.0
+  C  C8  1  0.09836000  0.18863000  0.61785000  1.0
+  C  C9  1  0.23437000  0.21982000  0.60664000  1.0
+  C  C10  1  0.42763000  0.99594000  0.49360000  1.0
+  C  C11  1  0.24840000  0.92406000  0.73874000  1.0
+  C  C12  1  0.40654000  0.91562000  0.74450000  1.0
+  C  C13  1  0.40484000  0.31137000  0.88215000  1.0
+  C  C14  1  0.56083000  0.28018000  0.89336000  1.0
+  C  C15  1  0.41717000  0.50406000  0.00640000  1.0
+  C  C16  1  0.41120000  0.57594000  0.76126000  1.0
+  C  C17  1  0.56666000  0.58438000  0.75550000  1.0
+  C  C18  1  0.71621000  0.38215000  0.68863000  1.0
+  C  C19  1  0.84101000  0.39336000  0.71982000  1.0
+  C  C20  1  0.92123000  0.50640000  0.49594000  1.0
+  C  C21  1  0.98714000  0.26126000  0.42406000  1.0
+  C  C22  1  0.15104000  0.25550000  0.41562000  1.0
+  C  C23  1  0.28699000  0.11785000  0.81137000  1.0
+  C  C24  1  0.45419000  0.10664000  0.78018000  1.0
+  C  C25  1  0.42357000  0.99360000  0.00406000  1.0
+  C  C26  1  0.17246000  0.23874000  0.07594000  1.0
+  C  C27  1  0.32216000  0.24450000  0.08438000  1.0
+  C  C28  1  0.90164000  0.81137000  0.38215000  1.0
+  C  C29  1  0.76563000  0.78018000  0.39336000  1.0
+  C  C30  1  0.57237000  0.00406000  0.50640000  1.0
+  C  C31  1  0.75160000  0.07594000  0.26126000  1.0
+  C  C32  1  0.59346000  0.08438000  0.25550000  1.0
+  C  C33  1  0.59516000  0.68863000  0.11785000  1.0
+  C  C34  1  0.43917000  0.71982000  0.10664000  1.0
+  C  C35  1  0.58283000  0.49594000  0.99360000  1.0
+  C  C36  1  0.58880000  0.42406000  0.23874000  1.0
+  C  C37  1  0.43334000  0.41562000  0.24450000  1.0
+  C  C38  1  0.28379000  0.61785000  0.31137000  1.0
+  C  C39  1  0.15899000  0.60664000  0.28018000  1.0
+  C  C40  1  0.07877000  0.49360000  0.50406000  1.0
+  C  C41  1  0.01286000  0.73874000  0.57594000  1.0
+  C  C42  1  0.84896000  0.74450000  0.58438000  1.0
+  C  C43  1  0.71301000  0.88215000  0.18863000  1.0
+  C  C44  1  0.54581000  0.89336000  0.21982000  1.0
+  C  C45  1  0.57643000  0.00640000  0.99594000  1.0
+  C  C46  1  0.82754000  0.76126000  0.92406000  1.0
+  C  C47  1  0.67784000  0.75550000  0.91562000  1.0
+  O  O48  1  0.11037000  0.12222000  0.64104000  1.0
+  O  O49  1  0.98753000  0.23160000  0.60234000  1.0
+  O  O50  1  0.35210000  0.17305000  0.61115000  1.0
+  O  O51  1  0.21794000  0.28815000  0.59257000  1.0
+  O  O52  1  0.31546000  0.01521000  0.54647000  1.0
+  O  O53  1  0.43495000  0.96927000  0.43183000  1.0
+  O  O54  1  0.20346000  0.97582000  0.69506000  1.0
+  O  O55  1  0.17744000  0.88115000  0.77497000  1.0
+  O  O56  1  0.47608000  0.95697000  0.69927000  1.0
+  O  O57  1  0.45785000  0.87215000  0.78935000  1.0
+  O  O58  1  0.37363000  0.37778000  0.85896000  1.0
+  O  O59  1  0.32147000  0.26840000  0.89766000  1.0
+  O  O60  1  0.63630000  0.32695000  0.88885000  1.0
+  O  O61  1  0.59866000  0.21185000  0.90743000  1.0
+  O  O62  1  0.37714000  0.48479000  0.95353000  1.0
+  O  O63  1  0.33605000  0.53073000  0.06817000  1.0
+  O  O64  1  0.37434000  0.52418000  0.80494000  1.0
+  O  O65  1  0.33356000  0.61885000  0.72503000  1.0
+  O  O66  1  0.63232000  0.54303000  0.80073000  1.0
+  O  O67  1  0.61935000  0.62785000  0.71065000  1.0
+  O  O68  1  0.75141000  0.35896000  0.62222000  1.0
+  O  O69  1  0.58987000  0.39766000  0.73160000  1.0
+  O  O70  1  0.96325000  0.38885000  0.67305000  1.0
+  O  O71  1  0.81051000  0.40743000  0.78815000  1.0
+  O  O72  1  0.86193000  0.45353000  0.51521000  1.0
+  O  O73  1  0.86678000  0.56817000  0.46927000  1.0
+  O  O74  1  0.89852000  0.30494000  0.47582000  1.0
+  O  O75  1  0.95241000  0.22503000  0.38115000  1.0
+  O  O76  1  0.17535000  0.30073000  0.45697000  1.0
+  O  O77  1  0.24720000  0.21065000  0.37215000  1.0
+  O  O78  1  0.23259000  0.14104000  0.87778000  1.0
+  O  O79  1  0.21913000  0.10234000  0.76840000  1.0
+  O  O80  1  0.52515000  0.11115000  0.82695000  1.0
+  O  O81  1  0.50609000  0.09257000  0.71185000  1.0
+  O  O82  1  0.33067000  0.04647000  0.98479000  1.0
+  O  O83  1  0.40422000  0.93183000  0.03073000  1.0
+  O  O84  1  0.17928000  0.19506000  0.02418000  1.0
+  O  O85  1  0.05859000  0.27497000  0.11885000  1.0
+  O  O86  1  0.43305000  0.19927000  0.04303000  1.0
+  O  O87  1  0.33000000  0.28935000  0.12785000  1.0
+  O  O88  1  0.88963000  0.87778000  0.35896000  1.0
+  O  O89  1  0.01247000  0.76840000  0.39766000  1.0
+  O  O90  1  0.64790000  0.82695000  0.38885000  1.0
+  O  O91  1  0.78206000  0.71185000  0.40743000  1.0
+  O  O92  1  0.68454000  0.98479000  0.45353000  1.0
+  O  O93  1  0.56505000  0.03073000  0.56817000  1.0
+  O  O94  1  0.79654000  0.02418000  0.30494000  1.0
+  O  O95  1  0.82256000  0.11885000  0.22503000  1.0
+  O  O96  1  0.52392000  0.04303000  0.30073000  1.0
+  O  O97  1  0.54215000  0.12785000  0.21065000  1.0
+  O  O98  1  0.62637000  0.62222000  0.14104000  1.0
+  O  O99  1  0.67853000  0.73160000  0.10234000  1.0
+  O  O100  1  0.36370000  0.67305000  0.11115000  1.0
+  O  O101  1  0.40134000  0.78815000  0.09257000  1.0
+  O  O102  1  0.62286000  0.51521000  0.04647000  1.0
+  O  O103  1  0.66395000  0.46927000  0.93183000  1.0
+  O  O104  1  0.62566000  0.47582000  0.19506000  1.0
+  O  O105  1  0.66644000  0.38115000  0.27497000  1.0
+  O  O106  1  0.36768000  0.45697000  0.19927000  1.0
+  O  O107  1  0.38065000  0.37215000  0.28935000  1.0
+  O  O108  1  0.24859000  0.64104000  0.37778000  1.0
+  O  O109  1  0.41013000  0.60234000  0.26840000  1.0
+  O  O110  1  0.03675000  0.61115000  0.32695000  1.0
+  O  O111  1  0.18949000  0.59257000  0.21185000  1.0
+  O  O112  1  0.13807000  0.54647000  0.48479000  1.0
+  O  O113  1  0.13322000  0.43183000  0.53073000  1.0
+  O  O114  1  0.10148000  0.69506000  0.52418000  1.0
+  O  O115  1  0.04759000  0.77497000  0.61885000  1.0
+  O  O116  1  0.82465000  0.69927000  0.54303000  1.0
+  O  O117  1  0.75280000  0.78935000  0.62785000  1.0
+  O  O118  1  0.76741000  0.85896000  0.12222000  1.0
+  O  O119  1  0.78087000  0.89766000  0.23160000  1.0
+  O  O120  1  0.47485000  0.88885000  0.17305000  1.0
+  O  O121  1  0.49391000  0.90743000  0.28815000  1.0
+  O  O122  1  0.66933000  0.95353000  0.01521000  1.0
+  O  O123  1  0.59578000  0.06817000  0.96927000  1.0
+  O  O124  1  0.82072000  0.80494000  0.97582000  1.0
+  O  O125  1  0.94141000  0.72503000  0.88115000  1.0
+  O  O126  1  0.56695000  0.80073000  0.95697000  1.0
+  O  O127  1  0.67000000  0.71065000  0.87215000  1.0
diff --git a/tests/testresources/inputs/cif_files/FAVGUH_clean.cif b/tests/testresources/inputs/cif_files/FAVGUH_clean.cif
new file mode 100644
index 00000000..301d6ef3
--- /dev/null
+++ b/tests/testresources/inputs/cif_files/FAVGUH_clean.cif
@@ -0,0 +1,164 @@
+# generated using pymatgen
+data_Eu2H24C26O17
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   11.88800000
+_cell_length_b   12.47500000
+_cell_length_c   12.54200000
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   98.94000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Eu2H24C26O17
+_chemical_formula_sum   'Eu4 H48 C52 O34'
+_cell_volume   1837.41755819
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Eu  Eu0  1  0.37264000  0.44573000  0.13151000  1.0
+  Eu  Eu1  1  0.64118000  0.22932000  0.18708000  1.0
+  Eu  Eu2  1  0.62736000  0.94573000  0.86849000  1.0
+  Eu  Eu3  1  0.35882000  0.72932000  0.81292000  1.0
+  H  H4  1  0.32600000  0.40020000  0.48240000  1.0
+  H  H5  1  0.47980000  0.33020000  0.78490000  1.0
+  H  H6  1  0.64410000  0.28080000  0.53120000  1.0
+  H  H7  1  0.30320000  0.30650000  0.80430000  1.0
+  H  H8  1  0.11100000  0.34160000  0.75110000  1.0
+  H  H9  1  0.13090000  0.46380000  0.77640000  1.0
+  H  H10  1  0.14680000  0.37990000  0.87060000  1.0
+  H  H11  1  0.66150000  0.36640000  0.85520000  1.0
+  H  H12  1  0.85310000  0.35160000  0.84330000  1.0
+  H  H13  1  0.85100000  0.22930000  0.87160000  1.0
+  H  H14  1  0.83250000  0.31530000  0.95840000  1.0
+  H  H15  1  0.00030000  0.53390000  0.92920000  1.0
+  H  H16  1  0.71280000  0.60600000  0.04600000  1.0
+  H  H17  1  0.00750000  0.56590000  0.24940000  1.0
+  H  H18  1  0.63580000  0.61990000  0.19960000  1.0
+  H  H19  1  0.67390000  0.65320000  0.38990000  1.0
+  H  H20  1  0.70690000  0.53240000  0.40970000  1.0
+  H  H21  1  0.58090000  0.56380000  0.36410000  1.0
+  H  H22  1  0.63390000  0.55220000  0.87380000  1.0
+  H  H23  1  0.66190000  0.51250000  0.69580000  1.0
+  H  H24  1  0.70260000  0.63010000  0.68000000  1.0
+  H  H25  1  0.57520000  0.60770000  0.69120000  1.0
+  H  H26  1  0.77150000  0.11100000  0.31380000  1.0
+  H  H27  1  0.80440000  0.16290000  0.41170000  1.0
+  H  H28  1  0.67400000  0.90020000  0.51760000  1.0
+  H  H29  1  0.52020000  0.83020000  0.21510000  1.0
+  H  H30  1  0.35590000  0.78080000  0.46880000  1.0
+  H  H31  1  0.69680000  0.80650000  0.19570000  1.0
+  H  H32  1  0.88900000  0.84160000  0.24890000  1.0
+  H  H33  1  0.86910000  0.96380000  0.22360000  1.0
+  H  H34  1  0.85320000  0.87990000  0.12940000  1.0
+  H  H35  1  0.33850000  0.86640000  0.14480000  1.0
+  H  H36  1  0.14690000  0.85160000  0.15670000  1.0
+  H  H37  1  0.14900000  0.72930000  0.12840000  1.0
+  H  H38  1  0.16750000  0.81530000  0.04160000  1.0
+  H  H39  1  0.99970000  0.03390000  0.07080000  1.0
+  H  H40  1  0.28720000  0.10600000  0.95400000  1.0
+  H  H41  1  0.99250000  0.06590000  0.75060000  1.0
+  H  H42  1  0.36420000  0.11990000  0.80040000  1.0
+  H  H43  1  0.32610000  0.15320000  0.61010000  1.0
+  H  H44  1  0.29310000  0.03240000  0.59030000  1.0
+  H  H45  1  0.41910000  0.06380000  0.63590000  1.0
+  H  H46  1  0.36610000  0.05220000  0.12620000  1.0
+  H  H47  1  0.33810000  0.01250000  0.30420000  1.0
+  H  H48  1  0.29740000  0.13010000  0.32000000  1.0
+  H  H49  1  0.42480000  0.10770000  0.30880000  1.0
+  H  H50  1  0.22850000  0.61100000  0.68620000  1.0
+  H  H51  1  0.19560000  0.66290000  0.58830000  1.0
+  C  C52  1  0.48470000  0.33970000  0.48980000  1.0
+  C  C53  1  0.38870000  0.37430000  0.52890000  1.0
+  C  C54  1  0.38770000  0.36950000  0.64070000  1.0
+  C  C55  1  0.48170000  0.33380000  0.71110000  1.0
+  C  C56  1  0.57920000  0.30350000  0.66950000  1.0
+  C  C57  1  0.58010000  0.30410000  0.55880000  1.0
+  C  C58  1  0.48740000  0.34140000  0.37030000  1.0
+  C  C59  1  0.27940000  0.38020000  0.78520000  1.0
+  C  C60  1  0.35650000  0.45790000  0.85910000  1.0
+  C  C61  1  0.15580000  0.39250000  0.79690000  1.0
+  C  C62  1  0.69290000  0.29530000  0.84430000  1.0
+  C  C63  1  0.63240000  0.21280000  0.90700000  1.0
+  C  C64  1  0.81870000  0.29810000  0.88290000  1.0
+  C  C65  1  0.02210000  0.54650000  0.09100000  1.0
+  C  C66  1  0.96300000  0.54850000  0.98740000  1.0
+  C  C67  1  0.84630000  0.57250000  0.97020000  1.0
+  C  C68  1  0.79040000  0.59120000  0.05720000  1.0
+  C  C69  1  0.85170000  0.58760000  0.16300000  1.0
+  C  C70  1  0.96680000  0.56670000  0.17970000  1.0
+  C  C71  1  0.14590000  0.52040000  0.10840000  1.0
+  C  C72  1  0.68650000  0.57280000  0.24780000  1.0
+  C  C73  1  0.67250000  0.45860000  0.20910000  1.0
+  C  C74  1  0.65950000  0.58140000  0.36380000  1.0
+  C  C75  1  0.68180000  0.59940000  0.83730000  1.0
+  C  C76  1  0.66130000  0.71610000  0.86420000  1.0
+  C  C77  1  0.65270000  0.58620000  0.71460000  1.0
+  C  C78  1  0.51530000  0.83970000  0.51020000  1.0
+  C  C79  1  0.61130000  0.87430000  0.47110000  1.0
+  C  C80  1  0.61230000  0.86950000  0.35930000  1.0
+  C  C81  1  0.51830000  0.83380000  0.28890000  1.0
+  C  C82  1  0.42080000  0.80350000  0.33050000  1.0
+  C  C83  1  0.41990000  0.80410000  0.44120000  1.0
+  C  C84  1  0.51260000  0.84140000  0.62970000  1.0
+  C  C85  1  0.72060000  0.88020000  0.21480000  1.0
+  C  C86  1  0.64350000  0.95790000  0.14090000  1.0
+  C  C87  1  0.84420000  0.89250000  0.20310000  1.0
+  C  C88  1  0.30710000  0.79530000  0.15570000  1.0
+  C  C89  1  0.36760000  0.71280000  0.09300000  1.0
+  C  C90  1  0.18130000  0.79810000  0.11710000  1.0
+  C  C91  1  0.97790000  0.04650000  0.90900000  1.0
+  C  C92  1  0.03700000  0.04850000  0.01260000  1.0
+  C  C93  1  0.15370000  0.07250000  0.02980000  1.0
+  C  C94  1  0.20960000  0.09120000  0.94280000  1.0
+  C  C95  1  0.14830000  0.08760000  0.83700000  1.0
+  C  C96  1  0.03320000  0.06670000  0.82030000  1.0
+  C  C97  1  0.85410000  0.02040000  0.89160000  1.0
+  C  C98  1  0.31350000  0.07280000  0.75220000  1.0
+  C  C99  1  0.32750000  0.95860000  0.79090000  1.0
+  C  C100  1  0.34050000  0.08140000  0.63620000  1.0
+  C  C101  1  0.31820000  0.09940000  0.16270000  1.0
+  C  C102  1  0.33870000  0.21610000  0.13580000  1.0
+  C  C103  1  0.34730000  0.08620000  0.28540000  1.0
+  O  O104  1  0.56360000  0.28520000  0.33750000  1.0
+  O  O105  1  0.41700000  0.39750000  0.31330000  1.0
+  O  O106  1  0.28810000  0.39790000  0.67480000  1.0
+  O  O107  1  0.37910000  0.54550000  0.82630000  1.0
+  O  O108  1  0.39050000  0.42110000  0.95390000  1.0
+  O  O109  1  0.67880000  0.27460000  0.73240000  1.0
+  O  O110  1  0.62530000  0.23840000  0.00150000  1.0
+  O  O111  1  0.59290000  0.12810000  0.85990000  1.0
+  O  O112  1  0.19740000  0.49690000  0.20030000  1.0
+  O  O113  1  0.19850000  0.52210000  0.02770000  1.0
+  O  O114  1  0.79740000  0.57040000  0.86450000  1.0
+  O  O115  1  0.74290000  0.78170000  0.87730000  1.0
+  O  O116  1  0.56120000  0.74520000  0.87100000  1.0
+  O  O117  1  0.80200000  0.60610000  0.25150000  1.0
+  O  O118  1  0.75000000  0.39120000  0.23220000  1.0
+  O  O119  1  0.57590000  0.43150000  0.15600000  1.0
+  O  O120  1  0.76370000  0.16770000  0.34980000  1.0
+  O  O121  1  0.43640000  0.78520000  0.66250000  1.0
+  O  O122  1  0.58300000  0.89750000  0.68670000  1.0
+  O  O123  1  0.71190000  0.89790000  0.32520000  1.0
+  O  O124  1  0.62090000  0.04550000  0.17370000  1.0
+  O  O125  1  0.60950000  0.92110000  0.04610000  1.0
+  O  O126  1  0.32120000  0.77460000  0.26760000  1.0
+  O  O127  1  0.37470000  0.73840000  0.99850000  1.0
+  O  O128  1  0.40710000  0.62810000  0.14010000  1.0
+  O  O129  1  0.80260000  0.99690000  0.79970000  1.0
+  O  O130  1  0.80150000  0.02210000  0.97230000  1.0
+  O  O131  1  0.20260000  0.07040000  0.13550000  1.0
+  O  O132  1  0.25710000  0.28170000  0.12270000  1.0
+  O  O133  1  0.43880000  0.24520000  0.12900000  1.0
+  O  O134  1  0.19800000  0.10610000  0.74850000  1.0
+  O  O135  1  0.25000000  0.89120000  0.76780000  1.0
+  O  O136  1  0.42410000  0.93150000  0.84400000  1.0
+  O  O137  1  0.23630000  0.66770000  0.65020000  1.0
diff --git a/tests/testresources/refs/MOF_descriptors/ETECIR_clean/ETECIR_clean.json b/tests/testresources/refs/MOF_descriptors/ETECIR_clean/ETECIR_clean.json
new file mode 100644
index 00000000..1bc70182
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/ETECIR_clean/ETECIR_clean.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all"], "descriptors": [1161.1336, 2342.12559999999, 7985.3856, 8370.20799999997, 25384.0, 58720.0, 77760.0, 87328.0, 122.0, 316.0, 792.0, 962.0, 1108.0, 3182.0, 5804.0, 6402.0, 79.2817999999998, 239.5916, 498.122399999998, 593.504599999999, 3.1684, 48.9855999999999, 36.312, 48.9855999999999, 2401.0, 3136.0, 2352.0, 3136.0, 1.0, 8.0, 8.0, 8.0, 64.0, 128.0, 192.0, 112.0, 2.0164, 8.2928, 8.7472, 8.2928, 0.0, -13.28, -6.15999999999999, -13.28, 0.0, 328.0, 344.0, 328.0, 0.0, 0.0, 0.0, 0.0, 0.0, 48.0, 40.0, 50.0, 0.0, 5.52, 5.19999999999999, 5.52, 60.3393999999999, 83.181, 117.510399999999, 94.6687999999999, 328.0, 456.0, 640.0, 512.0, 6.0, 10.0, 12.0, 8.0, 22.0, 42.0, 28.0, 8.0, 3.31739999999999, 5.6826, 6.62839999999999, 4.26319999999999, 11.8335999999999, 8.77199999999999, 20.6055999999999, 23.6671999999999, 64.0, 48.0, 112.0, 128.0, 1.0, 1.0, 2.0, 2.0, 1.0, 3.0, 4.0, 2.0, 0.532899999999999, 0.5621, 1.095, 1.06579999999999, 0.0, 0.89, 0.89, 0.0, 0.0, 2.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -2.0, -2.0, 0.0, 0.0, -0.04, -0.04, 0.0, 4.73344, 3.50879999999999, 8.24223999999999, 9.46688, 25.6, 19.2, 44.8, 51.2, 0.4, 0.4, 0.8, 0.8, 0.4, 1.2, 1.6, 0.8, 0.21316, 0.22484, 0.438, 0.426319999999999, 0.0, 0.356, 0.356, 0.0, 0.0, 0.8, 0.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.8, -0.8, 0.0, 0.0, -0.016, -0.016, 0.0]}
diff --git a/tests/testresources/refs/MOF_descriptors/FAVGUH_clean/FAVGUH_clean.json b/tests/testresources/refs/MOF_descriptors/FAVGUH_clean/FAVGUH_clean.json
new file mode 100644
index 00000000..22aedf45
--- /dev/null
+++ b/tests/testresources/refs/MOF_descriptors/FAVGUH_clean/FAVGUH_clean.json
@@ -0,0 +1 @@
+{"names": ["f-chi-0-all", "f-chi-1-all", "f-chi-2-all", "f-chi-3-all", "f-Z-0-all", "f-Z-1-all", "f-Z-2-all", "f-Z-3-all", "f-I-0-all", "f-I-1-all", "f-I-2-all", "f-I-3-all", "f-T-0-all", "f-T-1-all", "f-T-2-all", "f-T-3-all", "f-S-0-all", "f-S-1-all", "f-S-2-all", "f-S-3-all", "mc-chi-0-all", "mc-chi-1-all", "mc-chi-2-all", "mc-chi-3-all", "mc-Z-0-all", "mc-Z-1-all", "mc-Z-2-all", "mc-Z-3-all", "mc-I-0-all", "mc-I-1-all", "mc-I-2-all", "mc-I-3-all", "mc-T-0-all", "mc-T-1-all", "mc-T-2-all", "mc-T-3-all", "mc-S-0-all", "mc-S-1-all", "mc-S-2-all", "mc-S-3-all", "D_mc-chi-0-all", "D_mc-chi-1-all", "D_mc-chi-2-all", "D_mc-chi-3-all", "D_mc-Z-0-all", "D_mc-Z-1-all", "D_mc-Z-2-all", "D_mc-Z-3-all", "D_mc-I-0-all", "D_mc-I-1-all", "D_mc-I-2-all", "D_mc-I-3-all", "D_mc-T-0-all", "D_mc-T-1-all", "D_mc-T-2-all", "D_mc-T-3-all", "D_mc-S-0-all", "D_mc-S-1-all", "D_mc-S-2-all", "D_mc-S-3-all", "f-lig-chi-0", "f-lig-chi-1", "f-lig-chi-2", "f-lig-chi-3", "f-lig-Z-0", "f-lig-Z-1", "f-lig-Z-2", "f-lig-Z-3", "f-lig-I-0", "f-lig-I-1", "f-lig-I-2", "f-lig-I-3", "f-lig-T-0", "f-lig-T-1", "f-lig-T-2", "f-lig-T-3", "f-lig-S-0", "f-lig-S-1", "f-lig-S-2", "f-lig-S-3", "lc-chi-0-all", "lc-chi-1-all", "lc-chi-2-all", "lc-chi-3-all", "lc-Z-0-all", "lc-Z-1-all", "lc-Z-2-all", "lc-Z-3-all", "lc-I-0-all", "lc-I-1-all", "lc-I-2-all", "lc-I-3-all", "lc-T-0-all", "lc-T-1-all", "lc-T-2-all", "lc-T-3-all", "lc-S-0-all", "lc-S-1-all", "lc-S-2-all", "lc-S-3-all", "D_lc-chi-0-all", "D_lc-chi-1-all", "D_lc-chi-2-all", "D_lc-chi-3-all", "D_lc-Z-0-all", "D_lc-Z-1-all", "D_lc-Z-2-all", "D_lc-Z-3-all", "D_lc-I-0-all", "D_lc-I-1-all", "D_lc-I-2-all", "D_lc-I-3-all", "D_lc-T-0-all", "D_lc-T-1-all", "D_lc-T-2-all", "D_lc-T-3-all", "D_lc-S-0-all", "D_lc-S-1-all", "D_lc-S-2-all", "D_lc-S-3-all", "func-chi-0-all", "func-chi-1-all", "func-chi-2-all", "func-chi-3-all", "func-Z-0-all", "func-Z-1-all", "func-Z-2-all", "func-Z-3-all", "func-I-0-all", "func-I-1-all", "func-I-2-all", "func-I-3-all", "func-T-0-all", "func-T-1-all", "func-T-2-all", "func-T-3-all", "func-S-0-all", "func-S-1-all", "func-S-2-all", "func-S-3-all", "D_func-chi-0-all", "D_func-chi-1-all", "D_func-chi-2-all", "D_func-chi-3-all", "D_func-Z-0-all", "D_func-Z-1-all", "D_func-Z-2-all", "D_func-Z-3-all", "D_func-I-0-all", "D_func-I-1-all", "D_func-I-2-all", "D_func-I-3-all", "D_func-T-0-all", "D_func-T-1-all", "D_func-T-2-all", "D_func-T-3-all", "D_func-S-0-all", "D_func-S-1-all", "D_func-S-2-all", "D_func-S-3-all"], "descriptors": [423.828599999999, 767.529999999999, 2875.63839999999, 3033.95399999999, 18048.0, 34264.0, 47608.0, 45336.0, 48.0, 124.0, 296.0, 392.0, 472.0, 1548.0, 2296.0, 2508.0, 33.9932, 110.271599999999, 200.427199999999, 249.727199999999, 1.44, 32.49, 20.91, 50.85, 3969.0, 3969.0, 6111.0, 6237.0, 1.0, 8.0, 7.5, 14.0, 65.0, 158.5, 203.5, 316.5, 2.8224, 9.8448, 10.5587999999999, 17.6064, 0.0, -17.475, -8.425, -25.575, 0.0, 441.0, 375.5, 783.0, 0.0, 0.0, 0.0, 0.0, 0.0, 45.5, 34.0, 72.5, 0.0, 7.58, 6.315, 13.04, 232.4413, 441.914999999999, 740.549599999999, 923.7658, 991.0, 1884.0, 2828.0, 3028.0, 32.0, 64.0, 106.0, 130.0, 170.0, 412.0, 526.0, 546.0, 13.4768, 30.5536, 45.0058, 51.4914, 11.4528071428571, 9.86303571428571, 20.0627, 24.6014428571428, 62.0, 54.0, 109.142857142857, 110.0, 1.0, 1.14285714285714, 2.0, 2.76190476190476, 1.57142857142857, 3.85714285714285, 5.61904761904762, 7.9047619047619, 0.537185714285714, 0.6446, 1.10148571428571, 1.31842857142857, 0.0, 0.699285714285714, 0.826428571428571, 1.9195238095238, 0.0, 1.57142857142857, 1.85714285714285, 7.52380952380952, 0.0, 0.0, 0.0, 0.0, 0.0, -1.57142857142857, -2.47619047619047, -3.42857142857142, 0.0, -0.0314285714285714, -0.0371428571428571, 0.23047619047619, 11.8336, 17.5439999999999, 42.656, 79.0512, 64.0, 96.0, 200.0, 264.0, 1.0, 2.0, 5.0, 9.0, 4.0, 14.0, 28.0, 26.0, 0.532899999999999, 1.1242, 2.5185, 3.5405, 0.0, 1.78, 4.8, 7.98, 0.0, 4.0, 15.0, 39.0, 0.0, 0.0, 0.0, 0.0, 0.0, -3.0, -4.0, 5.0, 0.0, -0.08, 0.199999999999999, 1.71999999999999]}

From b8b79227a97858dd70b61538a3881dba2abc89ab Mon Sep 17 00:00:00 2001
From: Ralf Meyer <meyer.ralf@yahoo.com>
Date: Mon, 26 Feb 2024 16:20:54 -0500
Subject: [PATCH 19/19] Squashed commit of the following:
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

commit 9481fd800a6ad115816c58400bf5c3320610d104
Merge: 21b7db13 5369b242
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 26 16:11:39 2024 -0500

    Merge pull request #169 from hjkgrp/type-hinting

    Type hinting

commit 21b7db13af1cf67a5f705cf66fc2aea4fb9a8c04
Merge: 56ab21b3 04ad9292
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 19 21:40:41 2024 -0500

    Merge pull request #203 from hjkgrp/more_ligand_fixes

    Improve documentation of the test case

commit 04ad9292d32237c2e361fa17145ee87aa8d28f2f
Merge: d8cd523f 56ab21b3
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 19 21:27:56 2024 -0500

    Merge branch 'master' into more_ligand_fixes

commit 56ab21b3484e0db1d4f9a361ac830c0df5111810
Merge: e5a4d048 82640c53
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 19 21:20:13 2024 -0500

    Merge pull request #202 from hjkgrp/rmsd

    Add minimal example for issue 127

commit 82640c534fbcda70c71f1758893bf209f5317230
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 19 21:14:11 2024 -0500

    Add minimal example for issue 127

commit e5a4d048739e1e85421931d515ecd5aac0e598e4
Merge: 5ad401eb 8ecc724f
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 12 21:30:50 2024 -0500

    Merge pull request #201 from hjkgrp/mol3D_from_smiles

    mol3D from smiles

commit 8ecc724f181d8c5bd5b7289dc39f876aad1eea05
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 12 20:45:28 2024 -0500

    Add from_smiles constructor

commit 650a2220bb4827bb5b4bcbabfd8523b9d1f310cf
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 12 20:44:36 2024 -0500

    Fix get_geometry_type default argument

commit 5ad401eb4f611bb6e14b5ea9fb1a423330c0cec8
Author: Gianmarco Terrones <78051991+gianmarco-terrones@users.noreply.github.com>
Date:   Sat Feb 10 16:54:37 2024 -0500

    Update fragment_MOFs_for_pormake.py

commit e96d4245adde0779a6090ea90fb178d2436ef925
Merge: 9e428367 4836f075
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 5 16:29:06 2024 -0500

    Merge pull request #199 from hjkgrp/pre-commit-ci-update-config

    [pre-commit.ci] pre-commit autoupdate

commit 4836f075575401dd9977dc0a59165dfa28a5d7b2
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Feb 5 21:13:58 2024 +0000

    [pre-commit.ci] pre-commit autoupdate

    updates:
    - [github.com/pycqa/flake8: 6.1.0 → 7.0.0](https://github.com/pycqa/flake8/compare/6.1.0...7.0.0)

commit 9e4283678b3938d373927366a005bddd4cdac629
Merge: e8ee975e e5570d6f
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Mon Feb 5 16:07:27 2024 -0500

    Merge pull request #197 from hjkgrp/jwt_edits

    Jwt edits

commit e5570d6f598076dc2da8c40c56e3c2162458b96d
Author: jwtoney <jwt@mit.edu>
Date:   Mon Feb 5 13:45:46 2024 -0500

    Flake fixes

commit 71c2af113a3dccfb867704f02fc732c7a69322f6
Author: jwtoney <jwt@mit.edu>
Date:   Mon Feb 5 13:44:25 2024 -0500

    Remove print statement

commit e8ee975e120f311668a6cebfc481899c8346dffa
Author: davut-m <155399887+davut-m@users.noreply.github.com>
Date:   Wed Jan 24 10:11:50 2024 -0500

    Added a line to check geomnames (#195)

    * Added a line to check geomnames

    * [pre-commit.ci] auto fixes from pre-commit hooks

    ---------

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

commit 5369b24267cf48950066560b89d5b693661e132b
Merge: dd92b550 4e6d826e
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Fri Nov 10 19:00:41 2023 -0500

    Merge branch 'master' into type-hinting

commit 58c938419e6d2119b0192396f910474043912441
Merge: 9203f21a 62526bd6
Author: jwtoney <jwt@mit.edu>
Date:   Fri Oct 13 12:50:51 2023 -0400

    Merge branch 'master' into tutorial4
    Merge latest updates from master

commit 9203f21af8b8ad24a9afa43e02c0900447f6d74a
Author: jwtoney <jwt@mit.edu>
Date:   Fri Sep 29 11:04:19 2023 -0400

    Passed transition_metals_only flag

commit dd92b55018de559123fd7f24c6ca1366baea1c61
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Sat Aug 26 18:53:45 2023 -0400

    Fix mypy test for pandas index type

commit 944f9c6f486e460ce0e44707ff197c431286e862
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Sat Aug 26 18:46:54 2023 -0400

    type hints for rungen

commit fb50e107d76887dca9f4b134a69db27444f44d2c
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Sat Aug 26 18:08:22 2023 -0400

    Intermediate commit of new type hints

commit 65394d8364d2a9bd7659845b32448069342c33c0
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Fri Aug 25 16:24:30 2023 -0400

    remove mypy exclusions

commit d8cd523f2cb63df2effa9af205c37d380e78768e
Author: Ralf Meyer <meyer.ralf@yahoo.com>
Date:   Tue Aug 9 22:08:35 2022 -0400

    Improve documentation of the test case
---
 .github/workflows/python-linter.yaml          |   4 +-
 .pre-commit-config.yaml                       |   2 +-
 molSimplify/Classes/globalvars.py             |   5 +-
 molSimplify/Classes/ligand.py                 |   1 +
 molSimplify/Classes/mol3D.py                  |  48 +++-
 .../MOF_descriptors_alternate_functional.py   |   2 +-
 molSimplify/Informatics/MOF/PBC_functions.py  |   6 +-
 .../Informatics/MOF/cluster_extraction.py     |   2 +-
 .../MOF/fragment_MOFs_for_pormake.py          |   7 +-
 .../Informatics/macrocycle_synthesis.py       | 230 +++++++++---------
 molSimplify/Scripts/geometry.py               |   9 +-
 molSimplify/Scripts/io.py                     |   2 +-
 molSimplify/Scripts/nn_prep.py                |   2 +-
 molSimplify/Scripts/rungen.py                 |  86 ++++---
 molSimplify/Scripts/structgen.py              | 135 +++++-----
 molSimplify/Scripts/tf_nn_prep.py             |   8 +-
 molSimplify/python_nn/tf_ANN.py               |   2 +-
 tests/test_ligands.py                         |   2 +-
 tests/test_mol3D.py                           |  80 ++++++
 tests/test_rmsd.py                            |  28 +++
 20 files changed, 410 insertions(+), 251 deletions(-)

diff --git a/.github/workflows/python-linter.yaml b/.github/workflows/python-linter.yaml
index 8b59a33e..dca468c4 100644
--- a/.github/workflows/python-linter.yaml
+++ b/.github/workflows/python-linter.yaml
@@ -59,11 +59,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install mypy types-setuptools types-PyYAML types-requests
+        pip install mypy types-setuptools types-PyYAML types-requests types-tensorflow types-beautifulsoup4 pandas-stubs PyQt5-stubs
     - name: Typecheck with mypy
       run: |
         # Exclude parts of Informatics for now
-        mypy --ignore-missing-imports --exclude '(frag_functionalizer.py|bridge_functionalizer.py|macrocycle_synthesis.py)' molSimplify
+        mypy --ignore-missing-imports molSimplify
 
     - name: Report Status
       # Slack notifications only on the main repo
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index cb486a52..2df01fa7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/pycqa/flake8
-    rev: '6.1.0'
+    rev: '7.0.0'
     hooks:
     -   id: flake8
         args: ['--select=E9,F63,F7,F82', '--exclude=fragment_classes.py,frag_functionalizer.py,bridge_functionalizer.py']
diff --git a/molSimplify/Classes/globalvars.py b/molSimplify/Classes/globalvars.py
index 9d8787fb..372486c1 100644
--- a/molSimplify/Classes/globalvars.py
+++ b/molSimplify/Classes/globalvars.py
@@ -12,6 +12,7 @@
 import platform
 import sys
 import subprocess
+from typing import Dict, Tuple
 from molSimplify.utils.metaclasses import Singleton
 
 # Dictionary containing atomic mass, atomic number, covalent radius, num valence electrons
@@ -563,7 +564,7 @@ def __init__(self):
     # Returns atomic mass dictionary
     #  @param self The object pointer
     #  @return Atomic mass dictionary
-    def amass(self):
+    def amass(self) -> Dict[str, Tuple[float, int, float, int]]:
         """Get the atomic mass dictionary.
 
         Returns
@@ -573,7 +574,7 @@ def amass(self):
         """
         return amassdict
 
-    def polarizability(self):
+    def polarizability(self) -> Dict[str, float]:
         """Get the polarizability dictionary.
 
         Returns
diff --git a/molSimplify/Classes/ligand.py b/molSimplify/Classes/ligand.py
index da923965..10d676b0 100644
--- a/molSimplify/Classes/ligand.py
+++ b/molSimplify/Classes/ligand.py
@@ -286,6 +286,7 @@ def ligand_breakdown(mol, BondedOct=False, silent=True, transition_metals_only=T
     # this function takes an octahedral
     # complex and returns ligands
     metal_index = mol.findMetal(transition_metals_only=transition_metals_only)[0]
+    # print(BondedOct)
     bondedatoms = mol.getBondedAtomsSmart(metal_index, oct=BondedOct)
     # print('!!!!!boundatoms', bondedatoms)
     # print('from get oct' + str(bondedatoms))
diff --git a/molSimplify/Classes/mol3D.py b/molSimplify/Classes/mol3D.py
index fac36b70..ac75a16c 100644
--- a/molSimplify/Classes/mol3D.py
+++ b/molSimplify/Classes/mol3D.py
@@ -1345,6 +1345,7 @@ def findcloseMetal(self, atom0):
         return close_metal
 
     def findMetal(self, transition_metals_only: bool = True) -> List[int]:
+#        transition_metals_only = False
         """
         Find metal(s) in a mol3D class.
 
@@ -1438,6 +1439,35 @@ def findsubMol(self, atom0, atomN, smart=False):
                     conatoms.remove(atidx)  # remove from list to check
         return subm
 
+    @classmethod
+    def from_smiles(cls, smiles):
+        mol = cls()
+        mol.getOBMol(smiles, "smistring")
+
+        elem = globalvars().elementsbynum()
+        # Add atoms
+        for atom in openbabel.OBMolAtomIter(mol.OBMol):
+            # get coordinates
+            pos = [atom.GetX(), atom.GetY(), atom.GetZ()]
+            # get atomic symbol
+            sym = elem[atom.GetAtomicNum() - 1]
+            # add atom to molecule
+            # atom3D_list.append(atom3D(sym, pos))
+            mol.addAtom(atom3D(sym, pos))
+
+        # Add bonds
+        mol.graph = np.zeros([mol.natoms, mol.natoms])
+        mol.bo_graph = np.zeros([mol.natoms, mol.natoms])
+        for bond in openbabel.OBMolBondIter(mol.OBMol):
+            i = bond.GetBeginAtomIdx() - 1
+            j = bond.GetEndAtomIdx() - 1
+            bond_order = bond.GetBondOrder()
+            if bond.IsAromatic():
+                bond_order = 1.5
+            mol.graph[i, j] = mol.graph[j, i] = 1
+            mol.bo_graph[i, j] = mol.bo_graph[j, i] = bond_order
+        return mol
+
     def getAtom(self, idx):
         """
         Get atom with a given index.
@@ -5248,7 +5278,7 @@ def get_symmetry_denticity(self, return_eq_catoms=False, BondedOct=False):
                 eq_catoms = False
             return eqsym, maxdent, ligdents, homoleptic, ligsymmetry, eq_catoms
 
-    def is_sandwich_compound(self):
+    def is_sandwich_compound(self, transition_metals_only=True):
         """
         Evaluates whether a compound is a sandwich compound
 
@@ -5274,7 +5304,7 @@ def is_sandwich_compound(self):
 
         from molSimplify.Informatics.graph_analyze import obtain_truncation_metal
         mol_fcs = obtain_truncation_metal(self, hops=1)
-        metal_ind = mol_fcs.findMetal()[0]
+        metal_ind = mol_fcs.findMetal(transition_metals_only=transition_metals_only)[0]
         catoms = list(range(mol_fcs.natoms))
         catoms.remove(metal_ind)
         sandwich_ligands, _sl = list(), list()
@@ -5304,7 +5334,7 @@ def is_sandwich_compound(self):
                           for x in info_sandwich_lig])
         return num_sandwich_lig, info_sandwich_lig, aromatic, allconnect
 
-    def is_edge_compound(self):
+    def is_edge_compound(self, transition_metals_only=True):
         """
         Check if a structure is edge compound.
 
@@ -5321,10 +5351,10 @@ def is_edge_compound(self):
         # two connected non-metal atoms both connected to the metal.
 
         from molSimplify.Informatics.graph_analyze import obtain_truncation_metal
-        num_sandwich_lig, info_sandwich_lig, aromatic, allconnect = self.is_sandwich_compound()
+        num_sandwich_lig, info_sandwich_lig, aromatic, allconnect = self.is_sandwich_compound(transition_metals_only=transition_metals_only)
         if not num_sandwich_lig or (num_sandwich_lig and not allconnect):
             mol_fcs = obtain_truncation_metal(self, hops=1)
-            metal_ind = mol_fcs.findMetal()[0]
+            metal_ind = mol_fcs.findMetal(transition_metals_only=transition_metals_only)[0]
             catoms = list(range(mol_fcs.natoms))
             catoms.remove(metal_ind)
             edge_ligands, _el = list(), list()
@@ -5342,7 +5372,7 @@ def is_edge_compound(self):
             num_edge_lig, info_edge_lig = 0, list()
         return num_edge_lig, info_edge_lig
 
-    def get_geometry_type(self, dict_check=False, angle_ref=False, num_coord=False,
+    def get_geometry_type(self, dict_check=False, angle_ref=False, num_coord=None,
                           flag_catoms=False, catoms_arr=None, debug=False,
                           skip=False, transition_metals_only=False):
         """
@@ -5390,7 +5420,7 @@ def get_geometry_type(self, dict_check=False, angle_ref=False, num_coord=False,
             else:
                 raise ValueError('No metal centers exist in this complex.')
 
-        if num_coord is False:
+        if num_coord is None:
             # TODO: Implement the case where we don't know the coordination number.
             raise NotImplementedError(
                 "Not implemented yet. Please at least provide the coordination number.")
@@ -5398,8 +5428,8 @@ def get_geometry_type(self, dict_check=False, angle_ref=False, num_coord=False,
         if catoms_arr is not None and len(catoms_arr) != num_coord:
             raise ValueError("num_coord and the length of catoms_arr do not match.")
 
-        num_sandwich_lig, info_sandwich_lig, aromatic, allconnect = self.is_sandwich_compound()
-        num_edge_lig, info_edge_lig = self.is_edge_compound()
+        num_sandwich_lig, info_sandwich_lig, aromatic, allconnect = self.is_sandwich_compound(transition_metals_only=transition_metals_only)
+        num_edge_lig, info_edge_lig = self.is_edge_compound(transition_metals_only=transition_metals_only)
 
         if num_coord not in [3, 4, 5, 6, 7]:
             if num_sandwich_lig:
diff --git a/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py b/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py
index bc5a42ec..d1ca6d21 100644
--- a/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py
+++ b/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py
@@ -144,7 +144,7 @@ def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name,cell,anchoring_
                 for jj in range(len(temp_mol.graph)):
                     #print(link_list)
                     #print(main)
-                    if not jj in main:
+                    if jj not in main:
                         if not set({temp_mol.atoms[jj].sym}) & set({"H"}):
                             functional_atoms.append(jj)
                 print(functional_atoms)
diff --git a/molSimplify/Informatics/MOF/PBC_functions.py b/molSimplify/Informatics/MOF/PBC_functions.py
index 45408f94..0a544bc7 100644
--- a/molSimplify/Informatics/MOF/PBC_functions.py
+++ b/molSimplify/Informatics/MOF/PBC_functions.py
@@ -392,7 +392,7 @@ def returnXYZandGraph(filename, atoms, cell, fcoords, molgraph):
         cart_coord=np.dot(fcoord,cell)
         coord_list.append([cart_coord[0],cart_coord[1],cart_coord[2]])
     tmpstr=",".join([at for at in atoms])
-    if filename != None:
+    if filename is not None:
         np.savetxt(filename[:-4]+".net",molgraph,fmt="%i",delimiter=",",header=tmpstr)
     return coord_list, molgraph
 
@@ -936,7 +936,7 @@ def get_closed_subgraph(linkers, SBUlist, adj_matrix):
             current_linker_list = current_linker_list-SBUlist
             checked_list.add(start_idx)
             for val in loop_over:
-                if (not val in SBUlist):
+                if val not in SBUlist:
                     current_linker_list.update(np.nonzero(adj_matrix[val])[1]) # np.nonzero(adj_matrix[val])[1] are the indices of atoms with bonds to the atom with index val
             left_to_check = current_linker_list-checked_list-SBUlist # Linker atoms whose connecting atoms still need to be checked.
             if len(left_to_check) == 0:
@@ -1042,7 +1042,7 @@ def disorder_detector(name):
         disordered_atom_types = []
         disordered_atom_occupancies = []
 
-        if occupancy_index != False: # This means that occupancy information is available
+        if occupancy_index: # This means that occupancy information is available
             for idx, at in enumerate(atomlines): # Go through the lines of the cif with atom specific information. Atom by atom.
                 ln=at.strip().split()
 
diff --git a/molSimplify/Informatics/MOF/cluster_extraction.py b/molSimplify/Informatics/MOF/cluster_extraction.py
index f7941db5..c9ebb790 100644
--- a/molSimplify/Informatics/MOF/cluster_extraction.py
+++ b/molSimplify/Informatics/MOF/cluster_extraction.py
@@ -83,7 +83,7 @@ def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name,cell,anchoring_
                 """""""""
                 functional_atoms = []
                 for jj in range(len(temp_mol.graph)):
-                    if not jj in link_list:
+                    if jj not in link_list:
                         if not set({temp_mol.atoms[jj].sym}) & set({"C","H"}):
                             functional_atoms.append(jj)
         # At this point, we look at the cycles for the graph, then add atoms if they are part of a cycle
diff --git a/molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py b/molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
index 61558603..6a121ff4 100644
--- a/molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
+++ b/molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
@@ -682,15 +682,13 @@ def identify_short_linkers(molcif, initial_SBU_list, initial_SBU_subgraphlist, r
             else:
                 # check number of times we cross PBC :
                 # TODO: we still can fail in multidentate ligands!
-                linker_cart_coords = np.array([at.coords() \
-                        for at in [molcif.getAtom(val) for val in atoms_list]])
+                linker_cart_coords = np.array([at.coords() for at in [molcif.getAtom(val) for val in atoms_list]])
                 linker_adjmat = np.array(linker_subgraphlist[ii])
                 pr_image_organic = ligand_detect(cell_v, linker_cart_coords, linker_adjmat, linkeranchors_list)
                 sbu_temp = linkeranchors_atoms.copy()
                 sbu_temp.update({val for val in initial_SBU_list[list(sbu_connect_list)[0]]})
                 sbu_temp = list(sbu_temp)
-                sbu_cart_coords = np.array([at.coords() \
-                       for at in [molcif.getAtom(val) for val in sbu_temp]])
+                sbu_cart_coords = np.array([at.coords() for at in [molcif.getAtom(val) for val in sbu_temp]])
                 sbu_adjmat = slice_mat(adj_matrix.todense(), sbu_temp)
                 pr_image_sbu = ligand_detect(cell_v, sbu_cart_coords, sbu_adjmat,set(range(len(linkeranchors_list))))
                 if not (len(np.unique(pr_image_sbu, axis=0))==1 and len(np.unique(pr_image_organic, axis=0))==1): # linker
@@ -737,6 +735,7 @@ def identify_short_linkers(molcif, initial_SBU_list, initial_SBU_subgraphlist, r
 def make_MOF_fragments(data, path=False, xyzpath=False):
     """
     Breaks a MOF into fragments for use with pormake (in silico MOF construction).
+    cif for MOF should have P1 symmetry.
 
     Output codes are as follows:
     2: There exist short (i.e. 2 atom) and longer linkers. We could not split the MOF apart consistently.
diff --git a/molSimplify/Informatics/macrocycle_synthesis.py b/molSimplify/Informatics/macrocycle_synthesis.py
index 4ddaf0b8..fc2abbdc 100644
--- a/molSimplify/Informatics/macrocycle_synthesis.py
+++ b/molSimplify/Informatics/macrocycle_synthesis.py
@@ -4,11 +4,6 @@
 import itertools
 import pandas as pd
 
-# ## Below is RDKit dependency that this code uses
-# from rdkit import Chem
-# from rdkit.Chem import AllChem
-# ###
-
 
 def cyclic_equiv(u, v):
     n, i, j = len(u), 0, 0
@@ -62,114 +57,123 @@ def cyclic_equiv(u, v):
 bridges = list(itertools.product(list(bridge_options.keys()),
                                  list(bridge_options.keys()),
                                  list(bridge_options.keys())))
-print('---- ', len(bridges)*len(monodentates), ' possible combos being tried ')
-ligands_to_dump = []
-for i in monodentates:
-    # New set of monodentates, cannot be rotational repeats with other monodentates
-    checked_list = set()
-    for j in bridges:
-        temp_dict = {}
-        parts_list = [i[0], j[0], i[0], j[2], i[1], j[1], i[1], j[2]]
-        if any([cyclic_equiv(parts_list, list(val)) for val in checked_list]):
-            print('This is a rotational repeat. Skipping.', parts_list)
-            atoms = (bridge_options[j[0]][0]
-                     + bridge_options[j[1]][0]
-                     + bridge_options[j[2]][0]
-                     + frag_options[i[0]][0][0]
-                     + frag_options[i[1]][0][0])
-            heteroatoms = list(set([val for val in atoms if val.isalpha()])-set('C')-set('X'))
-            temp_dict['bridge1'] = j[0]
-            temp_dict['bridge2'] = j[1]
-            temp_dict['bridge3'] = j[2]
-            temp_dict['fragment1'] = i[0]
-            temp_dict['fragment2'] = i[0]
-            temp_dict['fragment3'] = i[1]
-            temp_dict['fragment4'] = i[1]
-            temp_dict['heteroatoms'] = heteroatoms
-            temp_dict['reason'] = 'rotational_repeat'
-            if not os.path.exists('failed_syntheses.csv'):
-                df = pd.DataFrame([temp_dict])
-                df.to_csv('failed_syntheses.csv', index=False)
-            else:
-                df = pd.read_csv('failed_syntheses.csv')
-                new_entry = pd.DataFrame([temp_dict])
-                new_df = pd.concat([df, new_entry], axis=0)
-                new_df.to_csv('failed_syntheses.csv', index=False)
-            continue
-        else:
-            checked_list.add(tuple(parts_list))
-        atoms = (bridge_options[j[0]][0]
-                 + bridge_options[j[1]][0]
-                 + bridge_options[j[2]][0]
-                 + frag_options[i[0]][0][0]
-                 + frag_options[i[1]][0][0])
-        heteroatoms = list(set([val for val in atoms if val.isalpha()])-set('C')-set('X'))
-        if len(heteroatoms) > 2:
-            temp_dict['bridge1'] = j[0]
-            temp_dict['bridge2'] = j[1]
-            temp_dict['bridge3'] = j[2]
-            temp_dict['fragment1'] = i[0]
-            temp_dict['fragment2'] = i[0]
-            temp_dict['fragment3'] = i[1]
-            temp_dict['fragment4'] = i[1]
-            temp_dict['heteroatoms'] = heteroatoms
-            temp_dict['reason'] = 'heteroatoms'
-            if not os.path.exists('failed_syntheses.csv'):
-                df = pd.DataFrame([temp_dict])
-                df.to_csv('failed_syntheses.csv', index=False)
-            else:
-                df = pd.read_csv('failed_syntheses.csv')
-                new_entry = pd.DataFrame([temp_dict])
-                new_df = pd.concat([df, new_entry], axis=0)
-                new_df.to_csv('failed_syntheses.csv', index=False)
-            continue
-        test_frag1 = fragment(i[0], frag_options[i[0]], start_macrocycle=True)
-        test_frag2 = fragment(i[0], frag_options[i[0]], ring_closure_ind=2)
-        test_frag3 = fragment(i[1], frag_options[i[1]], ring_closure_ind=3)
-        test_frag4 = fragment(i[1], frag_options[i[1]], ring_closure_ind=4)
-        test_bridge1 = bridge(bridge_options[j[0]][0], bridge_options[j[0]][1], bridge_options[j[0]][2])
-        test_bridge2 = bridge(bridge_options[j[1]][0], bridge_options[j[1]][1], bridge_options[j[1]][2])
-        test_bridge3 = bridge(bridge_options[j[2]][0], bridge_options[j[2]][1], bridge_options[j[2]][2])
-        test_tetra = tetradentate(test_frag1, test_frag2, test_frag3, test_frag4, test_bridge1, test_bridge2, test_bridge3)
-        possible_ligands = test_tetra.stitch()
-        ligands_to_dump += possible_ligands
-        if len(possible_ligands) == 0:
-            temp_dict['bridge1'] = j[0]
-            temp_dict['bridge2'] = j[1]
-            temp_dict['bridge3'] = j[2]
-            temp_dict['fragment1'] = i[0]
-            temp_dict['fragment2'] = i[0]
-            temp_dict['fragment3'] = i[1]
-            temp_dict['fragment4'] = i[1]
-            temp_dict['heteroatoms'] = heteroatoms
-            temp_dict['reason'] = 'no_compatible_combo'
-            if not os.path.exists('failed_syntheses.csv'):
-                df = pd.DataFrame([temp_dict])
-                df.to_csv('failed_syntheses.csv', index=False)
+
+
+def main():
+    print('---- ', len(bridges)*len(monodentates), ' possible combos being tried ')
+    ligands_to_dump = []
+    for i in monodentates:
+        # New set of monodentates, cannot be rotational repeats with other monodentates
+        checked_list = set()
+        for j in bridges:
+            temp_dict = {}
+            parts_list = [i[0], j[0], i[0], j[2], i[1], j[1], i[1], j[2]]
+            if any([cyclic_equiv(parts_list, list(val)) for val in checked_list]):
+                print('This is a rotational repeat. Skipping.', parts_list)
+                atoms = (
+                    bridge_options[j[0]][0]
+                    + bridge_options[j[1]][0]
+                    + bridge_options[j[2]][0]
+                    + frag_options[i[0]][0][0]
+                    + frag_options[i[1]][0][0])
+                heteroatoms = list(set([val for val in atoms if val.isalpha()])-set('C')-set('X'))
+                temp_dict['bridge1'] = j[0]
+                temp_dict['bridge2'] = j[1]
+                temp_dict['bridge3'] = j[2]
+                temp_dict['fragment1'] = i[0]
+                temp_dict['fragment2'] = i[0]
+                temp_dict['fragment3'] = i[1]
+                temp_dict['fragment4'] = i[1]
+                temp_dict['heteroatoms'] = heteroatoms
+                temp_dict['reason'] = 'rotational_repeat'
+                if not os.path.exists('failed_syntheses.csv'):
+                    df = pd.DataFrame([temp_dict])
+                    df.to_csv('failed_syntheses.csv', index=False)
+                else:
+                    df = pd.read_csv('failed_syntheses.csv')
+                    new_entry = pd.DataFrame([temp_dict])
+                    new_df = pd.concat([df, new_entry], axis=0)
+                    new_df.to_csv('failed_syntheses.csv', index=False)
+                continue
             else:
-                df = pd.read_csv('failed_syntheses.csv')
-                new_entry = pd.DataFrame([temp_dict])
-                new_df = pd.concat([df, new_entry], axis=0)
-                new_df.to_csv('failed_syntheses.csv', index=False)
-            continue
-        else:
-            temp_dict['bridge1'] = j[0]
-            temp_dict['bridge2'] = j[1]
-            temp_dict['bridge3'] = j[2]
-            temp_dict['fragment1'] = i[0]
-            temp_dict['fragment2'] = i[0]
-            temp_dict['fragment3'] = i[1]
-            temp_dict['fragment4'] = i[1]
-            temp_dict['heteroatoms'] = heteroatoms
-            temp_dict['num_macrocycles'] = len(possible_ligands)
-            if not os.path.exists('successful_syntheses.csv'):
-                df = pd.DataFrame([temp_dict])
-                df.to_csv('successful_syntheses.csv', index=False)
+                checked_list.add(tuple(parts_list))
+            atoms = (
+                bridge_options[j[0]][0]
+                + bridge_options[j[1]][0]
+                + bridge_options[j[2]][0]
+                + frag_options[i[0]][0][0]
+                + frag_options[i[1]][0][0])
+            heteroatoms = list(set([val for val in atoms if val.isalpha()])-set('C')-set('X'))
+            if len(heteroatoms) > 2:
+                temp_dict['bridge1'] = j[0]
+                temp_dict['bridge2'] = j[1]
+                temp_dict['bridge3'] = j[2]
+                temp_dict['fragment1'] = i[0]
+                temp_dict['fragment2'] = i[0]
+                temp_dict['fragment3'] = i[1]
+                temp_dict['fragment4'] = i[1]
+                temp_dict['heteroatoms'] = heteroatoms
+                temp_dict['reason'] = 'heteroatoms'
+                if not os.path.exists('failed_syntheses.csv'):
+                    df = pd.DataFrame([temp_dict])
+                    df.to_csv('failed_syntheses.csv', index=False)
+                else:
+                    df = pd.read_csv('failed_syntheses.csv')
+                    new_entry = pd.DataFrame([temp_dict])
+                    new_df = pd.concat([df, new_entry], axis=0)
+                    new_df.to_csv('failed_syntheses.csv', index=False)
+                continue
+            test_frag1 = fragment(i[0], frag_options[i[0]], start_macrocycle=True)
+            test_frag2 = fragment(i[0], frag_options[i[0]], ring_closure_ind=2)
+            test_frag3 = fragment(i[1], frag_options[i[1]], ring_closure_ind=3)
+            test_frag4 = fragment(i[1], frag_options[i[1]], ring_closure_ind=4)
+            test_bridge1 = bridge(bridge_options[j[0]][0], bridge_options[j[0]][1], bridge_options[j[0]][2])
+            test_bridge2 = bridge(bridge_options[j[1]][0], bridge_options[j[1]][1], bridge_options[j[1]][2])
+            test_bridge3 = bridge(bridge_options[j[2]][0], bridge_options[j[2]][1], bridge_options[j[2]][2])
+            test_tetra = tetradentate(test_frag1, test_frag2, test_frag3, test_frag4, test_bridge1, test_bridge2, test_bridge3)
+            possible_ligands = test_tetra.stitch()
+            ligands_to_dump += possible_ligands
+            if len(possible_ligands) == 0:
+                temp_dict['bridge1'] = j[0]
+                temp_dict['bridge2'] = j[1]
+                temp_dict['bridge3'] = j[2]
+                temp_dict['fragment1'] = i[0]
+                temp_dict['fragment2'] = i[0]
+                temp_dict['fragment3'] = i[1]
+                temp_dict['fragment4'] = i[1]
+                temp_dict['heteroatoms'] = heteroatoms
+                temp_dict['reason'] = 'no_compatible_combo'
+                if not os.path.exists('failed_syntheses.csv'):
+                    df = pd.DataFrame([temp_dict])
+                    df.to_csv('failed_syntheses.csv', index=False)
+                else:
+                    df = pd.read_csv('failed_syntheses.csv')
+                    new_entry = pd.DataFrame([temp_dict])
+                    new_df = pd.concat([df, new_entry], axis=0)
+                    new_df.to_csv('failed_syntheses.csv', index=False)
+                continue
             else:
-                df = pd.read_csv('successful_syntheses.csv')
-                new_entry = pd.DataFrame([temp_dict])
-                new_df = pd.concat([df, new_entry], axis=0)
-                new_df.to_csv('successful_syntheses.csv', index=False)
+                temp_dict['bridge1'] = j[0]
+                temp_dict['bridge2'] = j[1]
+                temp_dict['bridge3'] = j[2]
+                temp_dict['fragment1'] = i[0]
+                temp_dict['fragment2'] = i[0]
+                temp_dict['fragment3'] = i[1]
+                temp_dict['fragment4'] = i[1]
+                temp_dict['heteroatoms'] = heteroatoms
+                temp_dict['num_macrocycles'] = len(possible_ligands)
+                if not os.path.exists('successful_syntheses.csv'):
+                    df = pd.DataFrame([temp_dict])
+                    df.to_csv('successful_syntheses.csv', index=False)
+                else:
+                    df = pd.read_csv('successful_syntheses.csv')
+                    new_entry = pd.DataFrame([temp_dict])
+                    new_df = pd.concat([df, new_entry], axis=0)
+                    new_df.to_csv('successful_syntheses.csv', index=False)
+
+    with open(os.getcwd()+'/synthesized_ligands.json', 'w') as fout:
+        json.dump(ligands_to_dump, fout, indent=2)
+
 
-with open(os.getcwd()+'/synthesized_ligands.json', 'w') as fout:
-    json.dump(ligands_to_dump, fout, indent=2)
+if __name__ == "__main__":
+    main()
diff --git a/molSimplify/Scripts/geometry.py b/molSimplify/Scripts/geometry.py
index 0ba841ce..0ea3d8b7 100644
--- a/molSimplify/Scripts/geometry.py
+++ b/molSimplify/Scripts/geometry.py
@@ -8,6 +8,7 @@
 #  Department of Chemical Engineering, MIT
 
 import numpy as np
+from typing import List
 
 
 def norm(u):
@@ -498,7 +499,7 @@ def PointRotateMat(r, R):
     return rn
 
 
-def PointTranslateSph(Rp, p0, D):
+def PointTranslateSph(Rp, p0, D) -> List[float]:
     """Translates point in spherical coordinates.
 
     Parameters
@@ -517,7 +518,7 @@ def PointTranslateSph(Rp, p0, D):
 
     """
     # translate to origin
-    ps = [0, 0, 0]
+    ps = [0., 0., 0.]
     ps[0] = p0[0] - Rp[0]
     ps[1] = p0[1] - Rp[1]
     ps[2] = p0[2] - Rp[2]
@@ -525,12 +526,12 @@ def PointTranslateSph(Rp, p0, D):
     r0 = norm(ps)
     if (r0 < 1e-16):
         phi0 = 0.5 * np.pi
-        theta0 = 0
+        theta0 = 0.
     else:
         phi0 = np.arccos(ps[2] / r0)  # z/r
         theta0 = np.arctan2(ps[1], ps[0])  # y/x
     # get new point
-    p = [0, 0, 0]
+    p = [0., 0., 0.]
     p[0] = (D[0]) * np.sin(phi0 + D[2]) * np.cos(theta0 + D[1]) + Rp[0]
     p[1] = (D[0]) * np.sin(phi0 + D[2]) * np.sin(theta0 + D[1]) + Rp[1]
     p[2] = (D[0]) * np.cos(phi0 + D[2]) + Rp[2]
diff --git a/molSimplify/Scripts/io.py b/molSimplify/Scripts/io.py
index 1b5f9198..5bfaa3c5 100644
--- a/molSimplify/Scripts/io.py
+++ b/molSimplify/Scripts/io.py
@@ -927,7 +927,7 @@ def plugin_defs() -> str:
 #  @return Complex name
 
 
-def name_complex(rootdir: str, core, geometry, ligs, ligoc, sernum,
+def name_complex(rootdir: str, core, geometry, ligs, ligoc, sernum: int,
                  args, nconf=False, sanity=False, bind=False, bsmi=False) -> str:
     # new version of the above, designed to
     # produce more human and machine-readable formats
diff --git a/molSimplify/Scripts/nn_prep.py b/molSimplify/Scripts/nn_prep.py
index 8a5f472c..9d1eaf83 100644
--- a/molSimplify/Scripts/nn_prep.py
+++ b/molSimplify/Scripts/nn_prep.py
@@ -178,7 +178,7 @@ def get_con_at_type(mol, connection_atoms: List[Union[int, str]]) -> Tuple[bool,
 
 
 def ANN_preproc(args, ligs: List[str], occs: List[int], dents: List[int],
-                batslist: List[List[int]], tcats: List[str],
+                batslist: List[List[int]], tcats: List[List[Union[int, str]]],
                 licores: dict) -> Tuple[bool, str, dict]:
     # prepares and runs ANN calculation
 
diff --git a/molSimplify/Scripts/rungen.py b/molSimplify/Scripts/rungen.py
index b7800f9e..30571b25 100644
--- a/molSimplify/Scripts/rungen.py
+++ b/molSimplify/Scripts/rungen.py
@@ -12,7 +12,9 @@
 import sys
 from collections import Counter
 import glob
+from typing import List, Union, Tuple
 
+from argparse import Namespace
 from molSimplify.Classes.globalvars import globalvars
 from molSimplify.Scripts.isomers import generateisomers
 from molSimplify.Scripts.jobgen import (sgejobgen,
@@ -31,20 +33,20 @@
                                        multitcgen)
 from molSimplify.Scripts.structgen import (structgen)
 
-###################################################################
-### define input for cross-compatibility between python 2 and 3 ###
-###################################################################
+# ##################################################################
+# ## define input for cross-compatibility between python 2 and 3 ###
+# ##################################################################
 get_input = input
 if sys.version_info[:2] <= (2, 7):
     get_input = raw_input  # noqa: F821
 
-#####################################
-### constrained random generation ###
-#####################################
+# ####################################
+# ## constrained random generation ###
+# ####################################
 
 
-def constrgen(rundir, args):
-    emsg = False
+def constrgen(rundir: str, args: Namespace) -> Tuple[Union[Namespace, bool], str]:
+    emsg = ""
     # load global variables
     licores = getlicores()
     print('Random generation started..\n\n')
@@ -145,9 +147,9 @@ def constrgen(rundir, args):
     return args, emsg
 
 
-###############################################
-### get sample aggreeing to the constraints ###
-###############################################
+# ##############################################
+# ## get sample aggreeing to the constraints ###
+# ##############################################
 
 
 def getconstsample(no_rgen, args, licores, coord):
@@ -302,14 +304,14 @@ def multigenruns(rundir, args, write_files=True):
 #  @return Ligand list, connecting atoms, multiple ligand flag
 
 
-def checkmultilig(ligs):
+def checkmultilig(ligs: List[str]) -> Tuple[List[List[str]], List[List[str]], int]:
     mligs = []
     tcats = []
     multidx = -1
     # loop over ligands
 
     for i, lig in enumerate(ligs):
-        connatoms = []
+        connatoms: List[str] = []
         if '.smi' in lig:
             if '~' in lig:
                 lig = lig.replace('~', os.path.expanduser("~"))
@@ -321,12 +323,9 @@ def checkmultilig(ligs):
                 for ss in s:
                     ss = ss.replace('\t', ' ')
                     sf = [_f for _f in ss.split(' ') if _f]
-                    print(sf)
                     if len(sf) > 0:
                         connatoms.append(sf[-1])
                         multidx = i
-                    else:
-                        connatoms.append(False)
                 if len(s) > 1:
                     mligs.append(s)
                 else:
@@ -337,6 +336,7 @@ def checkmultilig(ligs):
             mligs.append([lig])
         tcats.append(connatoms)
     ligandslist = list(itertools.product(*mligs))
+
     # convert tuple to list
     llist = []
     for l0 in ligandslist:
@@ -353,13 +353,14 @@ def checkmultilig(ligs):
 #  @param rundir Run directory
 
 
-def draw_supervisor(args, rundir):
+def draw_supervisor(args: Namespace, rundir: str):
     if args.lig:
         print('Due to technical limitations, we will draw only the first ligand.')
         print('To view multiple ligands at once, consider using the GUI instead.')
         li = args.lig[0]
         lig, emsg = lig_load(li)
-        lig.draw_svg(li)
+        if lig is not None:
+            lig.draw_svg(li)
     elif args.core:
         if len(args.core) > 1:
             print('Due to technical limitations, we will draw only the first core.')
@@ -368,14 +369,16 @@ def draw_supervisor(args, rundir):
             print('Due to technical limitations, we can draw only one structure per run. '
                   'To draw the substrate, run the program again.')
         cc, emsg = core_load(args.core[0])
-        cc.draw_svg(args.core[0])
+        if cc is not None:
+            cc.draw_svg(args.core[0])
     elif args.substrate:
         if len(args.substrate) > 1:
             print('Due to technical limitations, we will draw only the first substrate.')
         print('Drawing the substrate.')
         print((args.substrate[0]))
         substrate, subcatoms, emsg = substr_load(args.substrate[0], 0, args.subcatoms)
-        substrate.draw_svg(args.substrate[0])
+        if substrate is not None:
+            substrate.draw_svg(args.substrate[0])
     else:
         print('You have not specified anything to draw. Currently supported: ligand, core, substrate')
 
@@ -386,14 +389,15 @@ def draw_supervisor(args, rundir):
 #  @return Error messages
 
 
-def rungen(rundir, args, chspfname=None, write_files=True):
+def rungen(rundir, args: Namespace, chspfname=None, write_files: bool = True):
     emsg = ''
     globs = globalvars()
     globs.nosmiles = 0  # reset smiles ligands for each run
     # check for specified ligands/functionalization
     ligocc = []
     # check for files specified for multiple ligands
-    mligs, catoms = [False], [False]
+    mligs: List[List[str]] = [[]]
+    catoms: List[List[str]] = [[]]
     if args.lig is not None:
         if args.lig:
             mligs, catoms, multidx = checkmultilig(args.lig)
@@ -401,10 +405,10 @@ def rungen(rundir, args, chspfname=None, write_files=True):
                 print('after checking for multiple ligs, we found '
                       f'{multidx} ligands')
     # save initial
-    smicat0 = [ss for ss in args.smicat] if args.smicat else False
+    smicat0 = [ss for ss in args.smicat] if args.smicat else []
     # loop over ligands
     for mcount, mlig in enumerate(mligs):
-        args.smicat = [ss for ss in smicat0] if smicat0 else False
+        args.smicat = [ss for ss in smicat0] if smicat0 else []
         args.checkdir, skip = False, False  # initialize flags
         if len(mligs) > 0 and mligs[0]:
             args.lig = mlig  # get combination
@@ -447,8 +451,8 @@ def rungen(rundir, args, chspfname=None, write_files=True):
         else:
             ligands = []
             lig = ''
-            ligocc = ''
-    # fetch smart name
+            ligocc = []
+        # fetch smart name
         fname = name_complex(rundir, args.core, args.geometry, ligands, ligocc,
                              mcount, args, nconf=False, sanity=False, bind=args.bind, bsmi=args.nambsmi)
         if args.tsgen:
@@ -458,13 +462,15 @@ def rungen(rundir, args, chspfname=None, write_files=True):
                 subcatoms = args.subcatoms
             mlig = args.mlig
             mligcatoms = args.mligcatoms
-            fname = name_ts_complex(rundir, args.core, args.geometry, ligands, ligocc, substrate, subcatoms,
-                                    mlig, mligcatoms, mcount, args, nconf=False, sanity=False, bind=args.bind, bsmi=args.nambsmi)
+            fname = name_ts_complex(rundir, args.core, args.geometry, ligands, ligocc,
+                                    substrate, subcatoms, mlig, mligcatoms, mcount,
+                                    args, nconf=False, sanity=False, bind=args.bind,
+                                    bsmi=args.nambsmi)
         if args.debug:
             print(('fname is ' + str(fname)))
         rootdir = fname
         # check for charges/spin
-        rootcheck = False
+        rootcheck = ""
         if chspfname is not None:
             rootcheck = rootdir
             rootdir = rootdir + '/' + chspfname
@@ -487,7 +493,8 @@ def rungen(rundir, args, chspfname=None, write_files=True):
                 else:
                     flagdir = 'replace'
             else:
-                # qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootcheck+' already exists. What do you want to do?')
+                # qqb = qBoxFolder(args.gui.wmain,'Folder exists',
+                #                  'Directory '+rootcheck+' already exists. What do you want to do?')
                 # flagdir = qqb.getaction()
                 flagdir = 'replace'
                 # replace existing directory
@@ -526,7 +533,8 @@ def rungen(rundir, args, chspfname=None, write_files=True):
                 else:
                     flagdir = 'replace'
             else:
-                # qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootdir+' already exists. What do you want to do?')
+                # qqb = qBoxFolder(args.gui.wmain,'Folder exists',
+                #                  'Directory '+rootdir+' already exists. What do you want to do?')
                 # flagdir = qqb.getaction()
                 flagdir = 'replace'
             # replace existing directory
@@ -548,9 +556,9 @@ def rungen(rundir, args, chspfname=None, write_files=True):
                 if write_files:
                     args.checkdirb = True
                     os.mkdir(rootdir)
-            ####################################
-            ############ GENERATION ############
-            ####################################
+        # ###################################
+        # ########### GENERATION ############
+        # ###################################
         if not skip:
             # check for generate all
             if args.genall:
@@ -560,14 +568,14 @@ def rungen(rundir, args, chspfname=None, write_files=True):
                 args.ffoption = 'ba'
                 args.MLbonds = False
                 strfiles, emsg, this_diag = structgen(
-                    args, rootdir, ligands, ligocc, globs, mcount, write_files=write_files)
+                    args, rootdir, ligands, ligocc, mcount, write_files=write_files)
                 for strf in strfiles:
                     tstrfiles.append(strf+'FFML')
                     os.rename(strf+'.xyz', strf+'FFML.xyz')
                 # generate xyz with FF and covalent
                 args.MLbonds = ['c' for i in range(0, len(args.lig))]
                 strfiles, emsg, this_diag = structgen(
-                    args, rootdir, ligands, ligocc, globs, mcount, write_files=write_files)
+                    args, rootdir, ligands, ligocc, mcount, write_files=write_files)
                 for strf in strfiles:
                     tstrfiles.append(strf+'FFc')
                     os.rename(strf+'.xyz', strf+'FFc.xyz')
@@ -576,14 +584,14 @@ def rungen(rundir, args, chspfname=None, write_files=True):
                 args.MLbonds = False
                 # generate xyz without FF and trained ML
                 strfiles, emsg, this_diag = structgen(
-                    args, rootdir, ligands, ligocc, globs, mcount, write_files=write_files)
+                    args, rootdir, ligands, ligocc, mcount, write_files=write_files)
                 for strf in strfiles:
                     tstrfiles.append(strf+'ML')
                     os.rename(strf+'.xyz', strf+'ML.xyz')
                 args.MLbonds = ['c' for i in range(0, len(args.lig))]
                 # generate xyz without FF and covalent ML
                 strfiles, emsg, this_diag = structgen(
-                    args, rootdir, ligands, ligocc, globs, mcount, write_files=write_files)
+                    args, rootdir, ligands, ligocc, mcount, write_files=write_files)
                 for strf in strfiles:
                     tstrfiles.append(strf+'c')
                     os.rename(strf+'.xyz', strf+'c.xyz')
@@ -591,7 +599,7 @@ def rungen(rundir, args, chspfname=None, write_files=True):
             else:
                 # generate xyz files
                 strfiles, emsg, this_diag = structgen(
-                    args, rootdir, ligands, ligocc, globs, mcount, write_files=write_files)
+                    args, rootdir, ligands, ligocc, mcount, write_files=write_files)
             # generate QC input files
             if args.qccode and (not emsg) and write_files:
                 if args.charge and (isinstance(args.charge, list)):
diff --git a/molSimplify/Scripts/structgen.py b/molSimplify/Scripts/structgen.py
index 79a77f04..64e77238 100644
--- a/molSimplify/Scripts/structgen.py
+++ b/molSimplify/Scripts/structgen.py
@@ -16,6 +16,7 @@
 import itertools
 import numpy as np
 from typing import Any, List, Tuple, Dict, Union, Optional
+from argparse import Namespace
 from molSimplify.Scripts.distgeom import GetConf
 from molSimplify.Scripts.geometry import (aligntoaxis2,
                                           best_fit_plane,
@@ -119,8 +120,8 @@ def getnupdateb(backbatoms: List[List[int]], denticity: int) -> Tuple[List[int],
 
 
 def init_ANN(args, ligands: List[str], occs: List[int], dents: List[int],
-             batslist: List[List[int]], tcats: List[str], licores: dict
-             ) -> Tuple[bool, List[Any], str, Dict[str, Any], bool]:
+             batslist: List[List[int]], tcats: List[List[Union[int, str]]],
+             licores: dict) -> Tuple[bool, List[Any], str, Dict[str, Any], bool]:
     """Initializes ANN.
 
     Parameters
@@ -215,8 +216,7 @@ def init_ANN(args, ligands: List[str], occs: List[int], dents: List[int],
     return ANN_flag, ANN_bondl, ANN_reason, ANN_attributes, catalysis_flag
 
 
-def init_template(args, cpoints_required: int,
-                  globs) -> Tuple[mol3D, mol3D, str, list, int, mol3D]:
+def init_template(args: Namespace, cpoints_required: int) -> Tuple[mol3D, mol3D, str, list, int, mol3D]:
     """Initializes core and template mol3Ds and properties.
 
     Parameters
@@ -225,8 +225,6 @@ def init_template(args, cpoints_required: int,
             Namespace of arguments.
         cpoints_required : int
             Number of connecting points required.
-        globs : dict
-            Globalvars dictionary. Globalvars class in molSimplify.
 
     Returns
     -------
@@ -244,6 +242,7 @@ def init_template(args, cpoints_required: int,
             Core reference atom index, mol3D instance.
 
     """
+    globs = globalvars()
     # initialize core and template
     core3D = mol3D()
     m3D = mol3D()
@@ -266,6 +265,8 @@ def init_template(args, cpoints_required: int,
         # check if geometry is defined and overwrite
         if args.geometry in geomshorts:
             geom = args.geometry
+        elif  args.geometry in geomnames:
+            geom = geomshorts[geomnames.index(args.geometry)]
         else:
             emsg = "Requested geometry not available." + \
                 "Defaulting to "+geomgroups[coord-1][0]
@@ -403,7 +404,8 @@ def init_template(args, cpoints_required: int,
     return m3D, core3D, geom, backbatoms, coord, corerefatoms
 
 
-def init_ligand(args, lig, tcats, keepHs, i):
+def init_ligand(args: Namespace, lig: mol3D, tcats,
+                keepHs: List[List[Union[bool, str]]], i: int):
     """Initializes ligand 3D geometry and properties.
 
     Parameters
@@ -603,8 +605,10 @@ def smartreorderligs(ligs: List[str], dentl: List[int],
     return indices
 
 
-def ffopt(ff: str, mol: mol3D, connected, constopt, frozenats: List[int], frozenangles,
-          mlbonds, nsteps: Union[int, str], spin: int = 1, debug: bool = False):
+def ffopt(ff: str, mol: mol3D, connected: List[int], constopt: int,
+          frozenats: List[int], frozenangles: bool,
+          mlbonds: List[float], nsteps: Union[int, str],
+          spin: int = 1, debug: bool = False) -> Tuple[mol3D, float]:
     """Main constrained FF opt routine.
 
     Parameters
@@ -658,8 +662,10 @@ def ffopt(ff: str, mol: mol3D, connected, constopt, frozenats: List[int], frozen
                            frozenangles, mlbonds, nsteps, debug=debug)
 
 
-def openbabel_ffopt(ff: str, mol: mol3D, connected, constopt, frozenats, frozenangles,
-                    mlbonds, nsteps: Union[int, str], debug: bool = False) -> Tuple[mol3D, float]:
+def openbabel_ffopt(ff: str, mol: mol3D, connected: List[int], constopt: int,
+                    frozenats: List[int], frozenangles: bool,
+                    mlbonds: List[float], nsteps: Union[int, str],
+                    debug: bool = False) -> Tuple[mol3D, float]:
     """ OpenBabel constraint optimization. To optimize metal-containing
     complexes with MMFF94, an intricate procedure of masking the metal
     atoms and manually editing their valences is applied. OpenBabel's
@@ -848,9 +854,10 @@ def openbabel_ffopt(ff: str, mol: mol3D, connected, constopt, frozenats, frozena
     return mol, en
 
 
-def xtb_opt(ff: str, mol: mol3D, connected, constopt, frozenats, frozenangles,
-            mlbonds, nsteps: Union[int, str], spin: int = 1, inertial: bool = False,
-            debug: bool = False) -> Tuple[mol3D, float]:
+def xtb_opt(ff: str, mol: mol3D, connected: List[int], constopt: int,
+            frozenats: List[int], frozenangles: bool,
+            mlbonds: List[float], nsteps: Union[int, str], spin: int = 1,
+            inertial: bool = False, debug: bool = False) -> Tuple[mol3D, float]:
     """ XTB optimization. Writes an input file (xtb.in) containing
     all the constraints and parameters to a temporary folder,
     executes the XTB program using the subprocess module and parses
@@ -975,7 +982,7 @@ def xtb_opt(ff: str, mol: mol3D, connected, constopt, frozenats, frozenangles,
     return mol, en
 
 
-def getconnection(core, cidx, BL):
+def getconnection(core: mol3D, cidx: int, BL: float) -> List[float]:
     """Finds the optimum attachment point for an atom/group to a central atom given the desired bond length.
     Objective function maximizes the minimum distance between attachment point and other groups bonded to the central atom.
 
@@ -1012,7 +1019,7 @@ def getconnection(core, cidx, BL):
     return cpoint
 
 
-def findsmarts(lig3D, smarts, catom):
+def findsmarts(lig3D: mol3D, smarts: List[str], catom: int) -> bool:
     """Checks if connecting atom of lig3D is part of SMARTS pattern.
 
     Parameters
@@ -1247,15 +1254,15 @@ def align_pi_ring_lig(corerefcoords, lig3D, atom0, ligpiatoms, u):
             mol3D class instance of aligned ligand.
 
     """
-    x_vec = np.array([1, 0, 0])
-    y_vec = np.array([0, 1, 0])
-    z_vec = np.array([0, 0, 1])
+    x_vec = np.array([1., 0., 0.])
+    y_vec = np.array([0., 1., 0.])
+    z_vec = np.array([0., 0., 1.])
     directional_vectors = [x_vec, y_vec, z_vec]
 
     # use a solver to find the rotations around the three vectors (x, y, z) required such that
     # the plane formed by the aromatic ring atoms is perpendicular to u
     from scipy.optimize import fsolve
-    initial_guess = [0, 0, 0]
+    initial_guess = [0., 0., 0.]
     rotations = fsolve(rotation_objective_func, initial_guess,
                        args=(lig3D, atom0, ligpiatoms, np.array(u), directional_vectors))
 
@@ -2252,7 +2259,8 @@ def align_dent3_lig(args, cpoint, batoms, m3D, core3D, coreref, ligand, lig3D,
     return lig3D_aligned, frozenats, MLoptbds
 
 
-def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D], str, run_diag, List, List]:
+def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
+             ) -> Tuple[mol3D, List[mol3D], str, run_diag, List[int], List[int]]:
     """Main ligand placement routine
 
     Parameters
@@ -2265,8 +2273,6 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
             List of ligand occupations.
         licores : dict
             Ligand dictionary as in molSimplify.
-        globs : dict
-            Globalvars dictionary. molSimplify Class.
 
     Returns
     -------
@@ -2284,6 +2290,9 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
             Ligand connection atoms from TSGen. Deprecated.
 
     """
+    globs = globalvars()
+    # load ligand dictionary
+    licores = getlicores()
     this_diag = run_diag()
     if globs.debug:
         print(('\nGenerating complex with ligands and occupations:', ligs, ligoc))
@@ -2299,16 +2308,16 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
     occs0 = []      # occurrences of each ligand
     toccs = 0       # total occurrence count (number of ligands)
     smilesligs = 0  # count how many smiles strings
-    cats0 = []      # connection atoms for ligands
+    cats0: List[List[Union[int, str]]] = []  # connection atoms for ligands
     dentl = []      # denticity of ligands
     connected = []  # indices in core3D of ligand atoms connected to metal
     frozenats = []  # atoms to be frozen in optimization
     freezeangles = False  # custom angles imposed
-    MLoptbds = []   # list of bond lengths
+    MLoptbds: List[float] = []   # list of bond lengths
     rempi = False   # remove dummy pi orbital center of mass atom
-    backbatoms = []
-    batslist = []
-    bats = []
+    backbatoms: List[List[int]] = []
+    batslist: List[List[int]] = []
+    bats: List[int] = []
     ffoption_list = []  # for each ligand, keeps track of what the forcefield option is.
     # load bond data
     MLbonds = loaddata('/Data/ML.dat')
@@ -2326,7 +2335,7 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
             dent_i = len(cats0[-1])
             smilesligs += 1
         else:
-            cats0.append(False)
+            cats0.append([])
         # otherwise get denticity from ligands dictionary
             if 'pi' in licores[ligname][2]:
                 dent_i = 1
@@ -2408,16 +2417,16 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
     for i, keepH in enumerate(keepHs):
         keepHs[i] = [keepHs[i]] * dents[i]
     # sort M-L bond list
-    MLb = False
+    MLb = []
     if args.MLbonds:
         MLb = [k for k in args.MLbonds]
         for j in range(len(args.MLbonds), len(ligs)):
             MLb.append(False)
         MLb = [MLb[i] for i in indcs]  # sort MLbonds list
     # sort ligands custom angles
-    pangles = False
+    pangles = []
     if args.pangles:
-        pangles = []
+        pangles = [k for k in args.pangles]
         for j in range(len(args.pangles), len(ligs)):
             pangles.append(False)
         pangles = [args.pangles[i] for i in indcs]  # sort custom langles list
@@ -2430,7 +2439,7 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
 
     # load core and initialize template
     m3D, core3D, geom, backbatoms, coord, corerefatoms = init_template(
-        args, cpoints_required, globs)
+        args, cpoints_required)
     # Get connection points for all the ligands
     # smart alignment and forced order
 
@@ -2456,10 +2465,10 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
                 bats, backbatoms = getnupdateb(backbatoms, dents[i])
                 batslist.append(bats)
     if not geom:
-        for comb in batslist:
+        for comb_i, comb in enumerate(batslist):
             for i in comb:
                 if i == 1:
-                    batslist[comb][i] = m3D.natoms - coord + 1
+                    batslist[comb_i][i] = m3D.natoms - coord + 1
     # initialize ANN
     ANN_flag, ANN_bondl, ANN_reason, ANN_attributes, catalysis_flag = init_ANN(
         args, ligands, occs, dents, batslist, tcats, licores)
@@ -2474,8 +2483,8 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
     # loop over ligands
     totlig = 0  # total number of ligands added
     ligsused = 0  # total number of ligands used
-    subcatoms_ext = []
-    mligcatoms_ext = []
+    subcatoms_ext: List[int] = []
+    mligcatoms_ext: List[int] = []
     if args.mligcatoms:
         for i in range(len(args.mligcatoms)):
             mligcatoms_ext.append(0)
@@ -2496,10 +2505,7 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
                             print(('decorating ' + str(ligand) + ' with ' + str(
                                 args.decoration[i]) + ' at sites ' + str(args.decoration_index)))
                         lig = decorate_ligand(
-                            ligand, args.decoration[i], args.decoration_index[i], args.debug)
-                    else:
-                        # keeps ligands that are not being decorated
-                        lig, emsg = lig_load(ligand)
+                            lig, args.decoration[i], args.decoration_index[i], args.debug)
             lig.convert2mol3D()
             # initialize ligand
             lig3D, rempi, ligpiatoms = init_ligand(args, lig, tcats, keepHs, i)
@@ -2789,8 +2795,11 @@ def mcomplex(args, ligs, ligoc, licores, globs):  # -> Tuple[mol3D, List[mol3D],
     return core3D, complex3D, emsg, this_diag, subcatoms_ext, mligcatoms_ext
 
 
-def generate_report(args, ligands, ligoc, licores, globs):
-    ligs = []
+def generate_report(args: Namespace, ligands: List[str], ligoc: List[int]
+                    ) -> Tuple[mol3D, List[mol3D], str, run_diag, List[int], List[int]]:
+    # load ligand dictionary
+    licores = getlicores()
+    ligs: List[ligand_class] = []
     cons = []
     # Bunch of unused variables?? RM 2022/02/17
     # mono_inds = []
@@ -2798,21 +2807,22 @@ def generate_report(args, ligands, ligoc, licores, globs):
     # tri_inds = []
     # tetra_inds = []
     # penta_inds = []
-    emsg, complex3D = False, []
+    emsg = ""
+    complex3D: List[mol3D] = []
     occs0 = []      # occurrences of each ligand
     toccs = 0       # total occurrence count (number of ligands)
     # catsmi = []     # SMILES ligands connection atoms
     smilesligs = 0  # count how many smiles strings
-    cats0 = []      # connection atoms for ligands
+    cats0: List[List[Union[int, str]]] = []      # connection atoms for ligands
     dentl = []      # denticity of ligands
     # connected = []  # indices in core3D of ligand atoms connected to metal
     # frozenats = []  # atoms to be frozen in optimization
     # freezeangles = False  # custom angles imposed
     # MLoptbds = []   # list of bond lengths
     # rempi = False   # remove dummy pi orbital center of mass atom
-    backbatoms = []
-    batslist = []
-    bats = []
+    backbatoms: List[List[int]] = []
+    batslist: List[List[int]] = []
+    bats: List[int] = []
     print('ONLY report wanted. Not building structure.')
     metal_mol = mol3D()
     metal_mol.addAtom(atom3D(args.core))
@@ -2836,7 +2846,7 @@ def generate_report(args, ligands, ligoc, licores, globs):
             dent_i = len(cats0[-1])
             smilesligs += 1
         else:
-            cats0.append(False)
+            cats0.append([])
         # otherwise get denticity from ligands dictionary
             if 'pi' in licores[name][2]:
                 dent_i = 1
@@ -2854,7 +2864,7 @@ def generate_report(args, ligands, ligoc, licores, globs):
             toccs += dent_i
     # sort by descending denticity (needed for adjacent connection atoms)
     ligandsU, occsU, dentsU = ligs, occs0, dentl  # save unordered lists
-    indcs = smartreorderligs(ligs, dentl, args.ligalign)
+    indcs = smartreorderligs(ligands, dentl, args.ligalign)
     occs = [occs0[i] for i in indcs]    # sort occurrences list
     tcats = [cats0[i] for i in indcs]   # sort connections list
     dents = [dentl[i] for i in indcs]   # sort denticities list
@@ -2866,14 +2876,14 @@ def generate_report(args, ligands, ligoc, licores, globs):
 
     # load core and initialize template
     m3D, core3D, geom, backbatoms, coord, corerefatoms = init_template(
-        args, cpoints_required, globs)
+        args, cpoints_required)
     # Get connection points for all the ligands
     # smart alignment and forced order
 
     # if geom:
     if args.ligloc and args.ligalign:
         batslist0 = []
-        for i, ligand_val in enumerate(ligandsU):
+        for i, ligandU_val in enumerate(ligandsU):
             for j in range(0, occsU[i]):
                 # get correct atoms
                 bats, backbatoms = getnupdateb(backbatoms, dentsU[i])
@@ -2893,10 +2903,10 @@ def generate_report(args, ligands, ligoc, licores, globs):
                 bats, backbatoms = getnupdateb(backbatoms, dents[i])
                 batslist.append(bats)
     if not geom:
-        for comb in batslist:
+        for comb_i, comb in enumerate(batslist):
             for i in comb:
                 if i == 1:
-                    batslist[comb][i] = m3D.natoms - coord + 1
+                    batslist[comb_i][i] = m3D.natoms - coord + 1
     ANN_flag, ANN_bondl, ANN_reason, ANN_attributes, catalysis_flag = init_ANN(
         args, ligands, occs, dents, batslist, tcats, licores)
 
@@ -2904,8 +2914,8 @@ def generate_report(args, ligands, ligoc, licores, globs):
     this_diag.set_ANN(ANN_flag, ANN_reason, ANN_attributes, catalysis_flag)
 
     # Unused return arguments
-    subcatoms_ext = []
-    mligcatoms_ext = []
+    subcatoms_ext: List[int] = []
+    mligcatoms_ext: List[int] = []
     if args.mligcatoms:
         for i in range(len(args.mligcatoms)):
             mligcatoms_ext.append(0)
@@ -2913,7 +2923,8 @@ def generate_report(args, ligands, ligoc, licores, globs):
     return core3D, complex3D, emsg, this_diag, subcatoms_ext, mligcatoms_ext
 
 
-def structgen(args, rootdir, ligands, ligoc, globs, sernum, write_files=True) -> Tuple[List[str], str, run_diag]:
+def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int],
+              sernum: int, write_files: bool = True) -> Tuple[List[str], str, run_diag]:
     """Main structure generation routine - multiple structures
 
     Parameters
@@ -2926,9 +2937,7 @@ def structgen(args, rootdir, ligands, ligoc, globs, sernum, write_files=True) ->
             List of ligand names.
         ligoc : list
             List of ligand occupations.
-        globs : dict
-            Globalvars dictionary. molSimplify Class.
-        sernum : str
+        sernum : int
             Serial number of complex for naming.
         write_files : bool, optional
             Flag to write files. Default is True. False for pythonic generation.
@@ -2947,20 +2956,18 @@ def structgen(args, rootdir, ligands, ligoc, globs, sernum, write_files=True) ->
     emsg = ''
 
     strfiles: List[str] = []
-    # load ligand dictionary
-    licores = getlicores()
     # build structure
     sanity = False
     this_diag = run_diag()
     if (ligands):
         if args.reportonly:
             core3D, complex3D, emsg, this_diag, subcatoms_ext, mligcatoms_ext = generate_report(
-                args, ligands, ligoc, licores, globs)
+                args, ligands, ligoc)
             if emsg:
                 return strfiles, emsg, this_diag
         else:
             core3D, complex3D, emsg, this_diag, subcatoms_ext, mligcatoms_ext = mcomplex(
-                args, ligands, ligoc, licores, globs)
+                args, ligands, ligoc)
             if args.debug:
                 print(('subcatoms_ext are ' + str(subcatoms_ext)))
             if emsg:
diff --git a/molSimplify/Scripts/tf_nn_prep.py b/molSimplify/Scripts/tf_nn_prep.py
index 48ac6fc1..c85c8914 100644
--- a/molSimplify/Scripts/tf_nn_prep.py
+++ b/molSimplify/Scripts/tf_nn_prep.py
@@ -93,7 +93,7 @@ def invoke_ANNs_from_mol3d(mol: mol3D, oxidation_state: int,
 
 
 def tf_check_ligands(ligs: List[str], batslist: List[List[int]],
-                     dents: List[int], tcats: List[str],
+                     dents: List[int], tcats: List[List[Union[int, str]]],
                      occs: List[int], debug: bool):
     # tests if ligand combination
     # is compatible with the ANN
@@ -121,8 +121,8 @@ def tf_check_ligands(ligs: List[str], batslist: List[List[int]],
     equatorial_ligs = []
     ax_dent = 0
     eq_dent = 0
-    eq_tcat = ''
-    ax_tcat = ''
+    eq_tcat = []
+    ax_tcat = []
     pentadentate = False
     ax_occs = []
     eq_occs = []
@@ -274,7 +274,7 @@ def check_metal(metal: str, oxidation_state: str) -> Tuple[bool, str]:
 
 
 def tf_ANN_preproc(metal: str, oxstate, spin, ligs: List[str], occs: List[int], dents: List[int],
-                   batslist: List[List[int]], tcats: List[str],
+                   batslist: List[List[int]], tcats: List[List[Union[int, str]]],
                    licores: dict, decoration, decoration_index, exchange, geometry: str = "oct",
                    debug: bool = False) -> Tuple[bool, str, dict, bool]:
     # prepares and runs ANN calculation
diff --git a/molSimplify/python_nn/tf_ANN.py b/molSimplify/python_nn/tf_ANN.py
index 6381a080..92f653aa 100644
--- a/molSimplify/python_nn/tf_ANN.py
+++ b/molSimplify/python_nn/tf_ANN.py
@@ -51,7 +51,7 @@ def perform_ANN_prediction(RAC_dataframe: pd.DataFrame, predictor_name: str,
     if len(missing_labels) > 0:
         # Try checking if there is anything in the column `RAC_column`. If so, deserialize it and re-run.
         if RAC_column in RAC_dataframe.columns:
-            deserialized_RACs = pd.DataFrame.from_records(RAC_dataframe[RAC_column].values, index=RAC_dataframe.index)
+            deserialized_RACs = pd.DataFrame.from_records(RAC_dataframe[RAC_column].values, index=RAC_dataframe.index.values)
             deserialized_RACs = deserialized_RACs.astype(float)
             RAC_dataframe = RAC_dataframe.join(deserialized_RACs)
             return perform_ANN_prediction(RAC_dataframe, predictor_name, RAC_column='RACs')
diff --git a/tests/test_ligands.py b/tests/test_ligands.py
index 5cdf8234..c07a0b64 100644
--- a/tests/test_ligands.py
+++ b/tests/test_ligands.py
@@ -40,7 +40,7 @@ def test_ligands_dict(lig_name):
         for line in lines:
             if 'CHG' in line:
                 # Should be in the following format:
-                # "M  CHGnn8 aaa vvv\n"
+                # "M  CHG  n aaa vvv\n"
                 # Where 'n' the number first number after 'CHG' states how
                 # many atom/charge pairs (8 characters each) follow.
                 n_charges = int(line[6:9])
diff --git a/tests/test_mol3D.py b/tests/test_mol3D.py
index 32d98de8..a69c5ff2 100644
--- a/tests/test_mol3D.py
+++ b/tests/test_mol3D.py
@@ -182,3 +182,83 @@ def test_readfromxyzfile(resource_path_root):
 
     for atom, ref in zip(mol.atoms, atoms_ref):
         assert (atom.symbol(), atom.coords()) == ref
+
+
+def test_mol3D_from_smiles_macrocycles():
+    """Uses an examples from Aditya's macrocycles that were previously
+    converted wrong.
+    """
+    smiles = "C9SC(=CCSC(CSC(=NCSC9)))"
+    mol = mol3D.from_smiles(smiles)
+    assert mol.natoms == 29
+
+    ref_graph = np.zeros([mol.natoms, mol.natoms])
+    ref_bo_graph = np.zeros([mol.natoms, mol.natoms])
+    bonds = [
+        (21, 7, 1.0),
+        (29, 14, 1.0),
+        (13, 14, 1.0),
+        (13, 12, 1.0),
+        (9, 10, 1.0),
+        (9, 8, 1.0),
+        (27, 12, 1.0),
+        (6, 7, 1.0),
+        (6, 5, 1.0),
+        (14, 28, 1.0),
+        (14, 1, 1.0),
+        (7, 8, 1.0),
+        (7, 22, 1.0),
+        (2, 1, 1.0),
+        (2, 3, 1.0),
+        (24, 8, 1.0),
+        (12, 11, 1.0),
+        (12, 26, 1.0),
+        (10, 11, 2.0),
+        (10, 25, 1.0),
+        (8, 23, 1.0),
+        (1, 15, 1.0),
+        (1, 16, 1.0),
+        (3, 17, 1.0),
+        (3, 4, 2.0),
+        (5, 19, 1.0),
+        (5, 4, 1.0),
+        (5, 20, 1.0),
+        (4, 18, 1.0),
+    ]
+    for bond in bonds:
+        i, j = bond[0] - 1, bond[1] - 1
+        ref_graph[i, j] = ref_graph[j, i] = 1
+        ref_bo_graph[i, j] = ref_bo_graph[j, i] = bond[2]
+
+    np.testing.assert_allclose(mol.graph, ref_graph)
+    np.testing.assert_allclose(mol.bo_graph, ref_bo_graph)
+
+
+def test_mol3D_from_smiles_benzene():
+    smiles = "c1ccccc1"
+    mol = mol3D.from_smiles(smiles)
+    assert mol.natoms == 12
+
+    ref_graph = np.zeros([mol.natoms, mol.natoms])
+    ref_bo_graph = np.zeros([mol.natoms, mol.natoms])
+    bonds = [
+        (1, 2, 1.5),
+        (2, 3, 1.5),
+        (3, 4, 1.5),
+        (4, 5, 1.5),
+        (5, 6, 1.5),
+        (1, 6, 1.5),
+        (1, 7, 1.0),
+        (2, 8, 1.0),
+        (3, 9, 1.0),
+        (4, 10, 1.0),
+        (5, 11, 1.0),
+        (6, 12, 1.0),
+    ]
+    for bond in bonds:
+        i, j = bond[0] - 1, bond[1] - 1
+        ref_graph[i, j] = ref_graph[j, i] = 1
+        ref_bo_graph[i, j] = ref_bo_graph[j, i] = bond[2]
+
+    np.testing.assert_allclose(mol.graph, ref_graph)
+    np.testing.assert_allclose(mol.bo_graph, ref_bo_graph)
diff --git a/tests/test_rmsd.py b/tests/test_rmsd.py
index bba5bd5e..a755e8db 100644
--- a/tests/test_rmsd.py
+++ b/tests/test_rmsd.py
@@ -1,6 +1,8 @@
 import pytest
+import numpy as np
 from molSimplify.Classes.mol3D import mol3D
 from molSimplify.Scripts.rmsd import rigorous_rmsd
+from molSimplify.Scripts.geometry import rotate_around_axis
 
 
 @pytest.mark.parametrize(
@@ -27,3 +29,29 @@ def test_rigorous_rmsd(resource_path_root, path1, path2, ref_hungarian, ref_none
 
     r = rigorous_rmsd(mol1, mol2, reorder='none')
     assert abs(r - ref_none) < atol
+
+
+@pytest.mark.skip
+def test_methane_rotation(atol=1e-3):
+    """This test case is intended to show the problem with our current RMSD implementation"""
+    # XYZ data copied from
+    # https://github.com/OpenChemistry/avogadrodata/blob/master/data/methane.xyz
+    d = 1.02672
+    theta = 110 * np.pi / 180
+    xyz_string = (
+        "C      0.00000    0.00000    0.0000\n"
+        "H      0.00000    0.00000    1.08900\n"
+        "H      1.02672    0.00000   -0.36300\n"
+        f"H    {d * np.cos(theta):8.5f}   {d * np.sin(theta):8.5f}   -0.36300\n"
+        f"H    {d * np.cos(theta):8.5f}   {-d * np.sin(theta):8.5f}   -0.36300\n"
+    )
+    mol1 = mol3D()
+    mol1.readfromstring(xyz_string)
+
+    mol2 = mol3D()
+    mol2.readfromstring(xyz_string)
+    # rotate 180 degrees around the z axis
+    mol2 = rotate_around_axis(mol2, [0.0, 0.0, 0.0], [0.0, 0.0, 1.0], 180)
+    assert rigorous_rmsd(mol1, mol2, reorder='none') < atol
+
+    assert rigorous_rmsd(mol1, mol2, reorder='hungarian') < atol