def set_aromaticity_mdl(self):
"""
Sets the aromaticity flags in this molecule to use the MDL model
"""
oechem.OEClearAromaticFlags(self.mol)
oechem.OEAssignAromaticFlags(self.mol, oechem.OEAroModel_MDL)
oechem.OEAssignHybridization(self.mol)
def createOEMolFromSDF(sdf_filename, index=0):
"""
Load an SDF file into an OEMol. Since SDF files can contain multiple molecules, an index can be provided as well.
Parameters
----------
sdf_filename : str
The name of the SDF file
index : int, default 0
The index of the molecule in the SDF file
Returns
-------
mol : openeye.oechem.OEMol object
The loaded oemol object
"""
#TODO this needs a test
ifs = oechem.oemolistream()
ifs.open(sdf_filename)
# get the list of molecules
mol_list = [oechem.OEMol(mol) for mol in ifs.GetOEMols()]
# we'll always take the first for now
# Assign aromaticity and hydrogens.
for molecule in mol_list:
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
oechem.OEAssignHybridization(molecule)
oechem.OEAddExplicitHydrogens(molecule)
mol_to_return = mol_list[index]
return mol_to_return
def smiles_to_oemol(smiles, title='MOL', max_confs=1):
"""
Generate an oemol from a SMILES string
Parameters
----------
smiles : str
SMILES string of molecule
title : str, default 'MOL'
title of OEMol molecule
max_confs : int, default 1
maximum number of conformers to generate
Returns
-------
molecule : openeye.oechem.OEMol
OEMol object of the molecule
"""
from openeye import oeomega
# Create molecule
molecule = oechem.OEMol()
oechem.OESmilesToMol(molecule, smiles)
# create unique atom names
if len([atom.GetName() for atom in molecule.GetAtoms()]) > len(
set([atom.GetName() for atom in molecule.GetAtoms()])):
# the atom names are not unique
molecule = generate_unique_atom_names(molecule)
else:
pass
# Set title.
molecule.SetTitle(title)
# Assign aromaticity and hydrogens.
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
oechem.OEAssignHybridization(molecule)
oechem.OEAddExplicitHydrogens(molecule)
oechem.OEPerceiveChiral(molecule)
# Create atom names.
oechem.OETriposAtomNames(molecule)
oechem.OETriposBondTypeNames(molecule)
# perceive chirality before attempting omega geometry proposal
assert oechem.OEPerceiveChiral(molecule), f"chirality perception failed"
# Assign geometry
omega = oeomega.OEOmega()
omega.SetMaxConfs(max_confs)
omega.SetIncludeInput(False)
omega.SetStrictStereo(True)
omega(molecule)
return molecule
def createOEMolFromSDF(sdf_filename,
index=0,
add_hydrogens=True,
allow_undefined_stereo=False):
"""
# TODO change this to return a list of all the mols if required
Load an SDF file into an OEMol. Since SDF files can contain multiple
molecules, an index can be provided as well.
Parameters
----------
sdf_filename : str
The name of the SDF file
index : int, default 0
The index of the molecule in the SDF file
allow_undefined_stereo : bool, default=False
wether to skip stereo perception
Returns
-------
mol : openeye.oechem.OEMol object
The loaded oemol object
"""
# TODO this needs a test
ifs = oechem.oemolistream()
ifs.open(sdf_filename)
# get the list of molecules
mol_list = [oechem.OEMol(mol) for mol in ifs.GetOEMols()]
# we'll always take the first for now
# pick out molecule of interest
molecule = mol_list[index]
# Generate unique atom names
if len([atom.GetName() for atom in molecule.GetAtoms()]) > len(
set([atom.GetName() for atom in molecule.GetAtoms()])):
molecule = generate_unique_atom_names(molecule)
# Assign aromaticity and hydrogens.
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
oechem.OEAssignHybridization(molecule)
if add_hydrogens:
oechem.OEAddExplicitHydrogens(molecule)
oechem.OEPerceiveChiral(molecule)
# perceive chirality
if not allow_undefined_stereo:
assert oechem.OE3DToInternalStereo(
molecule
), f"the stereochemistry perception from 3D coordinates failed"
assert not has_undefined_stereocenters(
molecule), f"there is an atom with an undefined stereochemistry"
return molecule
def _process_mol(mol: oechem.OEMol, explicit_H: Optional[str] = None):
if explicit_H == 'all':
oechem.OEAddExplicitHydrogens(mol)
elif explicit_H == 'polar':
oechem.OESuppressHydrogens(mol, explicit_H)
elif explicit_H is None:
oechem.OESuppressHydrogens(mol)
else:
raise ValueError
oechem.OEAssignAromaticFlags(mol)
oechem.OEAssignHybridization(mol)
oechem.OEAssignFormalCharges(mol)
mol.Sweep()
def get_sf_elements(mol):
sfObj = SymmetryFunction()
oechem.OEAssignFormalCharges(mol)
oechem.OEAssignHybridization(mol)
rsf, asf = sfObj.CalculateSymmetryFunction(mol)
tsf1 = sfObj.CalculateTorsionSymmetryFunction(mol, 1)
tsf2 = sfObj.CalculateTorsionSymmetryFunction(mol, 2)
tsf = []
for elem1, elem2 in zip(tsf1, tsf2):
tsf.append(elem1 + elem2)
sf_elements = rsf
sf_elements.extend(asf)
sf_elements.extend(tsf)
return sf_elements
def generate_initial_molecule(mol_smiles):
"""
Generate an oemol with a geometry
"""
import openeye.oechem as oechem
import openeye.oeomega as oeomega
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, mol_smiles)
mol.SetTitle("MOL")
# Assign aromaticity and hydrogens and hybridization.
oechem.OEAddExplicitHydrogens(mol)
oechem.OEAssignAromaticFlags(mol, oechem.OEAroModelOpenEye)
oechem.OEAssignHybridization(mol)
oechem.OETriposAtomNames(mol)
oechem.OETriposBondTypeNames(mol)
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega(mol)
return mol
def iupac_to_oemol(iupac, title='MOL', max_confs=1):
"""
Generate an oemol from an IUPAC name
Parameters
----------
iupac : str
iupac name of molecule
title : str, default 'MOL'
title of OEMol molecule
max_confs : int, default 1
maximum number of conformers to generate
Returns
-------
molecule : openeye.oechem.OEMol
OEMol object of the molecule
"""
from openeye import oeiupac, oeomega
# Create molecule
molecule = oechem.OEMol()
oeiupac.OEParseIUPACName(molecule, iupac)
# Set title.
molecule.SetTitle(title)
# Assign aromaticity and hydrogens.
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
oechem.OEAssignHybridization(molecule)
oechem.OEAddExplicitHydrogens(molecule)
oechem.OEPerceiveChiral(molecule)
# Create atom names.
oechem.OETriposAtomNames(molecule)
oechem.OETriposBondTypeNames(molecule)
# Assign geometry
omega = oeomega.OEOmega()
omega.SetMaxConfs(max_confs)
omega.SetIncludeInput(False)
omega.SetStrictStereo(True)
omega(molecule)
return molecule
def smiles_to_oemol(smiles, title='MOL',max_confs=1):
"""
Generate an oemol from a SMILES string
Parameters
----------
smiles : str
SMILES string of molecule
title : str, default 'MOL'
title of OEMol molecule
max_confs : int, default 1
maximum number of conformers to generate
Returns
-------
molecule : openeye.oechem.OEMol
OEMol object of the molecule
"""
from openeye import oeiupac, oeomega
# Create molecule
molecule = oechem.OEMol()
oechem.OESmilesToMol(molecule, smiles)
# Set title.
molecule.SetTitle(title)
# Assign aromaticity and hydrogens.
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
oechem.OEAssignHybridization(molecule)
oechem.OEAddExplicitHydrogens(molecule)
# Create atom names.
oechem.OETriposAtomNames(molecule)
# Assign geometry
omega = oeomega.OEOmega()
omega.SetMaxConfs(max_confs)
omega.SetIncludeInput(False)
omega.SetStrictStereo(True)
omega(molecule)
return molecule
def addCoordFiles(self, *coordFiles):
# print(f'\n\033[1m Read Coordinate files... \033[0m')
if len(coordFiles) == 0:
print(
'Skip this molecule? Empty molecule object will be created since no conformers is provided.'
)
self.mols.append(oechem.OEMol())
self.atomids.append([])
self.elems.append([])
self.resnames.append([])
self.atomnames.append([])
self.resnumbers.append([])
self.listofpolars.append([])
self.listofburieds.append([])
xyzs = []
self.nmols.append(len(xyzs))
indices = []
charge = 0
number = len(self.elems)
resname = 'mol%d' % (number)
chargeinfo = [[indices, resname, charge]]
self.listofchargeinfo.append(chargeinfo)
else:
xyzs = []
listofoemol = []
firstconf = True
for coordFile in coordFiles:
fbmol = Molecule(coordFile)
xyz = fbmol.xyzs[0]
xyz = np.array(xyz) / bohr2Ang
xyzs.append(xyz)
# Making oemol using openeye toolkit : for atomID(?), equivGroup and listofpolar
ifs = oechem.oemolistream(coordFile)
oemol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, oemol)
listofoemol.append(oemol)
oechem.OEPerceiveSymmetry(oemol)
if firstconf == True:
firstconf = False
atomicNum = []
elem = fbmol.elem
if 'resid' not in list(fbmol.Data.keys()):
print(
' - Are you using xyz file? Default resid, resname, atomname will be assigned.'
)
resnumber = [1 for i in elem]
resname = list('MOL' for i in elem)
atomname = [
'%s%d' % (i, idx + 1) for idx, i in enumerate(elem)
]
else:
resnumber = fbmol.resid
resname = fbmol.resname
atomname = fbmol.atomname
for elm in elem:
atomicNum.append(
list(PeriodicTable.keys()).index(elm) + 1)
atomid = []
if len(self.atomidinfo) == 0:
atmid = 1
else:
atmid = max(list(self.atomidinfo.keys())) + 1
# if resname is 'MOL', assign resname to be moli
if resname == list('MOL' for i in elem):
fnm = Path(coordFile).stem
newresname = fnm.split('_')[0]
print(
' - Is this file generated from esp_generator? The residue name is MOL, which is a default residue name for small organic molecule.'
)
print(
' It reassigns the residue name to %s not to confuse with other molecules while forcing symmetry.'
% newresname)
resname = list(newresname for i in elem)
num = 1
for res, atom in zip(resname, elem):
val = {
'resname': res,
'atomname': '%s%d' % (atom, num)
}
atomid.append(atmid)
self.atomidinfo[atmid] = [val]
atmid += 1
num += 1
else:
for res, atom in zip(resname, atomname):
val = {'resname': res, 'atomname': atom}
if len(self.atomidinfo) == 0:
atomid.append(atmid)
self.atomidinfo[atmid] = [val]
atmid += 1
elif any(val in v
for v in list(self.atomidinfo.values())):
for k, v in self.atomidinfo.items():
if val in v:
atomid.append(int(k))
else:
atomid.append(atmid)
self.atomidinfo[atmid] = [val]
atmid += 1
# Using openeye tool, make listofpolar,
symmetryClass = []
listofpolar = []
listofburied = []
oechem.OEAssignHybridization(oemol)
for atom in oemol.GetAtoms():
symmetryClass.append(atom.GetSymmetryClass())
if atom.IsCarbon() and int(atom.GetHyb()) != 3:
listofpolar.append(atom.GetIdx())
if len([bond for bond in atom.GetBonds()]) > 3:
listofburied.append(atom.GetIdx())
# ispolar = False
# for bond in atom.GetBonds():
# atom2 = bond.GetNbr(atom)
# if bond.GetOrder() == 1 and ispolar == False:
# continue
# else:
# ispolar = True
# break
# if ispolar == True:
# listofpolar.append(atom.GetIdx())
for atom in oemol.GetAtoms():
if atom.IsHydrogen():
for bond in atom.GetBonds():
atom2 = bond.GetNbr(atom)
if atom2.IsPolar():
listofpolar.append(atom.GetIdx())
elif atom2.IsCarbon() and atom2.GetIdx(
) in listofpolar:
listofpolar.append(atom.GetIdx())
if atom2.GetIdx() in listofburied:
listofburied.append(
atom.GetIdx()
) # store hydrogens bonded to buried atoms
if atom.IsPolar():
listofpolar.append(atom.GetIdx())
listofpolar = sorted(set(listofpolar))
listofburied = sorted(set(listofburied))
idxof1statm, resnameof1statm = self.getidxof1statm(
resnumber, resname)
unique_resid = set(resnameof1statm)
sameresid = [[
i for i, v in enumerate(resnameof1statm) if v == value
] for value in unique_resid]
sameresid.sort()
#sameresid = self.removeSingleElemList(sameresid)
idxof1statm.append(len(resnumber))
equiv_ids = []
#print('symmetryClass', symmetryClass)
#print('sameresid', sameresid)
for equivresidgroup in sameresid:
resnum = equivresidgroup[0]
listofsym = symmetryClass[
idxof1statm[resnum]:idxof1statm[resnum + 1]]
#print(listofsym)
unique_sym = set(listofsym)
equiv_sym = [[
i + idxof1statm[resnum]
for i, v in enumerate(listofsym) if v == value
] for value in unique_sym]
equiv_sym = self.removeSingleElemList(equiv_sym)
#print('equiv_sym', equiv_sym)
# change index to ID
equiv_ID = []
for lst in equiv_sym:
newlist = []
for item in lst:
newlist.append(atomid[item])
equiv_ID.append(newlist)
for i in equiv_ID:
i.sort()
equiv_ids.append(i) # weird:\
needtoremove = []
for idx, equiv_id in enumerate(equiv_ids):
if len(set(equiv_id)) == 1:
needtoremove.append(idx)
needtoremove.sort(reverse=True)
for i in needtoremove:
del equiv_ids[i]
if self.inp is not None:
list_of_new_equiv_atoms = self.convert_equiv_atoms(
self.inp.equiv_atoms, self.atomidinfo)
else:
list_of_new_equiv_atoms = []
equiv_ids_comb = []
for i in equiv_ids:
equiv_ids_comb.append(i)
for i in list_of_new_equiv_atoms:
equiv_ids_comb.append(i)
for i in equiv_ids_comb:
i.sort()
equiv_ids_comb.sort()
newatomid = atomid.copy()
newatomidinfo = copy.deepcopy(self.atomidinfo)
for equiv_id in equiv_ids_comb:
newid = equiv_id[0]
for i in equiv_id[1:]:
newatomid = [
newid if x == i else x for x in newatomid
]
for j in self.atomidinfo[i]:
newatomidinfo[newid].append(j)
del newatomidinfo[i]
# print('newatomidinfo', newatomidinfo)
# print('oldatomidinfo', self.atomidinfo)
# print('newatomid', newatomid)
# print('oldatomid', atomid)
if self.inp is not None:
# print( f' * symmetry: {self.inp.symmetry}')
if self.inp.symmetry == False:
self.atomids.append(atomid)
self.atomidinfo = self.atomidinfo
else:
self.atomids.append(newatomid)
self.atomidinfo = newatomidinfo
else:
self.atomids.append(newatomid)
self.atomidinfo = newatomidinfo
self.elems.append(atomicNum)
self.resnames.append(resname)
self.atomnames.append(atomname)
self.resnumbers.append(resnumber)
self.listofpolars.append(listofpolar)
self.listofburieds.append(listofburied)
if self.inp is not None:
chargeinfo = self.gen_chargeinfo(
self.inp.resChargeDict, newatomid, self.atomidinfo,
resnumber)
else:
indices = list(range(len(elem)))
charge = None
number = len(self.elems) + 1
resname = 'mol%d' % (number)
chargeinfo = [[indices, resname, charge]]
self.listofchargeinfo.append(chargeinfo)
self.nmols.append(len(xyzs))
for xyz in xyzs:
self.xyzs.append(xyz)
for oemol in listofoemol:
self.mols.append(oemol)
def set_aromaticity_mdl(self):
oechem.OEClearAromaticFlags(self.mol)
oechem.OEAssignAromaticFlags(self.mol, oechem.OEAroModel_MDL)
oechem.OEAssignHybridization(self.mol)
# 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.
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme
# @ <SNIPPET-ANNOTATE-ATOM-PROPERTY>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cc(N)cc(S(=O)(=O)O)c1")
oechem.OEAssignHybridization(mol)
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(350, 250, oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
disp = oedepict.OE2DMolDisplay(mol, opts)
sp2pen = oedepict.OEPen(oechem.OEWhite, oechem.OEBlueTint, oedepict.OEFill_Off,
1.5)
glyphSP2 = oegrapheme.OEAtomGlyphCircle(sp2pen, oegrapheme.OECircleStyle_Sun,
1.2)
oegrapheme.OEAddGlyph(disp, glyphSP2,
oechem.OEIsAtomHybridization(oechem.OEHybridization_sp2))
sp3pen = oedepict.OEPen(oechem.OEWhite, oechem.OEPinkTint, oedepict.OEFill_Off,
1.5)
def GetTorsions(mol):
'''
Goes through each rotatable bond in the molecule
and extracts torsion atoms (a-b-c-d)
Core torsion atoms are extended by one bond
If core or extended atoms are part of a ring,
then entire ring is kept
Keep ortho substitution
Keep functional groups that have at least one atom overlap
with the core/extended torsion atoms
Functional group inclusion criteria:
- <= 5 heavy atoms
- must contain at least one hetero atom
- non-ring
Add methyl cap if bond involving hetero atom is broken
@param mol: OEGraphMol
@type mol: OEGraphMol
@return: list[OEGraphMol]
'''
# mol = OEGraphMol(input_mol)
oechem.OEAssignHybridization(mol)
funcGrps = TorsionGenerator.GetFuncGroups(mol)
includedTorsions = oechem.OEAtomBondSet()
torsionMols = []
for atom in mol.GetAtoms():
atom.SetData("idx", atom.GetIdx() + 1)
torsions = get_canonical_torsions(mol)
if torsions is None:
torsions = oechem.OEGetTorsions(mol, oechem.OEIsRotor())
for torsion in torsions:
if torsion.a.IsHydrogen() or torsion.b.IsHydrogen() or \
torsion.c.IsHydrogen() or torsion.d.IsHydrogen():
continue
torsion_bond = mol.GetBond(torsion.b, torsion.c)
if includedTorsions.HasBond(torsion_bond):
continue
# if includedTorsions.HasAtom(torsion.b) and \
# includedTorsions.HasAtom(torsion.c):
# continue
# revert map idx to zero in original mol
for atom in mol.GetAtoms():
atom.SetMapIdx(0)
# includedTorsions.AddAtom(torsion.b)
# includedTorsions.AddAtom(torsion.c)
includedTorsions.AddBond(torsion_bond)
torsionSet = oechem.OEAtomBondSet(mol.GetBonds())
torsionSet.AddAtoms([torsion.a, torsion.b, torsion.c, torsion.d])
for atom in torsionSet.GetAtoms():
atom.SetMapIdx(1)
# extend core torsion atoms by one bond
nbrs = TorsionGenerator.GetNbrs(torsionSet)
torsionSet.AddAtoms(nbrs)
# include ring atoms
ringAtoms = TorsionGenerator.GetSameRingAtoms(mol, torsionSet)
torsionSet.AddAtoms(ringAtoms)
for atom in torsionSet.GetAtoms():
if not atom.GetMapIdx() == 1:
atom.SetMapIdx(2)
# add functional groups that overlap with torsion set
TorsionGenerator.AddFuncGroupAtoms(funcGrps, torsionSet)
# add relevant ring atoms (ortho substituents and ring H)
TorsionGenerator.AddRelevantRingAtoms(mol, torsion, torsionSet)
# special treatment for C=O
for atom in torsionSet.GetAtoms(
oechem.OEAndAtom(
oechem.OEIsOxygen(),
oechem.OEIsAtomHybridization(
oechem.OEHybridization_sp2))):
for nbr in atom.GetAtoms():
if torsionSet.HasAtom(nbr):
for nbr2 in nbr.GetAtoms(oechem.OEIsHeavy()):
if not torsionSet.HasAtom(nbr2):
nbr2.SetMapIdx(2)
torsionSet.AddAtom(nbr2)
# mark bridging atom and cap if needed
BRIDGE_ATOM_IDX = 4
TorsionGenerator.MarkBridgingAtoms(BRIDGE_ATOM_IDX, mol,
torsionSet)
A_IDX = 11
B_IDX = 12
C_IDX = 13
D_IDX = 14
torsion.a.SetMapIdx(A_IDX)
torsion.b.SetMapIdx(B_IDX)
torsion.c.SetMapIdx(C_IDX)
torsion.d.SetMapIdx(D_IDX)
torsionMol = oechem.OEGraphMol()
oechem.OESubsetMol(torsionMol, mol, torsionSet, True)
torsionMol.Sweep()
torsionMols.append(torsionMol)
# change bridge atom to Carbon
for atom in torsionMol.GetAtoms(
oechem.OEHasMapIdx(BRIDGE_ATOM_IDX)):
atom.SetAtomicNum(oechem.OEElemNo_C)
explicit_valence = atom.GetExplicitValence()
if explicit_valence < 4:
atom.SetImplicitHCount(4 - explicit_valence)
TorsionGenerator.SetSDData(A_IDX, B_IDX, C_IDX, D_IDX, torsion,
torsionMol)
# set map idx to zero in torsion mol
for atom in torsionMol.GetAtoms():
atom.SetMapIdx(0)
# revert map idx to zero in original mol
for atom in mol.GetAtoms():
atom.SetMapIdx(0)
return torsionMols
