def get_ani_mol(coordinates, species, smiles):
""" Given smiles string and list of elements as reference,
get the RDKit mol with xyz.
"""
mol = oechem.OEGraphMol()
for symbol in species:
mol.NewAtom(getattr(oechem, 'OEElemNo_' + symbol))
mol.SetCoords(coordinates.reshape([-1]))
mol.SetDimension(3)
oechem.OEDetermineConnectivity(mol)
oechem.OEFindRingAtomsAndBonds(mol)
oechem.OEPerceiveBondOrders(mol)
smiles_can = oechem.OECreateCanSmiString(mol)
ims = oechem.oemolistream()
ims.SetFormat(oechem.OEFormat_SMI)
ims.openstring(smiles)
mol_ref = next(ims.GetOEMols())
smiles_ref = oechem.OECreateCanSmiString(mol_ref)
assert smiles_can == smiles_ref
g = hgfp.graph.from_oemol(mol, use_fp=True)
return g, mol
def descriptorToMol(self,
descr,
descrType,
limitPerceptions=False,
messageTag=None):
"""Parse the input descriptor string and return a molecule object (OeGraphMol/OeQMol).
Args:
descr (str): descriptor
descrType (str): descriptor type
limitPerceptions (bool): flag to limit the perceptions/transformations of input descriptor
messageTag (srt, optional): prefix string for error messages. Defaults to None.
Returns:
object: OeGraphMol()/OeQmol() object or None for failure
ifs.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_Default | oechem.OEIFlavor_PDB_DATA | oechem.OEIFlavor_PDB_ALTLOC) # noq
"""
try:
if "SMILES" in descrType.upper() and "ISO" in descrType.upper():
oeMol = self.smilesToMol(descr,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
if oeMol:
isoSmiles = oechem.OECreateIsoSmiString(oeMol)
return self.smilesToMol(isoSmiles,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
else:
return None
if "SMILES" in descrType.upper():
oeMol = self.smilesToMol(descr,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
if oeMol:
smiles = oechem.OECreateCanSmiString(oeMol)
return self.smilesToMol(smiles,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
else:
return None
elif "INCHI" in descrType.upper():
oeMol = self.inchiToMol(descr,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
if oeMol:
isoSmiles = oechem.OECreateIsoSmiString(oeMol)
return self.smilesToMol(isoSmiles,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
elif "SMARTS" in descrType.upper():
return self.smartsToQmol(descr, messageTag=messageTag)
else:
return None
except Exception as e:
logger.exception("Failing with %s", str(e))
return None
def __makeChemCompDescriptorCategory(self, ccId, oeMol):
"""
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
ARG SMILES ACDLabs 10.04 "O=C(O)C(N)CCCNC(=[NH2+])N"
ARG SMILES_CANONICAL CACTVS 3.341 "N[C@@H](CCCNC(N)=[NH2+])C(O)=O"
ARG SMILES CACTVS 3.341 "N[CH](CCCNC(N)=[NH2+])C(O)=O"
ARG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N"
ARG SMILES "OpenEye OEToolkits" 1.5.0 "C(CC(C(=O)O)N)CNC(=[NH2+])N"
ARG InChI InChI 1.03 "InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-1..... "
ARG InChIKey InChI 1.03 ODKSFYDXXFIFQN-BYPYZUCNSA-O
#
"""
rowL = []
#
aRow = {}
aRow["comp_id"] = ccId
aRow["type"] = "SMILES_CANONICAL"
aRow["program"] = "OpenEye OEToolkits"
aRow["program_version"] = self.__oeVersion
aRow["descriptor"] = oechem.OECreateIsoSmiString(oeMol)
rowL.append(aRow)
#
aRow = {}
aRow["comp_id"] = ccId
aRow["type"] = "SMILES"
aRow["program"] = "OpenEye OEToolkits"
aRow["program_version"] = self.__oeVersion
aRow["descriptor"] = oechem.OECreateCanSmiString(oeMol)
rowL.append(aRow)
#
aRow = {}
aRow["comp_id"] = ccId
aRow["type"] = "InChI"
aRow["program"] = "OpenEye OEToolkits"
aRow["program_version"] = self.__oeVersion
aRow["descriptor"] = oechem.OECreateInChI(oeMol)
rowL.append(aRow)
#
aRow = {}
aRow["comp_id"] = ccId
aRow["type"] = "InChIKey"
aRow["program"] = "OpenEye OEToolkits"
aRow["program_version"] = self.__oeVersion
aRow["descriptor"] = oechem.OECreateInChIKey(oeMol)
rowL.append(aRow)
#
return rowL
def serializeOe(self, oeMol):
"""Create a string representing the content of the current OE molecule. This
serialization uses the OE internal binary format.
"""
try:
oms = oechem.oemolostream()
oms.SetFormat(oechem.OEFormat_OEB)
oms.openstring()
oechem.OEWriteMolecule(oms, oeMol)
logger.debug("SMILES %s", oechem.OECreateCanSmiString(oeMol))
logger.debug("Atoms = %d", oeMol.NumAtoms())
return oms.GetString()
except Exception as e:
logger.exception("Failing with %s", str(e))
def test_atom_map(self):
"""Test get atom map"""
from openeye import oechem
tagged_smiles = '[H:5][C:1]#[N+:4][C:3]([H:9])([H:10])[C:2]([H:6])([H:7])[H:8]'
mol_1 = openeye.smiles_to_oemol('CC[N+]#C')
inf = get_fn('ethylmethylidyneamonium.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = utils.get_atom_map(tagged_smiles, mol_1)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i + 1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping - 1))
atom_2.SetAtomicNum(i + 1)
self.assertEqual(oechem.OECreateCanSmiString(mol_1),
oechem.OECreateCanSmiString(mol_2))
# Test aromatic molecule
tagged_smiles = '[H:10][c:4]1[c:3]([c:2]([c:1]([c:6]([c:5]1[H:11])[H:12])[C:7]([H:13])([H:14])[H:15])[H:8])[H:9]'
mol_1 = openeye.smiles_to_oemol('Cc1ccccc1')
inf = get_fn('toluene.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = utils.get_atom_map(tagged_smiles, mol_1)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i + 1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping - 1))
atom_2.SetAtomicNum(i + 1)
self.assertEqual(oechem.OECreateCanSmiString(mol_1),
oechem.OECreateCanSmiString(mol_2))
def get_d3rmolecule(self, source):
"""Gets D3RMolecule from `source`
"""
openeye_mol = self._get_molecule_from_openeye(source)
d3ratoms = []
for atom in openeye_mol.GetAtoms():
d3ratom = D3RAtom()
d3ratom.set_atomic_name(atom.GetName())
d3ratom.set_atomic_number(atom.GetAtomicNum())
d3ratom.set_is_hydrogen(atom.IsHydrogen())
d3ratoms.append(d3ratom)
d3rmol = D3RMolecule()
d3rmol.set_atoms(d3ratoms)
smi_str = oechem.OECreateCanSmiString(openeye_mol)
d3rmol.set_canonical_smiles_str(smi_str)
return d3rmol
def descriptorToSmiles(self,
descr,
descrType,
limitPerceptions=False,
messageTag=None):
"""Parse the input descriptor string and return an OE smiles.
Args:
descr (str): descriptor
descrType (str): descriptor type
limitPerceptions (bool): flag to limit the perceptions/transformations of input descriptor
messageTag (srt, optional): prefix string for error messages. Defaults to None.
Returns:
str: SMILES string
"""
try:
if "SMILES" in descrType.upper() and "ISO" in descrType.upper():
oeMol = self.smilesToMol(descr,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
if oeMol:
return oechem.OECreateIsoSmiString(oeMol)
else:
return None
if "SMILES" in descrType.upper():
oeMol = self.smilesToMol(descr,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
if oeMol:
return oechem.OECreateCanSmiString(oeMol)
else:
return None
elif "INCHI" in descrType.upper():
oeMol = self.inchiToMol(descr,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
if oeMol:
return oechem.OECreateIsoSmiString(oeMol)
else:
return None
except Exception as e:
logger.exception("Failing with %s", str(e))
return None
def standardizeSmiles(self, smiles, type="ISOMERIC"): # pylint: disable=redefined-builtin
""" Return a standardized SMILES (type) or None
"""
smilesOut = None
try:
mol = oechem.OEGraphMol()
if (oechem.OEParseSmiles(mol, smiles) == 1):
oechem.OEAssignAromaticFlags(mol)
if type == "CANNONICAL":
smilesOut = oechem.OECreateCanSmiString(mol)
elif type == "ISOMERIC":
smilesOut = oechem.OECreateIsoSmiString(mol)
else:
logger.error("Unable to parse input SMILES '%s'", smiles)
except Exception as e:
logger.exception("Error '%s' occured. Arguments %s.", str(e), e.args)
return smilesOut
def deserializeOe(self, oeS):
"""Reconstruct an OE molecule from the input string serialization (OE binary).
The deserialized molecule is used to initialize the internal OE molecule
within this object.
Returns:
list: OE GraphMol list
"""
molList = []
try:
ims = oechem.oemolistream()
ims.SetFormat(oechem.OEFormat_OEB)
ims.openstring(oeS)
for mol in ims.GetOEGraphMols():
logger.debug("SMILES %s", oechem.OECreateCanSmiString(mol))
logger.debug("title %s", mol.GetTitle())
logger.debug("atoms %d", mol.NumAtoms())
molList.append(oechem.OEGraphMol(mol))
except Exception as e:
logger.exception("Failing with %s", str(e))
return molList
def PerceiveAromaticity(mol, modelname, aromodel):
oechem.OEAssignAromaticFlags(mol, aromodel)
cansmi = oechem.OECreateCanSmiString(mol)
print(modelname, ":", cansmi)
def smiles(self):
"""
Returns a SMILES string for this structure.
"""
return oechem.OECreateCanSmiString(self._struc)
topology.setPeriodicBoxVectors(system.getDefaultPeriodicBoxVectors())
ifs = oechem.oemolistream()
ifs.open(ligand_filename)
# get the list of molecules
mol_list = [oechem.OEMol(mol) for mol in ifs.GetOEMols()]
for idx, mol in enumerate(mol_list):
mol.SetTitle("MOL{}".format(idx))
oechem.OETriposAtomNames(mol)
initial_mol = mol_list[initial_ligand]
proposal_mol = mol_list[proposal_ligand]
proposal_smiles = SmallMoleculeSetProposalEngine.canonicalize_smiles(
oechem.OECreateCanSmiString(proposal_mol))
current_smiles = SmallMoleculeSetProposalEngine.canonicalize_smiles(
oechem.OECreateCanSmiString(initial_mol))
barostat = openmm.MonteCarloBarostat(1.0 * unit.atmosphere, temperature,
50)
system_generator = SystemGenerator(
[
'amber14/protein.ff14SB.xml', 'gaff.xml', 'amber14/tip3p.xml',
'MCL1_ligands.xml'
],
barostat=barostat,
forcefield_kwargs={
'nonbondedMethod': app.PME,
'constraints': app.HBonds,
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
import sys
mol = oechem.OEGraphMol()
for smi in sys.stdin:
mol.Clear()
smi = smi.strip()
if oechem.OEParseSmiles(mol, smi):
oechem.OEAssignAromaticFlags(mol)
print(oechem.OECreateCanSmiString(mol))
else:
oechem.OEThrow.Warning("%s is an invalid SMILES!" % smi)
# @ </SNIPPET>
#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
mol = oechem.OEGraphMol()
oechem.OEParseSmiles(mol, "n1ccncc1")
print("Canonical smiles :", oechem.OECreateCanSmiString(mol))
oechem.OEClearAromaticFlags(mol)
oechem.OEKekulize(mol)
print("Kekule smiles :", oechem.OECreateCanSmiString(mol))
# @ </SNIPPET>
def infer_mol_from_coordinates(
coordinates,
species,
smiles_ref=None,
coordinates_unit="angstrom",
):
# local import
from openeye import oechem
from simtk import unit
from simtk.unit import Quantity
if isinstance(coordinates_unit, str):
coordinates_unit = getattr(unit, coordinates_unit)
# make sure we have the coordinates
# in the unit system
coordinates = Quantity(coordinates, coordinates_unit).value_in_unit(
unit.angstrom # to make openeye happy
)
# initialize molecule
mol = oechem.OEGraphMol()
if all(isinstance(symbol, str) for symbol in species):
[
mol.NewAtom(getattr(oechem, "OEElemNo_" + symbol))
for symbol in species
]
elif all(isinstance(symbol, int) for symbol in species):
[
mol.NewAtom(
getattr(oechem,
"OEElemNo_" + oechem.OEGetAtomicSymbol(symbol)))
for symbol in species
]
else:
raise RuntimeError(
"The species can only be all strings or all integers.")
mol.SetCoords(coordinates.reshape([-1]))
mol.SetDimension(3)
oechem.OEDetermineConnectivity(mol)
oechem.OEFindRingAtomsAndBonds(mol)
oechem.OEPerceiveBondOrders(mol)
if smiles_ref is not None:
smiles_can = oechem.OECreateCanSmiString(mol)
ims = oechem.oemolistream()
ims.SetFormat(oechem.OEFormat_SMI)
ims.openstring(smiles_ref)
mol_ref = next(ims.GetOEMols())
smiles_ref = oechem.OECreateCanSmiString(mol_ref)
assert (smiles_ref == smiles_can
), "SMILES different. Input is %s, ref is %s" % (
smiles_can,
smiles_ref,
)
from openff.toolkit.topology import Molecule
_mol = Molecule.from_openeye(mol, allow_undefined_stereo=True)
g = esp.Graph(_mol)
return g
topology = topology.to_openmm()
topology.setPeriodicBoxVectors(system.getDefaultPeriodicBoxVectors())
ifs = oechem.oemolistream()
ifs.open(ligand_filename)
# get the list of molecules
mol_list = [oechem.OEMol(mol) for mol in ifs.GetOEMols()]
for idx, mol in enumerate(mol_list):
mol.SetTitle("MOL{}".format(idx))
oechem.OETriposAtomNames(mol)
initial_mol = mol_list[initial_ligand]
proposal_mol = mol_list[proposal_ligand]
proposal_smiles = SmallMoleculeSetProposalEngine.canonicalize_smiles(oechem.OECreateCanSmiString(proposal_mol))
current_smiles = SmallMoleculeSetProposalEngine.canonicalize_smiles(oechem.OECreateCanSmiString(initial_mol))
barostat = openmm.MonteCarloBarostat(1.0*unit.atmosphere, temperature, 50)
system_generator = SystemGenerator(['amber14/protein.ff14SB.xml', 'gaff.xml', 'amber14/tip3p.xml', 'MCL1_ligands.xml'], barostat=barostat, forcefield_kwargs={'constraints': app.HBonds,
'hydrogenMass': 4 * unit.amus}, periodic_forcefield_kwargs={'nonbondedMethod': app.PME} use_antechamber=False)
atom_mapper_filename = os.path.join(setup_directory, "{}_atom_mapper.json".format(project_prefix))
with open(atom_mapper_filename, 'r') as infile:
atom_mapper = SmallMoleculeAtomMapper.from_json(infile.read())
proposal_engine = PremappedSmallMoleculeSetProposalEngine(atom_mapper, system_generator)
topology_proposal = proposal_engine.propose(system, topology, current_smiles=current_smiles, proposed_mol=proposal_mol, map_index=map_index)
