def __makeChemCompBondCategory(self, ccId, oeMol):
idCode = ccId
rowL = []
iBondD = {1: "SING", 2: "DOUB", 3: "TRIP", 4: "QUAD", 5: "AROM", 0: "DELO"}
for ii, bond in enumerate(oeMol.GetBonds()):
oeOrder = str(bond.GetOrder()).upper()
b1 = bond.GetBgn().GetName().strip()
b2 = bond.GetEnd().GetName().strip()
if (b1 is None) or (len(b1) < 1):
continue
if (b2 is None) or (len(b1) < 1):
continue
if int(oeOrder) in iBondD:
bndRow = {}
bndRow["comp_id"] = idCode
bndRow["atom_id_1"] = b1
bndRow["atom_id_2"] = b2
bndRow["value_order"] = iBondD[int(oeOrder)]
if bond.IsAromatic():
bndRow["pdbx_aromatic_flag"] = "Y"
else:
bndRow["pdbx_aromatic_flag"] = "N"
oeSt = None
if bond.GetOrder() == 2:
cip = oechem.OEPerceiveCIPStereo(oeMol, bond)
if bond.HasStereoSpecified():
if cip == oechem.OECIPBondStereo_E:
oeSt = "E"
if cip == oechem.OECIPBondStereo_Z:
oeSt = "Z"
if cip == oechem.OECIPBondStereo_NotStereo:
oeSt = None
if cip == oechem.OECIPBondStereo_UnspecStereo:
oeSt = None
if oeSt is not None and (len(oeSt) > 0) and (oeSt == "E" or oeSt == "Z"):
bndRow["pdbx_stereo_config"] = oeSt
else:
bndRow["pdbx_stereo_config"] = "N"
bndRow["pdbx_ordinal"] = str(ii + 1)
rowL.append(bndRow)
return rowL
def rdmol_from_oemol(oemol):
"""
Create an RDKit molecule identical to the input OpenEye molecule.
Reference
---------
Written by Caitlin Bannan:
https://gist.github.com/bannanc/810ccc4636b930a4522636baab1965a6
May not be needed in newer openforcefield versions. See:
https://github.com/openforcefield/openforcefield/issues/135
Parameters
----------
oemol : OEMol
"""
#print("Starting OpenEye molecule: ", oechem.OEMolToSmiles(oemol))
# start function
rdmol = Chem.RWMol()
# RDKit keeps bond order as a type instead using these values, I don't really understand 7,
# I took them from Shuzhe's example linked above
_bondtypes = {
1: Chem.BondType.SINGLE,
1.5: Chem.BondType.AROMATIC,
2: Chem.BondType.DOUBLE,
3: Chem.BondType.TRIPLE,
4: Chem.BondType.QUADRUPLE,
5: Chem.BondType.QUINTUPLE,
6: Chem.BondType.HEXTUPLE,
7: Chem.BondType.ONEANDAHALF,
}
# atom map lets you find atoms again
map_atoms = dict() # {oe_idx: rd_idx}
for oea in oemol.GetAtoms():
oe_idx = oea.GetIdx()
rda = Chem.Atom(oea.GetAtomicNum())
rda.SetFormalCharge(oea.GetFormalCharge())
rda.SetIsAromatic(oea.IsAromatic())
# unlike OE, RDK lets you set chirality directly
cip = oechem.OEPerceiveCIPStereo(oemol, oea)
if cip == oechem.OECIPAtomStereo_S:
rda.SetChiralTag(Chem.CHI_TETRAHEDRAL_CW)
if cip == oechem.OECIPAtomStereo_R:
rda.SetChiralTag(Chem.CHI_TETRAHEDRAL_CCW)
map_atoms[oe_idx] = rdmol.AddAtom(rda)
# As discussed above, setting bond stereochemistry requires neighboring bonds
# so we will store that information by atom index in this list
stereo_bonds = list()
# stereo_bonds will have tuples with the form (rda1, rda2, rda3, rda4, is_cis)
# where rda[n] is an atom index for a double bond of form 1-2=3-4
# and is_cis is a Boolean is True then onds 1-2 and 3-4 are cis to each other
for oeb in oemol.GetBonds():
# get neighboring rd atoms
rd_a1 = map_atoms[oeb.GetBgnIdx()]
rd_a2 = map_atoms[oeb.GetEndIdx()]
# AddBond returns the total number of bonds, so addbond and then get it
rdmol.AddBond(rd_a1, rd_a2)
rdbond = rdmol.GetBondBetweenAtoms(rd_a1, rd_a2)
# Assign bond type, which is based on order unless it is aromatic
order = oeb.GetOrder()
if oeb.IsAromatic():
rdbond.SetBondType(_bondtypes[1.5])
rdbond.SetIsAromatic(True)
else:
rdbond.SetBondType(_bondtypes[order])
rdbond.SetIsAromatic(False)
# If the bond has specified stereo add the required information to stereo_bonds
if oeb.HasStereoSpecified(oechem.OEBondStereo_CisTrans):
# OpenEye determined stereo based on neighboring atoms so get two outside atoms
n1 = [n for n in oeb.GetBgn().GetAtoms() if n != oeb.GetEnd()][0]
n2 = [n for n in oeb.GetEnd().GetAtoms() if n != oeb.GetBgn()][0]
rd_n1 = map_atoms[n1.GetIdx()]
rd_n2 = map_atoms[n2.GetIdx()]
stereo = oeb.GetStereo([n1, n2], oechem.OEBondStereo_CisTrans)
if stereo == oechem.OEBondStereo_Cis:
print('cis')
stereo_bonds.append((rd_n1, rd_a1, rd_a2, rd_n2, True))
elif stereo == oechem.OEBondStereo_Trans:
print('trans')
stereo_bonds.append((rd_n1, rd_a1, rd_a2, rd_n2, False))
# add bond stereochemistry:
for (rda1, rda2, rda3, rda4, is_cis) in stereo_bonds:
# get neighbor bonds
bond1 = rdmol.GetBondBetweenAtoms(rda1, rda2)
bond2 = rdmol.GetBondBetweenAtoms(rda3, rda4)
# Since this is relative, the first bond always goes up
# as explained above these names come from SMILES slashes so UP/UP is Trans and Up/Down is cis
bond1.SetBondDir(Chem.BondDir.ENDUPRIGHT)
if is_cis:
bond2.SetBondDir(Chem.BondDir.ENDDOWNRIGHT)
else:
bond2.SetBondDir(Chem.BondDir.ENDUPRIGHT)
# if oemol has coordinates (The dimension is non-zero)
# add those coordinates to the rdmol
if oechem.OEGetDimensionFromCoords(oemol) > 0:
conformer = Chem.Conformer()
oecoords = oemol.GetCoords()
for oe_idx, rd_idx in map_atoms.items():
(x, y, z) = oecoords[oe_idx]
conformer.SetAtomPosition(rd_idx, Geometry.Point3D(x, y, z))
rdmol.AddConformer(conformer)
# Save the molecule title
rdmol.SetProp("_Name", oemol.GetTitle())
# Cleanup the rdmol
# Note I copied UpdatePropertyCache and GetSSSR from Shuzhe's code to convert oemol to rdmol here:
rdmol.UpdatePropertyCache(strict=False)
Chem.GetSSSR(rdmol)
# I added AssignStereochemistry which takes the directions of the bond set
# and assigns the stereochemistry tags on the double bonds
Chem.AssignStereochemistry(rdmol, force=False)
#print("Final RDKit molecule: ", Chem.MolToSmiles(Chem.RemoveHs(rdmol), isomericSmiles=True))
return rdmol.GetMol()
def oemol_from_rdmol(rdmol):
"""
Creates an openeye molecule object that is identical to the input rdkit molecule
"""
# RDK automatically includes explicit hydrogens in its SMILES patterns
print("Starting molecule: ", Chem.MolToSmiles(Chem.RemoveHs(rdmol)))
# openeye stores bond orders as integers regardless of aromaticity
# in order to properly extract these, we need to have the "Kekulized" version of the rdkit mol
kekul_mol = Chem.Mol(rdmol)
Chem.Kekulize(kekul_mol, True)
oemol = oechem.OEMol()
map_atoms = dict() # {rd_idx: oe_atom}
# setting chirality in openey requires using neighbor atoms
# therefore we can't do it until after the atoms and bonds are all added
chiral_atoms = dict() # {rd_idx: openeye chirality}
for rda in rdmol.GetAtoms():
rd_idx = rda.GetIdx()
# create a new atom
oe_a = oemol.NewAtom(rda.GetAtomicNum())
map_atoms[rd_idx] = oe_a
oe_a.SetFormalCharge(rda.GetFormalCharge())
oe_a.SetAromatic(rda.GetIsAromatic())
# If chiral, store the chirality to be set later
tag = rda.GetChiralTag()
if tag == Chem.CHI_TETRAHEDRAL_CCW:
chiral_atoms[rd_idx] = oechem.OECIPAtomStereo_R
if tag == Chem.CHI_TETRAHEDRAL_CW:
chiral_atoms[rd_idx] = oechem.OECIPAtomStereo_S
# Similar to chirality, stereochemistry of bonds in OE is set relative to their neighbors
stereo_bonds = list()
# stereo_bonds stores tuples in the form (oe_bond, rd_idx1, rd_idx2, OE stereo specification)
# where rd_idx1 and 2 are the atoms on the outside of the bond
# i.e. Cl and F in the example above
aro_bond = 0
for rdb in rdmol.GetBonds():
a1 = rdb.GetBeginAtomIdx()
a2 = rdb.GetEndAtomIdx()
# create a new bond
newbond = oemol.NewBond(map_atoms[a1], map_atoms[a2])
order = rdb.GetBondTypeAsDouble()
if order == 1.5:
# get the bond order for this bond in the kekulized molecule
order = kekul_mol.GetBondWithIdx(
rdb.GetIdx()).GetBondTypeAsDouble()
newbond.SetAromatic(True)
else:
newbond.SetAromatic(False)
newbond.SetOrder(int(order))
# determine if stereochemistry is needed
tag = rdb.GetStereo()
if tag == Chem.BondStereo.STEREOCIS or tag == Chem.BondStereo.STEREOZ:
stereo_atoms = rdb.GetStereoAtoms()
stereo_bonds.append((newbond, stereo_atoms[0], stereo_atoms[1],
oechem.OEBondStereo_Cis))
bond2 = rdmol.GetBondBetweenAtoms(stereo_atoms[0], a1)
bond4 = rdmol.GetBondBetweenAtoms(stereo_atoms[1], a2)
print(tag, bond2.GetBondDir(), bond4.GetBondDir())
if tag == Chem.BondStereo.STEREOTRANS or tag == Chem.BondStereo.STEREOE:
stereo_atoms = rdb.GetStereoAtoms()
stereo_bonds.append((newbond, stereo_atoms[0], stereo_atoms[1],
oechem.OEBondStereo_Trans))
bond2 = rdmol.GetBondBetweenAtoms(stereo_atoms[0], a1)
bond4 = rdmol.GetBondBetweenAtoms(stereo_atoms[1], a2)
print(tag, bond2.GetBondDir(), bond4.GetBondDir())
# Now that all of the atoms are connected we can set stereochemistry
# starting with atom chirality
for rd_idx, chirality in chiral_atoms.items():
# chirality is set relative to neighbors, so we will get neighboring atoms
# assign Right handed direction, check the cip stereochemistry
# if the cip stereochemistry isn't correct then we'll set left and double check
oea = map_atoms[rd_idx]
neighs = [n for n in oea.GetAtoms()]
# incase you look at the documentation oe has two options for handedness for example:
# oechem.OEAtomStereo_Left == oechem.OEAtomStereo_LeftHanded
oea.SetStereo(neighs, oechem.OEAtomStereo_Tetra,
oechem.OEAtomStereo_Right)
cip = oechem.OEPerceiveCIPStereo(oemol, oea)
if cip != chirality:
oea.SetStereo(neighs, oechem.OEAtomStereo_Tetra,
oechem.OEAtomStereo_Left)
new_cip = oechem.OEPerceiveCIPStereo(oemol, oea)
if new_cip != chirality:
# Note, I haven't seen this happen yet, but it shouldn't be a problem since there
# is only 2 directions for handedness and we're only running this for chiral atoms
print("PANIC!")
# Set stereochemistry using the reference atoms extracted above
for oeb, idx1, idx2, oestereo in stereo_bonds:
oeb.SetStereo([map_atoms[idx1], map_atoms[idx2]],
oechem.OEBondStereo_CisTrans, oestereo)
# If the rdmol has a conformer, add its coordinates to the oemol
# Note, this currently only adds the first conformer, it will need to be adjusted if the
# you wanted to convert multiple sets of coordinates
if rdmol.GetConformers():
conf = rdmol.GetConformer()
for rd_idx, oeatom in map_atoms.items():
coords = conf.GetAtomPosition(rd_idx)
oemol.SetCoords(oeatom, oechem.OEFloatArray(coords))
# If RDMol has a title save it
if rdmol.HasProp("_Name"):
oemol.SetTitle(rdmol.GetProp("_Name"))
# Clean Up phase
# The only feature of a molecule that wasn't perceived above seemed to be ring connectivity, better to run it
# here then for someone to inquire about ring sizes and get 0 when it shouldn't be
oechem.OEFindRingAtomsAndBonds(oemol)
print('Final Molecule: ', oechem.OEMolToSmiles(oemol))
return oemol
# 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.OESmilesToMol(mol, "N[C@@H]1N[C@@H](O)CC(O)C1.C2[C@@H](O)CC[C@@H](O)C2")
for atom in mol.GetAtoms():
cip = oechem.OEPerceiveCIPStereo(mol, atom)
if atom.HasStereoSpecified():
print("atom %d is" % atom.GetIdx(), end=" ")
if cip == oechem.OECIPAtomStereo_S:
print('S')
if cip == oechem.OECIPAtomStereo_R:
print('R')
if cip == oechem.OECIPAtomStereo_NotStereo:
print('not a CIP stereo center')
if cip == oechem.OECIPAtomStereo_UnspecStereo:
print("atom %d is" % atom.GetIdx(), end=" ")
print('a CIP stereo center without specified stereochemistry')
# @ </SNIPPET>
def __makeChemCompAtomCategory(self, ccId, oeMol, writeIdealXyz=True):
"""Populate elements of chemical component definition for atoms and bonds."""
#
idCode = ccId
#
rowL = []
for ii, atom in enumerate(oeMol.GetAtoms()):
#
atRow = {}
atRow["comp_id"] = idCode
atRow["atom_id"] = atom.GetName().strip()
atRow["alt_atom_id"] = atom.GetName().strip()
atRow["type_symbol"] = oechem.OEGetAtomicSymbol(atom.GetAtomicNum())
atRow["charge"] = atom.GetFormalCharge()
(xC, yC, zC) = oeMol.GetCoords(atom)
if writeIdealXyz:
atRow["pdbx_model_Cartn_x_ideal"] = "%0.3f" % xC
atRow["pdbx_model_Cartn_y_ideal"] = "%0.3f" % yC
atRow["pdbx_model_Cartn_z_ideal"] = "%0.3f" % zC
else:
atRow["model_Cartn_x"] = "%0.3f" % xC
atRow["model_Cartn_y"] = "%0.3f" % yC
atRow["model_Cartn_z"] = "%0.3f" % zC
if atom.GetStringData("pdbx_leaving_atom_flag") in ["Y", "N"]:
atRow["pdbx_leaving_atom_flag"] = atom.GetStringData("pdbx_leaving_atom_flag")
else:
atRow["pdbx_leaving_atom_flag"] = "N"
if len(atRow["atom_id"]) > 3 or len(atRow["type_symbol"]) == 2:
atRow["pdbx_align"] = 0
else:
atRow["pdbx_align"] = 1
if atom.IsAromatic():
atRow["pdbx_aromatic_flag"] = "Y"
else:
atRow["pdbx_aromatic_flag"] = "N"
# oeSt = oechem.OEGetCIPStereo(mol, atom)
oeSt = None
# if atom.IsChiral():
cip = oechem.OEPerceiveCIPStereo(oeMol, atom)
if atom.HasStereoSpecified():
if cip == oechem.OECIPAtomStereo_S:
oeSt = "S"
if cip == oechem.OECIPAtomStereo_R:
oeSt = "R"
if cip == oechem.OECIPAtomStereo_NotStereo:
oeSt = None
if cip == oechem.OECIPAtomStereo_UnspecStereo:
oeSt = "U"
# oeSt = oechem.OEGetCIPStereo(oeMol, atom)
# oeSt = atom.GetCIPStereo()
if oeSt is not None and (len(oeSt) > 0) and (oeSt == "R" or oeSt == "S"):
atRow["pdbx_stereo_config"] = oeSt
else:
atRow["pdbx_stereo_config"] = "N"
atRow["pdbx_component_atom_id"] = atom.GetName().strip()
atRow["pdbx_component_comp_id"] = idCode
atRow["pdbx_ordinal"] = str(ii + 1)
rowL.append(atRow)
#
return rowL
# 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.OESmilesToMol(mol, "C\\C(C)=C(\\C)C.O\\C(C)=C(\\C)O.O\\C(C)=C(\\O)C.CC(O)=C(O)C")
for bond in mol.GetBonds():
if bond.GetOrder() == 2:
cip = oechem.OEPerceiveCIPStereo(mol, bond)
print("bond %d is" % bond.GetIdx(), end=" ")
if bond.HasStereoSpecified():
if cip == oechem.OECIPBondStereo_E:
print('E')
if cip == oechem.OECIPBondStereo_Z:
print('Z')
if cip == oechem.OECIPBondStereo_NotStereo:
print('not a CIP stereo center')
if cip == oechem.OECIPBondStereo_UnspecStereo:
print('a CIP stereo center without specified stereochemistry')
# @ </SNIPPET>