Removed unused files incl. the older bio3d R script; Ruff formatting

JHKru · Sep 23, 2024 · d5ab251 · d5ab251
1 parent 6ba376e
commit d5ab251
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Showing 8 changed files with 26 additions and 14,271 deletions.
diff --git a/1l2y.pdb b/1l2y.pdb
diff --git a/7cal.pdb b/7cal.pdb
diff --git a/README.rst b/README.rst
@@ -41,6 +41,13 @@ via *pip*:
    $ git clone https://github.com/biotite-dev/springcraft.git
    $ pip install ./springcraft
 
+A development conda environment with all required dependencies for testing
+can be installed from `environment.yml`
+
+Scripts to generate reference files for tests are stored in tests/data; 
+a separate environment to rerun these locally can be found in `test_create_data_env.yml`.
+BioPhysConnectoR has to be installed separately. 
+
 Example
 =======
 

diff --git a/test_create_data_env.yaml → test_create_data_env.yml b/test_create_data_env.yaml → test_create_data_env.yml
diff --git a/tests/data/hessian_calpha_sdENM_pfENM_bio3d.R b/tests/data/hessian_calpha_sdENM_pfENM_bio3d.R
diff --git a/tests/data/test_data_prep_prody_bio3d.py b/tests/data/test_data_prep_prody_bio3d.py
@@ -17,13 +17,11 @@
 FETCH_PDB_IDS = ["1l2y", "7cal"]
 
 for pdb_fetch_id in FETCH_PDB_IDS:
-    in_pdb = pdb.PDBFile.read(
-        rcsb.fetch(pdb_fetch_id, format="pdb", overwrite=True)
-    )
+    in_pdb = pdb.PDBFile.read(rcsb.fetch(pdb_fetch_id, format="pdb", overwrite=True))
     in_struc = in_pdb.get_structure(model=1)
     # NOTE: Deprecated filter function -> Older Biotite version
     protein = in_struc[struc.filter_amino_acids(in_struc)]
-    
+
     outpdb = pdb.PDBFile()
     pdb.set_structure(outpdb, protein)
     outpdb.write(pdb_fetch_id + ".pdb")
@@ -33,6 +31,7 @@
 # Sequence funtion in R
 r_seq = robjects.r["seq"]
 
+
 # Convert AtomArray into bio3d-PDB objects
 def aarray_to_bio3d(aarray):
     coords = aarray.coord
@@ -98,6 +97,7 @@ def aarray_to_bio3d(aarray):
 
     return pdb_bio3d
 
+
 ## Test data-generating functions
 # -> Enforce consistent naming of output .csv
 def prody_enm_nma(enm_type, structure_path, cutoff_list, output_markers="all"):
@@ -216,10 +216,7 @@ def bio3d_anm_nma(structure_path, bio3d_ff, output_markers="all"):
     # Structure I/O w. biotite
     in_struc = bstio.load_structure(structure_path, model=1)
     ca = in_struc[
-        (
-            (struc.filter_canonical_amino_acids(in_struc))
-            & (in_struc.atom_name == "CA")
-        )
+        ((struc.filter_canonical_amino_acids(in_struc)) & (in_struc.atom_name == "CA"))
     ]
 
     for o in outputs:

diff --git a/tests/test_anm.py b/tests/test_anm.py
@@ -56,9 +56,7 @@ def test_mass_weights_simple():
     assert not np.allclose(different_anm.hessian, ref_anm.hessian)
 
 
-@pytest.mark.parametrize(
-        "file_path", glob.glob(join(data_dir(), "*.pdb"))
-)
+@pytest.mark.parametrize("file_path", glob.glob(join(data_dir(), "*.pdb")))
 def test_compare_eigenvals_BiophysConnectoR(file_path):
     """
     Compare non-mass-weighted eigenvalues with those computed with
@@ -86,11 +84,10 @@ def test_compare_eigenvals_BiophysConnectoR(file_path):
 
 
 @pytest.mark.parametrize(
-        "file_path, ff_name", 
-        itertools.product(
-            glob.glob(join(data_dir(), "*.pdb")), 
-            ["Hinsen", "sdENM", "pfENM"]
-        )
+    "file_path, ff_name",
+    itertools.product(
+        glob.glob(join(data_dir(), "*.pdb")), ["Hinsen", "sdENM", "pfENM"]
+    ),
 )
 def test_mass_weights_eigenvals(file_path, ff_name):
     """
@@ -110,25 +107,20 @@ def test_mass_weights_eigenvals(file_path, ff_name):
     if ff_name == "sdENM":
         ff = springcraft.TabulatedForceField.sd_enm(ca)
         ff_bio3d_str = "sdenm"
-        
+
         # NOTE: Different chains are not correctly identified in bio3d
         # -> Connect single chains with modified covalent contacts
         #    in springcraft
         if struc.get_chain_count(ca) > 1:
             after_chainbreak = struc.check_res_id_continuity(ca)
-            prior_chainbreak = after_chainbreak-1
-            contact_mod_pairs = np.array(
-                [prior_chainbreak, after_chainbreak]
-            ).T
-            bonded_force_constant = 43.52*0.0083144621*300*10
+            prior_chainbreak = after_chainbreak - 1
+            contact_mod_pairs = np.array([prior_chainbreak, after_chainbreak]).T
+            bonded_force_constant = 43.52 * 0.0083144621 * 300 * 10
             ff = springcraft.PatchedForceField(
-                    ff,
-                    contact_pair_off=contact_mod_pairs,
-                    contact_pair_on=contact_mod_pairs,
-                    force_constants=np.full(
-                        len(contact_mod_pairs), 
-                        bonded_force_constant
-                    )
+                ff,
+                contact_pair_off=contact_mod_pairs,
+                contact_pair_on=contact_mod_pairs,
+                force_constants=np.full(len(contact_mod_pairs), bonded_force_constant),
             )
     if ff_name == "pfENM":
         ff = springcraft.ParameterFreeForceField()

diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
@@ -364,7 +364,7 @@ def test_compare_with_biophysconnector_heterogenous(atoms_singlechain, ff_name):
 
     if ff_name == "e_anm":
         ff = springcraft.TabulatedForceField.e_anm(atoms_singlechain)
-        ref_file = "biophysconnector_anm_eanm_hessian_1l2y.csv.gz" 
+        ref_file = "biophysconnector_anm_eanm_hessian_1l2y.csv.gz"
     if ff_name == "e_anm_mj":
         ff = springcraft.TabulatedForceField.e_anm_mj(atoms_singlechain)
         ref_file = "biophysconnector_anm_eanm_mj_hessian_1l2y.csv"