def test_parity_method(id_1, id_2, score):
c1 = ccd_reader.read_pdb_cif_file(cif_filename(id_1)).component
c2 = ccd_reader.read_pdb_cif_file(cif_filename(id_2)).component
parity = compare_molecules(c1.mol, c2.mol)
assert round(parity.similarity_score, 2) == score
def test_scaffold_absent(ccd_id):
component = ccd_reader.read_pdb_cif_file(
cif_filename(ccd_id)).component
result = component.get_scaffolds()
assert result[0].GetNumAtoms() == 0
assert not component.scaffolds
def component(request):
reader = ccd_reader.read_pdb_cif_file(request.param)
c = reader.component
if c.id not in problematic_ids:
assert reader.warnings == []
return c
def test_unichem_download(het_code):
c = ccd_reader.read_pdb_cif_file(cif_filename(het_code)).component
c.fetch_external_mappings()
assert len(c.external_mappings) > 0
c.fetch_external_mappings(True)
assert len(c.external_mappings) > 0
def test_scaffold_present(ccd_id, smiles):
component = ccd_reader.read_pdb_cif_file(
cif_filename(ccd_id)).component
result = component.get_scaffolds()
mol = result[0]
assert Chem.MolToSmiles(mol) == smiles
assert component.scaffolds
assert component.scaffolds[0].smiles == smiles
def test_components_layouts_downloaded(tmpdir, het_code):
dl = PubChemDownloader(tmpdir)
to_download = os.path.join(tmpdir, f'{het_code}.sdf')
comp = ccd_reader.read_pdb_cif_file(cif_filename(het_code)).component
dl.process_template(comp)
assert os.path.isfile(to_download)
assert os.path.getsize(to_download) > 0
assert comp.mol_no_h.HasSubstructMatch(
Chem.MolFromMolFile(to_download, sanitize=True))
def update_ccd_dir(self, components: str):
"""Update 2D images of PDBeChem components which are available
in the pubchem database
Args:
components (str): Path to the directory with components in
.cif format
"""
for f in os.listdir(components):
c = ccd_reader.read_pdb_cif_file(os.path.join(components, f)).component
self.process_template(c)
def test_valid_properties(key):
physchem_props = ccd_reader.read_pdb_cif_file(
cif_filename(key)).component.physchem_properties
assert test_inputs[key]["logp"] == round(
physchem_props["CrippenClogP"], 3)
assert test_inputs[key]["heavy_atom_count"] == physchem_props[
"NumHeavyAtoms"]
assert test_inputs[key]["numH_acceptors"] == physchem_props["NumHBA"]
assert test_inputs[key]["numH_donors"] == physchem_props["NumHBD"]
assert (test_inputs[key]["num_rotable_bonds"] ==
physchem_props["NumRotatableBonds"])
assert test_inputs[key]["rings_count"] == physchem_props["NumRings"]
assert test_inputs[key]["TPSA"] == round(physchem_props["tpsa"], 3)
assert test_inputs[key]["molwt"] == round(physchem_props["exactmw"], 3)
def component_eoh():
"""
loads PDB-CCD for ethanol eoh.cif and returns the
component object
Returns:
pdbeccdutils.core.component.Component: component object for
eoh.cif
"""
cif_file = cif_filename('EOH')
reader = ccd_reader.read_pdb_cif_file(cif_file)
assert reader.warnings == []
assert reader.errors == []
component = reader.component
return component
def test_invalid_properties(key):
physchem_props = ccd_reader.read_pdb_cif_file(
cif_filename(key)).component.physchem_properties
assert physchem_props == {}
def load_molecule(id_):
c = ccd_reader.read_pdb_cif_file(cif_filename(id_)).component
c.compute_2d(depictions)
return c
def test_scaffolds(scaffold_type):
c = ccd_reader.read_pdb_cif_file(cif_filename("NAG")).component
c.get_scaffolds(scaffold_type)
assert len(c.scaffolds) > 0
