def __init__(self,
path: str,
multiconf: bool = True,
nr_mols: int = -1,
properties: list = None):
"""
:param path:
:param multiconf:
:param nr_mols:
:param properties: List of properties to be read from SDF file. Returns None if not found. Internally adds ' <'
and '>' before and after the property names in order to comply with the toolkit.
"""
self.r = Chem.FileSDFMoleculeReader(path)
self.multiconf = multiconf
self.nr_mols = nr_mols
self.nr_samples = None
self.properties = set([" <" + p + ">" for p in properties
]) if properties is not None else None
Chem.setMultiConfImportParameter(self.r, multiconf)
if multiconf:
Chem.setMultiConfInputProcessorParameter(
self.r,
Chem.DefaultMultiConfMoleculeInputProcessor(
False,
Chem.AtomPropertyFlag.TYPE | Chem.AtomPropertyFlag.ISOTOPE
| Chem.AtomPropertyFlag.FORMAL_CHARGE,
Chem.BondPropertyFlag.ORDER))
self._gen = iter(self)
def process():
if len(sys.argv) < 4:
print(
'Usage:',
sys.argv[0],
'[input torsion rules.xml] [structures.sdf] [output torsion histogram library.sdf]',
file=sys.stderr)
sys.exit(2)
tor_lib = ConfGen.TorsionLibrary()
try:
tor_lib.load(Base.FileIOStream(sys.argv[1], 'r'))
except:
print('Error while loading input torsion rules:',
sys.exc_info()[0],
file=sys.stderr)
sys.exit(2)
tor_matcher = ConfGen.TorsionRuleMatcher(tor_lib)
tor_matcher.findAllRuleMappings(True)
tor_matcher.findUniqueMappingsOnly(True)
tor_matcher.stopAtFirstMatchingRule(True)
mol = Chem.BasicMolecule()
mol_reader = Chem.FileSDFMoleculeReader(sys.argv[2])
Chem.setMultiConfImportParameter(mol_reader, False)
print('- Analyzing input structures...', file=sys.stderr)
i = 1
rule_to_angle_hists = {}
coords = Math.Vector3DArray()
while True:
try:
if not mol_reader.read(mol):
break
except IOError as e:
print('Error while reading input molecule',
i,
':',
e,
file=sys.stderr)
i += 1
continue
if i % 500 == 0:
print(' ... At input molecule', i, '...', file=sys.stderr)
Chem.initSubstructureSearchTarget(mol, False)
try:
Chem.get3DCoordinates(mol, coords)
except Base.ItemNotFound:
print('Could not get 3D-coordinates for molecule',
i,
file=sys.stderr)
i += 1
continue
for bond in mol.bonds:
if Chem.getRingFlag(bond):
continue
if Chem.isHydrogenBond(bond):
continue
if Chem.getExplicitBondCount(
bond.getBegin()) <= 1 or Chem.getExplicitBondCount(
bond.getEnd()) <= 1:
continue
tor_matcher.findMatches(bond, mol, False)
for match in tor_matcher:
processMatch(i, match, mol, coords, rule_to_angle_hists)
i += 1
print('- Processing torsion angle histograms...', file=sys.stderr)
processHistograms(tor_lib, rule_to_angle_hists)
print('- Writing output torsion library...', file=sys.stderr)
try:
tor_lib.save(Base.FileIOStream(sys.argv[3], 'w+'))
except:
print('Error while writing torsion library:',
sys.exc_info()[0],
file=sys.stderr)
sys.exit(2)
print('DONE!', file=sys.stderr)