def AtomPathLength(ifs, ofs, itf, atm1, atm2):
for mol in ifs.GetOEGraphMols():
oechem.OETriposAtomNames(mol)
a1 = None
a2 = None
for atm in mol.GetAtoms():
if atm.GetName() == atm1:
a1 = atm
if atm.GetName() == atm2:
a2 = atm
if a1 is not None and a2 is not None:
break
if a1 is None or a2 is None:
oechem.OEThrow.Warning(
"Failed to find atoms %s and %s in molecule" % (atm1, atm2))
continue
pathlen = oechem.OEGetPathLength(a1, a2)
if itf.GetBool("-verbose") or not itf.HasString("-o"):
print("Path length: %s in %s" %
(pathlen, oechem.OEMolToSmiles(mol)))
spath = oechem.OEShortestPath(a1, a2)
spathmol = oechem.OEGraphMol()
adjustHCount = True
oechem.OESubsetMol(spathmol, mol, oechem.OEIsAtomMember(spath),
adjustHCount)
spathsmiles = oechem.OEMolToSmiles(spathmol)
if itf.HasString("-o"):
oechem.OEWriteMolecule(ofs, spathmol)
elif itf.GetBool("-verbose"):
print(spathsmiles)
def atom_bond_set_to_mol(frag, oemol, adjust_hcount=False, RGroup=True):
from openeye import oechem
import warnings
fragatompred = oechem.OEIsAtomMember(frag.GetAtoms())
fragbondpred = oechem.OEIsBondMember(frag.GetBonds())
fragment_oemol = oechem.OEMol()
adjustHCount = adjust_hcount
oechem.OESubsetMol(fragment_oemol, oemol, fragatompred, fragbondpred,
adjustHCount, RGroup)
oechem.OEAddExplicitHydrogens(fragment_oemol)
# sanity check that all atoms are bonded
for atom in fragment_oemol.GetAtoms():
if not list(atom.GetBonds()):
warnings.warn(
"Yikes!!! An atom that is not bonded to any other atom in the fragment. "
"You probably ran into a bug. Please report the input molecule to the issue tracker"
)
# Perceive stereo and check that defined stereo did not change
oechem.OEPerceiveChiral(fragment_oemol)
oechem.OE3DToAtomStereo(fragment_oemol)
oechem.OE3DToBondStereo(fragment_oemol)
return fragment_oemol
def frag_to_smiles(frags, mol):
"""
Convert fragments (AtomBondSet) to smiles string
Parameters
----------
frags
mol
Returns
-------
smiles: list of smiles strings
"""
smiles = {}
for frag in frags:
fragatompred = oechem.OEIsAtomMember(frag.GetAtoms())
fragbondpred = oechem.OEIsBondMember(frag.GetBonds())
fragment = oechem.OEGraphMol()
adjustHCount = True
oechem.OESubsetMol(fragment, mol, fragatompred, fragbondpred,
adjustHCount)
s = oechem.OECreateIsoSmiString(fragment)
if s not in smiles:
smiles[s] = []
smiles[s].append(frag)
return smiles
def SmartsPathLength(ifs, ofs, itf, ss1, ss2):
for mol in ifs.GetOEGraphMols():
oechem.OEPrepareSearch(mol, ss1)
oechem.OEPrepareSearch(mol, ss2)
if not (ss1.SingleMatch(mol) and ss2.SingleMatch(mol)):
oechem.OEThrow.Warning(
"Unable to find SMARTS matches in %s, skipping" %
mol.GetTitle())
continue
unique = True
allminlen = sys.maxsize
for match1 in ss1.Match(mol, unique):
for match2 in ss2.Match(mol, unique):
minlen = sys.maxsize
for atom1 in match1.GetTargetAtoms():
for atom2 in match2.GetTargetAtoms():
pathlen = oechem.OEGetPathLength(atom1, atom2)
if minlen > pathlen:
minlen = pathlen
atompairs = []
atompairs.append([atom1, atom2])
elif minlen == pathlen:
atompairs.append([atom1, atom2])
if minlen < allminlen:
allminlen = minlen
allatompairs = atompairs[:]
elif minlen == allminlen:
allatompairs += atompairs[:]
if itf.GetBool("-verbose") or not itf.HasString("-o"):
print("Shortest path length: %s in %s" %
(allminlen, oechem.OEMolToSmiles(mol)))
spathlist = set()
for satom1, satom2, in allatompairs:
spath = oechem.OEShortestPath(satom1, satom2)
spathmol = oechem.OEGraphMol()
oechem.OESubsetMol(spathmol, mol, oechem.OEIsAtomMember(spath))
spathsmiles = oechem.OEMolToSmiles(spathmol)
if spathsmiles in spathlist:
continue
spathlist.add(spathsmiles)
if itf.HasString("-o"):
oechem.OEWriteMolecule(ofs, spathmol)
elif itf.GetBool("-verbose"):
print(spathsmiles)
return
def GetFragmentCombinations(mol, fraglist, frag_number):
fragments = []
fragcombs = GetFragmentAtomBondSetCombinations(mol, fraglist, frag_number)
for f in fragcombs:
fragatompred = oechem.OEIsAtomMember(f.GetAtoms())
fragbondpred = oechem.OEIsBondMember(f.GetBonds())
fragment = oechem.OEGraphMol()
adjustHCount = True
oechem.OESubsetMol(fragment, mol, fragatompred, fragbondpred,
adjustHCount)
fragments.append(fragment)
return fragments
def BackBone(ifs, ofs):
adjustHCount = True
mol = oechem.OEGraphMol()
backboneMol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
aiter = mol.GetAtoms(oechem.OEIsBackboneAtom())
member = oechem.OEIsAtomMember(aiter)
oechem.OESubsetMol(backboneMol, mol, member, adjustHCount)
oechem.OEWriteMolecule(ofs, backboneMol)
def GetFragments(mol, minbonds, maxbonds):
from openeye import oegraphsim
frags = []
fptype = oegraphsim.OEGetFPType("Tree,ver=2.0.0,size=4096,bonds=%d-%d,atype=AtmNum,btype=Order"
% (minbonds, maxbonds))
for abset in oegraphsim.OEGetFPCoverage(mol, fptype, True):
fragatompred = oechem.OEIsAtomMember(abset.GetAtoms())
frag = oechem.OEGraphMol()
adjustHCount = True
oechem.OESubsetMol(frag, mol, fragatompred, adjustHCount)
oechem.OEFindRingAtomsAndBonds(frag)
frags.append(oechem.OEGraphMol(frag))
return frags
def SubSetRes(ifs, ofs, chainid, resname, resnum):
adjustHCount = True
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
hv = oechem.OEHierView(mol)
res = hv.GetResidue(chainid, resname, resnum)
if res.GetOEResidue().GetName() is None:
oechem.OEThrow.Fatal("Failed to find residue")
atomiter = res.GetAtoms()
member = oechem.OEIsAtomMember(atomiter)
resmol = oechem.OEGraphMol()
oechem.OESubsetMol(resmol, mol, member, adjustHCount)
if chainid == " ":
resmol.SetTitle("%s %d" % (resname, resnum))
else:
resmol.SetTitle("%s %s %d" % (resname, chainid, resnum))
oechem.OEWriteMolecule(ofs, resmol)
def frag_to_smiles(frags, mol):
"""
Convert fragments (AtomBondSet) to canonical isomeric SMILES string
Parameters
----------
frags: list
mol: OEMol
OESMILESFlag: str
Either 'ISOMERIC' or 'DEFAULT'. This flag determines which OE function to use to generate SMILES string
Returns
-------
smiles: dict of smiles to frag
"""
smiles = {}
for frag in frags:
fragatompred = oechem.OEIsAtomMember(frag.GetAtoms())
fragbondpred = oechem.OEIsBondMember(frag.GetBonds())
#fragment = oechem.OEGraphMol()
fragment = oechem.OEMol()
adjustHCount = True
oechem.OESubsetMol(fragment, mol, fragatompred, fragbondpred, adjustHCount)
oechem.OEPerceiveChiral(fragment)
# sanity check that all atoms are bonded
for atom in fragment.GetAtoms():
if not list(atom.GetBonds()):
raise Warning("Yikes!!! An atom that is not bonded to any other atom in the fragment. "
"You probably ran into a bug. Please report the input molecule to the issue tracker")
#s = oechem.OEMolToSmiles(fragment)
#s2 = fragmenter.utils.create_mapped_smiles(fragment, tagged=False, explicit_hydrogen=False)
s = mol_to_smiles(fragment, mapped=False, explicit_hydrogen=True, isomeric=True)
if s not in smiles:
smiles[s] = []
smiles[s].append(frag)
return smiles
# 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
from openeye import oemedchem
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "COc1ccc(cc1)CC(=O)N")
for frag in oemedchem.OEGetRingChainFragments(mol):
fragatompred = oechem.OEIsAtomMember(frag.GetAtoms())
fragbondpred = oechem.OEIsBondMember(frag.GetBonds())
fragment = oechem.OEGraphMol()
adjustHCount = True
oechem.OESubsetMol(fragment, mol, fragatompred, fragbondpred, adjustHCount)
print(oechem.OEMolToSmiles(fragment))
# @ </SNIPPET>
def _extract_oe_fragment(
molecule: Molecule, atom_indices: Set[int], bond_indices: Set[Tuple[int, int]]
) -> Molecule:
from openeye import oechem
oe_molecule = molecule.to_openeye()
# Restore the map indices as to_openeye does not automatically add them.
for atom_index, map_index in molecule.properties["atom_map"].items():
oe_atom = oe_molecule.GetAtom(oechem.OEHasAtomIdx(atom_index))
oe_atom.SetMapIdx(map_index)
# Include any Hs bonded to the included atom set so we can retain their map
# indices.
for map_index in {*atom_indices}:
oe_atom = oe_molecule.GetAtom(oechem.OEHasMapIdx(map_index))
for neighbour in oe_atom.GetAtoms():
if (
neighbour.GetAtomicNum() != 1
or neighbour.GetMapIdx() < 1
or neighbour.GetMapIdx() in atom_indices
):
continue
atom_indices.add(neighbour.GetMapIdx())
bond_indices.add((map_index, neighbour.GetMapIdx()))
atom_bond_set = oechem.OEAtomBondSet()
for map_index in atom_indices:
atom = oe_molecule.GetAtom(oechem.OEHasMapIdx(map_index))
atom_bond_set.AddAtom(atom)
for map_index_1, map_index_2 in bond_indices:
atom_1 = oe_molecule.GetAtom(oechem.OEHasMapIdx(map_index_1))
atom_2 = oe_molecule.GetAtom(oechem.OEHasMapIdx(map_index_2))
bond = oe_molecule.GetBond(atom_1, atom_2)
if not bond:
raise ValueError(f"{(map_index_1, map_index_2)} is a disconnected bond")
atom_bond_set.AddBond(bond)
atom_predicate = oechem.OEIsAtomMember(atom_bond_set.GetAtoms())
bond_predicate = oechem.OEIsBondMember(atom_bond_set.GetBonds())
fragment = oechem.OEMol()
oechem.OESubsetMol(fragment, oe_molecule, atom_predicate, bond_predicate, True)
oechem.OEAddExplicitHydrogens(fragment)
oechem.OEPerceiveChiral(fragment)
# Always restore map?
# if restore_maps:
# In some cases (symmetric molecules) this changes the atom map so skip it
# restore_atom_map(fragment)
# atom map should be restored for combinatorial fragmentation
# Perceive stereo and check that defined stereo did not change
oechem.OEPerceiveChiral(fragment)
oechem.OE3DToAtomStereo(fragment)
oechem.OE3DToBondStereo(fragment)
return Molecule.from_openeye(fragment, allow_undefined_stereo=True)
def DepictMoleculeWithFragmentCombinations(report, mol, frags, opts): #fragcombs, opts):
""" This function was taken from https://docs.eyesopen.com/toolkits/cookbook/python/depiction/enumfrags.html with some modification
"""
stag = "fragment idx"
itag = oechem.OEGetTag(stag)
for fidx, frag in enumerate(frags):
for bond in frags[frag].GetBonds():
bond.SetData(itag, fidx)
# setup depiction styles
nrfrags = len(frags)
colors = [c for c in oechem.OEGetLightColors()]
if len(colors) < nrfrags:
colors = [c for c in oechem.OEGetColors(oechem.OEYellowTint, oechem.OEDarkOrange, nrfrags)]
bondglyph = ColorBondByFragmentIndex(colors, itag)
lineWidthScale = 0.75
fadehighlight = oedepict.OEHighlightByColor(oechem.OEGrey, lineWidthScale)
# depict each fragment combinations
for frag in frags:
cell = report.NewCell()
disp = oedepict.OE2DMolDisplay(mol, opts)
fragatoms = oechem.OEIsAtomMember(frags[frag].GetAtoms())
fragbonds = oechem.OEIsBondMember(frags[frag].GetBonds())
notfragatoms = oechem.OENotAtom(fragatoms)
notfragbonds = oechem.OENotBond(fragbonds)
oedepict.OEAddHighlighting(disp, fadehighlight, notfragatoms, notfragbonds)
bond = mol.GetBond(oechem.OEHasBondIdx(frag))
atomBondSet = oechem.OEAtomBondSet()
atomBondSet.AddBond(bond)
atomBondSet.AddAtom(bond.GetBgn())
atomBondSet.AddAtom(bond.GetEnd())
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atomBondSet)
#oegrapheme.OEAddGlyph(disp, bondglyph, fragbonds)
oedepict.OERenderMolecule(cell, disp)
# depict original fragmentation in each header
cellwidth, cellheight = report.GetHeaderWidth(), report.GetHeaderHeight()
opts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
bondlabel = LabelBondOrder()
opts.SetBondPropertyFunctor(bondlabel)
disp = oedepict.OE2DMolDisplay(mol, opts)
#oegrapheme.OEAddGlyph(disp, bondglyph, oechem.IsTrueBond())
headerpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey, oedepict.OEFill_Off, 2.0)
for header in report.GetHeaders():
oedepict.OERenderMolecule(header, disp)
oedepict.OEDrawBorder(header, headerpen)