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 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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 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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 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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 - C C163 1.0 0.20750 0.42129 0.65759 1.0000 - C C164 1.0 0.22431 0.61842 0.71759 1.0000 - C C165 1.0 0.24470 0.35448 0.71585 1.0000 - C C166 1.0 0.92547 0.52268 0.53446 1.0000 - C C167 1.0 0.85574 0.54693 0.53467 1.0000 - C C168 1.0 0.81812 0.56127 0.57188 1.0000 - C C169 1.0 0.81020 0.51555 0.63909 1.0000 - C C170 1.0 0.80591 0.45177 0.65921 1.0000 - C C171 1.0 0.78182 0.45068 0.69724 1.0000 - C C172 1.0 0.76263 0.51337 0.71571 1.0000 - C C173 1.0 0.76950 0.57714 0.69586 1.0000 - C C174 1.0 0.79250 0.57870 0.65759 1.0000 - C C175 1.0 0.77569 0.38158 0.71759 1.0000 - C C176 1.0 0.75530 0.64552 0.71585 1.0000 - C C177 1.0 0.01131 0.46250 0.99999 1.0000 - C C178 1.0 0.06101 0.32106 0.99999 1.0000 - C C179 1.0 0.98869 0.53750 0.99999 1.0000 - C C180 1.0 0.93899 0.67894 0.99999 1.0000 - C C181 1.0 0.53750 0.01131 0.99999 1.0000 - C C182 1.0 0.67894 0.06102 0.99999 1.0000 - C C183 1.0 0.46250 0.98869 0.99999 1.0000 - C C184 1.0 0.32106 0.93899 0.99999 1.0000 - C C185 1.0 0.48869 0.96250 0.50001 1.0000 - C C186 1.0 0.43899 0.82106 0.50001 1.0000 - C C187 1.0 0.51131 0.03750 0.50001 1.0000 - C C188 1.0 0.56102 0.17894 0.50001 1.0000 - C C189 1.0 0.96251 0.51131 0.50001 1.0000 - C C190 1.0 0.82106 0.56101 0.50001 1.0000 - C C191 1.0 0.03750 0.48869 0.50001 1.0000 - C C192 1.0 0.17894 0.43899 0.50001 1.0000 - N N1 1.0 0.01423 0.33489 0.10091 1.0000 - N N2 1.0 0.98577 0.66511 0.10091 1.0000 - N N3 1.0 0.66511 0.01424 0.10091 1.0000 - N N4 1.0 0.33489 0.98576 0.10091 1.0000 - N N5 1.0 0.48576 0.83489 0.39909 1.0000 - N N6 1.0 0.51424 0.16511 0.39909 1.0000 - N N7 1.0 0.83489 0.51423 0.39909 1.0000 - N N8 1.0 0.16511 0.48577 0.39909 1.0000 - N N9 1.0 0.98577 0.66510 0.89907 1.0000 - N N10 1.0 0.01423 0.33490 0.89907 1.0000 - N N11 1.0 0.33489 0.98577 0.89907 1.0000 - N N12 1.0 0.66512 0.01423 0.89906 1.0000 - N N13 1.0 0.51423 0.16511 0.60093 1.0000 - N N14 1.0 0.48577 0.83489 0.60093 1.0000 - N N15 1.0 0.16510 0.48577 0.60093 1.0000 - N N16 1.0 0.83490 0.51423 0.60093 1.0000 - O O1 1.0 0.11088 0.27687 0.07571 1.0000 - O O2 1.0 0.82726 0.29868 0.19968 1.0000 - O O3 1.0 0.88252 0.24752 0.25100 1.0000 - O O4 1.0 0.20061 0.28036 0.19948 1.0000 - O O5 1.0 0.14353 0.22109 0.24748 1.0000 - O O6 1.0 0.88912 0.72313 0.07571 1.0000 - O O7 1.0 0.17273 0.70131 0.19968 1.0000 - O O8 1.0 0.11748 0.75248 0.25100 1.0000 - O O9 1.0 0.79939 0.71964 0.19947 1.0000 - O O10 1.0 0.85647 0.77891 0.24748 1.0000 - O O11 1.0 0.72313 0.11088 0.07571 1.0000 - O O12 1.0 0.70132 0.82727 0.19968 1.0000 - O O13 1.0 0.75248 0.88252 0.25100 1.0000 - O O14 1.0 0.71964 0.20061 0.19947 1.0000 - O O15 1.0 0.77891 0.14353 0.24748 1.0000 - O O16 1.0 0.27687 0.88912 0.07571 1.0000 - O O17 1.0 0.29868 0.17273 0.19968 1.0000 - O O18 1.0 0.24752 0.11748 0.25100 1.0000 - O O19 1.0 0.28036 0.79939 0.19947 1.0000 - O O20 1.0 0.22109 0.85647 0.24748 1.0000 - O O21 1.0 0.38912 0.77687 0.42429 1.0000 - O O22 1.0 0.67273 0.79868 0.30032 1.0000 - O O23 1.0 0.61748 0.74752 0.24900 1.0000 - O O24 1.0 0.29939 0.78036 0.30053 1.0000 - O O25 1.0 0.35647 0.72109 0.25252 1.0000 - O O26 1.0 0.61088 0.22314 0.42429 1.0000 - O O27 1.0 0.32727 0.20132 0.30032 1.0000 - O O28 1.0 0.38252 0.25248 0.24900 1.0000 - O O29 1.0 0.70061 0.21964 0.30053 1.0000 - O O30 1.0 0.64353 0.27891 0.25252 1.0000 - O O31 1.0 0.77687 0.61088 0.42429 1.0000 - O O32 1.0 0.79869 0.32727 0.30032 1.0000 - O O33 1.0 0.74752 0.38252 0.24900 1.0000 - O O34 1.0 0.78036 0.70061 0.30053 1.0000 - O O35 1.0 0.72109 0.64353 0.25252 1.0000 - O O36 1.0 0.22313 0.38912 0.42429 1.0000 - O O37 1.0 0.20132 0.67274 0.30032 1.0000 - O O38 1.0 0.25248 0.61748 0.24900 1.0000 - O O39 1.0 0.21964 0.29939 0.30052 1.0000 - O O40 1.0 0.27891 0.35647 0.25252 1.0000 - O O41 1.0 0.88912 0.72312 0.92426 1.0000 - O O42 1.0 0.17273 0.70133 0.80031 1.0000 - O O43 1.0 0.11748 0.75249 0.74899 1.0000 - O O44 1.0 0.79940 0.71965 0.80051 1.0000 - O O45 1.0 0.85647 0.77892 0.75251 1.0000 - O O46 1.0 0.11088 0.27688 0.92426 1.0000 - O O47 1.0 0.82727 0.29866 0.80031 1.0000 - O O48 1.0 0.88251 0.24751 0.74899 1.0000 - O O49 1.0 0.20059 0.28035 0.80051 1.0000 - O O50 1.0 0.14352 0.22108 0.75251 1.0000 - O O51 1.0 0.27688 0.88911 0.92426 1.0000 - O O52 1.0 0.29864 0.17274 0.80031 1.0000 - O O53 1.0 0.24752 0.11747 0.74898 1.0000 - O O54 1.0 0.28036 0.79940 0.80051 1.0000 - O O55 1.0 0.22108 0.85647 0.75251 1.0000 - O O56 1.0 0.72313 0.11087 0.92425 1.0000 - O O57 1.0 0.70131 0.82728 0.80032 1.0000 - O O58 1.0 0.75251 0.88254 0.74900 1.0000 - O O59 1.0 0.71968 0.20061 0.80053 1.0000 - O O60 1.0 0.77886 0.14349 0.75250 1.0000 - O O61 1.0 0.61087 0.22313 0.57575 1.0000 - O O62 1.0 0.32728 0.20131 0.69968 1.0000 - O O63 1.0 0.38253 0.25251 0.75100 1.0000 - O O64 1.0 0.70059 0.21964 0.69949 1.0000 - O O65 1.0 0.64351 0.27892 0.74750 1.0000 - O O66 1.0 0.38911 0.77688 0.57574 1.0000 - O O67 1.0 0.67274 0.79864 0.69969 1.0000 - O O68 1.0 0.61747 0.74752 0.75102 1.0000 - O O69 1.0 0.29940 0.78036 0.69949 1.0000 - O O70 1.0 0.35647 0.72108 0.74749 1.0000 - O O71 1.0 0.22312 0.38912 0.57574 1.0000 - O O72 1.0 0.20133 0.67273 0.69969 1.0000 - O O73 1.0 0.25249 0.61748 0.75101 1.0000 - O O74 1.0 0.21965 0.29940 0.69949 1.0000 - O O75 1.0 0.27892 0.35647 0.74749 1.0000 - O O76 1.0 0.77688 0.61088 0.57574 1.0000 - O O77 1.0 0.79866 0.32727 0.69969 1.0000 - O O78 1.0 0.74751 0.38251 0.75101 1.0000 - O O79 1.0 0.78035 0.70059 0.69949 1.0000 - O O80 1.0 0.72108 0.64352 0.74749 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 + Cu Cu0 1 0.70750000 0.73250000 0.22324000 1.0 + Cu Cu1 1 0.29250000 0.26750000 0.22324000 1.0 + Cu Cu2 1 0.26750000 0.70750000 0.22324000 1.0 + Cu Cu3 1 0.73250000 0.29250000 0.22324000 1.0 + Cu Cu4 1 0.20750000 0.76750000 0.27676000 1.0 + Cu Cu5 1 0.79250000 0.23250000 0.27676000 1.0 + Cu Cu6 1 0.76750000 0.79250000 0.27676000 1.0 + Cu Cu7 1 0.23250000 0.20750000 0.27676000 1.0 + Cu Cu8 1 0.29250000 0.26750000 0.77676000 1.0 + Cu Cu9 1 0.70749000 0.73249000 0.77678000 1.0 + Cu Cu10 1 0.73251000 0.29251000 0.77678000 1.0 + Cu Cu11 1 0.26751000 0.70750000 0.77676000 1.0 + Cu Cu12 1 0.79250000 0.23249000 0.72324000 1.0 + Cu Cu13 1 0.20748000 0.76749000 0.72322000 1.0 + Cu Cu14 1 0.23250000 0.20750000 0.72324000 1.0 + Cu Cu15 1 0.76751000 0.79252000 0.72322000 1.0 + H H16 1 0.54827000 0.01520000 0.06202000 1.0 + H H17 1 0.64067000 0.96906000 0.09267000 1.0 + H H18 1 0.67961000 0.90202000 0.14556000 1.0 + H H19 1 0.75651000 0.01255000 0.24520000 1.0 + H H20 1 0.70351000 0.12878000 0.14259000 1.0 + H H21 1 0.45173000 0.98480000 0.06202000 1.0 + H H22 1 0.35933000 0.03094000 0.09267000 1.0 + H H23 1 0.32039000 0.09798000 0.14556000 1.0 + H H24 1 0.24349000 0.98745000 0.24520000 1.0 + H H25 1 0.29649000 0.87122000 0.14259000 1.0 + H H26 1 0.98480000 0.54827000 0.06202000 1.0 + H H27 1 0.03094000 0.64067000 0.09267000 1.0 + H H28 1 0.09798000 0.67961000 0.14556000 1.0 + H H29 1 0.98745000 0.75651000 0.24520000 1.0 + H H30 1 0.87121000 0.70351000 0.14259000 1.0 + H H31 1 0.01520000 0.45173000 0.06202000 1.0 + H H32 1 0.96906000 0.35933000 0.09267000 1.0 + H H33 1 0.90202000 0.32039000 0.14556000 1.0 + H H34 1 0.01255000 0.24349000 0.24520000 1.0 + H H35 1 0.12879000 0.29649000 0.14259000 1.0 + H H36 1 0.04827000 0.48480000 0.43798000 1.0 + H H37 1 0.14067000 0.53094000 0.40733000 1.0 + H H38 1 0.17961000 0.59798000 0.35444000 1.0 + H H39 1 0.25651000 0.48745000 0.25479000 1.0 + H H40 1 0.20351000 0.37121000 0.35741000 1.0 + H H41 1 0.95173000 0.51520000 0.43798000 1.0 + H H42 1 0.85933000 0.46906000 0.40733000 1.0 + H H43 1 0.82039000 0.40202000 0.35444000 1.0 + H H44 1 0.74349000 0.51255000 0.25480000 1.0 + H H45 1 0.79649000 0.62879000 0.35741000 1.0 + H H46 1 0.48480000 0.95173000 0.43798000 1.0 + H H47 1 0.53094000 0.85933000 0.40733000 1.0 + H H48 1 0.59798000 0.82039000 0.35444000 1.0 + H H49 1 0.48745000 0.74349000 0.25480000 1.0 + H H50 1 0.37122000 0.79649000 0.35741000 1.0 + H H51 1 0.51520000 0.04827000 0.43798000 1.0 + H H52 1 0.46906000 0.14067000 0.40733000 1.0 + H H53 1 0.40202000 0.17961000 0.35444000 1.0 + H H54 1 0.51255000 0.25651000 0.25480000 1.0 + H H55 1 0.62878000 0.20351000 0.35741000 1.0 + H H56 1 0.45173000 0.98480000 0.93795000 1.0 + H H57 1 0.35933000 0.03095000 0.90731000 1.0 + H H58 1 0.32039000 0.09799000 0.85442000 1.0 + H H59 1 0.24348000 0.98745000 0.75478000 1.0 + H H60 1 0.29649000 0.87122000 0.85739000 1.0 + H H61 1 0.54827000 0.01520000 0.93795000 1.0 + H H62 1 0.64067000 0.96905000 0.90731000 1.0 + H H63 1 0.67961000 0.90201000 0.85442000 1.0 + H H64 1 0.75652000 0.01255000 0.75478000 1.0 + H H65 1 0.70351000 0.12878000 0.85739000 1.0 + H H66 1 0.01520000 0.45173000 0.93795000 1.0 + H H67 1 0.96905000 0.35935000 0.90731000 1.0 + H H68 1 0.90202000 0.32041000 0.85442000 1.0 + H H69 1 0.01255000 0.24348000 0.75478000 1.0 + H H70 1 0.12878000 0.29649000 0.85739000 1.0 + H H71 1 0.98479000 0.54826000 0.93795000 1.0 + H H72 1 0.03094000 0.64066000 0.90730000 1.0 + H H73 1 0.09797000 0.67961000 0.85441000 1.0 + H H74 1 0.98747000 0.75653000 0.75476000 1.0 + H H75 1 0.87120000 0.70345000 0.85738000 1.0 + H H76 1 0.95174000 0.51521000 0.56205000 1.0 + H H77 1 0.85934000 0.46906000 0.59269000 1.0 + H H78 1 0.82039000 0.40203000 0.64559000 1.0 + H H79 1 0.74352000 0.51255000 0.74525000 1.0 + H H80 1 0.79655000 0.62880000 0.64262000 1.0 + H H81 1 0.04827000 0.48480000 0.56205000 1.0 + H H82 1 0.14065000 0.53095000 0.59269000 1.0 + H H83 1 0.17959000 0.59798000 0.64558000 1.0 + H H84 1 0.25653000 0.48745000 0.74522000 1.0 + H H85 1 0.20351000 0.37122000 0.64261000 1.0 + H H86 1 0.51520000 0.04827000 0.56205000 1.0 + H H87 1 0.46905000 0.14067000 0.59269000 1.0 + H H88 1 0.40201000 0.17961000 0.64558000 1.0 + H H89 1 0.51255000 0.25652000 0.74522000 1.0 + H H90 1 0.62878000 0.20351000 0.64261000 1.0 + H H91 1 0.48480000 0.95173000 0.56205000 1.0 + H H92 1 0.53095000 0.85933000 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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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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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+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 + O O101 1 0.04456000 0.14197000 0.39886000 1.0 + O O102 1 0.32768000 0.39703000 0.44554000 1.0 + O O103 1 0.36159000 0.55524000 0.60302000 1.0 + O O104 1 0.51580000 0.45116000 0.21294000 1.0 + O O105 1 0.52801000 0.27490000 0.16640000 1.0 + O O106 1 0.52902000 0.41509000 0.54442000 1.0 + O O107 1 0.54456000 0.25689000 0.39886000 1.0 + O O108 1 0.82768000 0.04851000 0.44554000 1.0 + O O109 1 0.86159000 0.04778000 0.60302000 1.0 + O O110 1 0.98420000 0.23822000 0.78706000 1.0 + O O111 1 0.97199000 0.10850000 0.83360000 1.0 + O O112 1 0.97098000 0.87067000 0.45558000 1.0 + O O113 1 0.95544000 0.85803000 0.60114000 1.0 + O O114 1 0.67232000 0.60297000 0.55446000 1.0 + 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 + Li Li0 1 0.99805000 0.48585000 0.04885000 1.0 + 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 + Li Li7 1 0.74820000 0.30490000 0.02130000 1.0 + Li Li8 1 0.49805000 0.04885000 0.48585000 1.0 + Li Li9 1 0.78441000 0.52242000 0.04596000 1.0 + Li Li10 1 0.13873000 0.56331000 0.99363000 1.0 + Li Li11 1 0.57440000 0.97870000 0.69510000 1.0 + Li Li12 1 0.03275000 0.95115000 0.51415000 1.0 + Li Li13 1 0.35279000 0.47758000 0.95404000 1.0 + Li Li14 1 0.69567000 0.43669000 0.00637000 1.0 + Li Li15 1 0.24820000 0.02130000 0.30490000 1.0 + H H16 1 0.97850000 0.42800000 0.94080000 1.0 + H H17 1 0.93190000 0.34790000 0.89490000 1.0 + H H18 1 0.25990000 0.27760000 0.78440000 1.0 + H H19 1 0.30380000 0.35740000 0.83020000 1.0 + H H20 1 0.38820000 0.08440000 0.75020000 1.0 + H H21 1 0.24650000 0.15960000 0.82880000 1.0 + H H22 1 0.07450000 0.23000000 0.69240000 1.0 + H H23 1 0.21280000 0.15200000 0.61620000 1.0 + H H24 1 0.94260000 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0.21483000 0.84119000 1.0 + C C193 1 0.62058000 0.23237000 0.79687000 1.0 + C C194 1 0.54228000 0.29591000 0.79933000 1.0 + C C195 1 0.53341000 0.34078000 0.84580000 1.0 + C C196 1 0.52439000 0.18351000 0.73911000 1.0 + C C197 1 0.19424000 0.47049000 0.08845000 1.0 + C C198 1 0.26810000 0.42699000 0.12713000 1.0 + C C199 1 0.38365000 0.41783000 0.10775000 1.0 + C C200 1 0.45277000 0.37442000 0.14184000 1.0 + C C201 1 0.40580000 0.34115000 0.19725000 1.0 + C C202 1 0.28920000 0.35092000 0.21708000 1.0 + C C203 1 0.22055000 0.39350000 0.18220000 1.0 + C C204 1 0.34726000 0.08641000 0.39053000 1.0 + C C205 1 0.38702000 0.13916000 0.34590000 1.0 + C C206 1 0.36064000 0.15615000 0.28737000 1.0 + C C207 1 0.39220000 0.20868000 0.25012000 1.0 + C C208 1 0.44500000 0.24671000 0.27069000 1.0 + C C209 1 0.47270000 0.22874000 0.32906000 1.0 + C C210 1 0.44465000 0.17509000 0.36541000 1.0 + C C211 1 0.56590000 0.32160000 0.24480000 1.0 + N N212 1 0.06621000 0.24953000 0.81501000 1.0 + N N213 1 0.50760000 0.76608000 0.70052000 1.0 + N N214 1 0.13075000 0.75047000 0.18499000 1.0 + N N215 1 0.97420000 0.23392000 0.29948000 1.0 + N N216 1 0.56621000 0.81501000 0.24953000 1.0 + N N217 1 0.00760000 0.70052000 0.76608000 1.0 + N N218 1 0.63075000 0.18499000 0.75047000 1.0 + N N219 1 0.47420000 0.29948000 0.23392000 1.0 + O O220 1 0.09712000 0.49261000 0.96123000 1.0 + O O221 1 0.27668000 0.45465000 0.89931000 1.0 + 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 + H H118 1 0.30110000 0.24430000 0.38930000 1.0 + H H119 1 0.26880000 0.32960000 0.39000000 1.0 + H H120 1 0.22850000 0.15230000 0.69580000 1.0 + H H121 1 0.18100000 0.24480000 0.60390000 1.0 + H H122 1 0.21730000 0.32870000 0.60860000 1.0 + H H123 1 0.17640000 0.41350000 0.39750000 1.0 + H H124 1 0.75130000 0.97820000 0.24580000 1.0 + H H125 1 0.47810000 0.85500000 0.46110000 1.0 + H H126 1 0.31320000 0.29830000 0.52120000 1.0 + H H127 1 0.29630000 0.20940000 0.52580000 1.0 + H H128 1 0.13690000 0.14130000 0.20550000 1.0 + H H129 1 0.85260000 0.06280000 0.21510000 1.0 + H H130 1 0.51570000 0.91550000 0.35500000 1.0 + H H131 1 0.84320000 0.55900000 0.27960000 1.0 + H H132 1 0.73600000 0.47590000 0.25590000 1.0 + H H133 1 0.68260000 0.49890000 0.03730000 1.0 + H H134 1 0.70380000 0.01310000 0.46350000 1.0 + H H135 1 0.00170000 0.55850000 0.33800000 1.0 + H H136 1 0.31640000 0.40500000 0.59910000 1.0 + H H137 1 0.77410000 0.21590000 0.37100000 1.0 + H H138 1 0.76380000 0.69770000 0.12440000 1.0 + H H139 1 0.95440000 0.46360000 0.25540000 1.0 + H H140 1 0.24940000 0.14980000 0.29470000 1.0 + H H141 1 0.66900000 0.13270000 0.39930000 1.0 + H H142 1 0.39100000 0.51750000 0.58520000 1.0 + H H143 1 0.65250000 0.61780000 0.10300000 1.0 + H H144 1 0.50550000 0.39600000 0.14690000 1.0 + H H145 1 0.66530000 0.95160000 0.56880000 1.0 + H H146 1 0.11330000 0.53300000 0.40970000 1.0 + H H147 1 0.34600000 0.13940000 0.77880000 1.0 + H H148 1 0.64040000 0.43560000 0.92900000 1.0 + H H149 1 0.55480000 0.43980000 0.72500000 1.0 + H H150 1 0.51170000 0.53460000 0.65000000 1.0 + H H151 1 0.46540000 0.33100000 0.03980000 1.0 + C C152 1 0.64490000 0.71570000 0.31244000 1.0 + C C153 1 0.45300000 0.14390000 0.40560000 1.0 + C C154 1 0.79000000 0.73590000 0.53510000 1.0 + C C155 1 0.74770000 0.72410000 0.60801000 1.0 + C C156 1 0.86550000 0.70780000 0.69926000 1.0 + C C157 1 0.72760000 0.81400000 0.29920000 1.0 + C C158 1 0.76890000 0.72570000 0.39779000 1.0 + C C159 1 0.89920000 0.63080000 0.68102000 1.0 + C C160 1 0.11250000 0.79580000 0.73430000 1.0 + C C161 1 0.17590000 0.85130000 0.71050000 1.0 + C C162 1 0.18500000 0.36310000 0.79520000 1.0 + C C163 1 0.40270000 0.54490000 0.89800000 1.0 + C C164 1 0.47360000 0.66740000 0.09730000 1.0 + C C165 1 0.30000000 0.95120000 0.67580000 1.0 + C C166 1 0.38590000 0.03060000 0.60120000 1.0 + C C167 1 0.86890000 0.57580000 0.63100000 1.0 + C C168 1 0.24480000 0.97350000 0.73000000 1.0 + C C169 1 0.47600000 0.11340000 0.53830000 1.0 + C C170 1 0.72910000 0.74000000 0.47241000 1.0 + C C171 1 0.31520000 0.46110000 0.82340000 1.0 + C C172 1 0.60500000 0.64300000 0.33119000 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N360 1 0.11170000 0.74076000 0.23853000 1.0 + N N361 1 0.39869000 0.74824000 0.74682000 1.0 + N N362 1 0.20018000 0.25581000 0.32783000 1.0 + N N363 1 0.28462000 0.25233000 0.66326000 1.0 + N N364 1 0.03364000 0.38405000 0.27827000 1.0 + N N365 1 0.46630000 0.36715000 0.70513000 1.0 + N N366 1 0.38830000 0.24076000 0.73853000 1.0 + N N367 1 0.10131000 0.24824000 0.24682000 1.0 + O O368 1 0.51630000 0.18637000 0.40457000 1.0 + O O369 1 0.36644000 0.00044000 0.66821000 1.0 + O O370 1 0.40861000 0.13614000 0.34937000 1.0 + O O371 1 0.07397000 0.81035000 0.79354000 1.0 + O O372 1 0.38245000 0.50975000 0.83038000 1.0 + O O373 1 0.09910000 0.73530000 0.69737000 1.0 + O O374 1 0.52720000 0.71810000 0.09891000 1.0 + O O375 1 0.43500000 0.65171000 0.15544000 1.0 + 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 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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", 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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 @@ +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 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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", 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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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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 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"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", 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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 @@ 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+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, 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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", 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-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 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<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