def has_protonated_double_bonded_ring_nitrogen(mol):
for atom in mol.GetAtoms(
oechem.OEAndAtom(
oechem.OEAndAtom(oechem.OEIsNitrogen(),
oechem.OEHasFormalCharge(1)),
oechem.OEAtomIsInRing(),
)):
for bond in atom.GetBonds():
if bond.GetOrder() == 2:
return True
return False
def AddRelevantRingAtoms(mol, torsion, torsionSet):
atom1or2 = oechem.OEOrAtom(oechem.OEHasMapIdx(1),
oechem.OEHasMapIdx(2))
ringNbrs = []
for atom in mol.GetAtoms(
oechem.OEAndAtom(oechem.OEAtomIsInRing(), atom1or2)):
for nbr in atom.GetAtoms(
oechem.OEAndAtom(oechem.OENotAtom(atom1or2),
oechem.OENotAtom(
oechem.OEAtomIsInRing()))):
if nbr.IsHydrogen():
ringNbrs.append(nbr)
continue
if nbr.IsOxygen() and mol.GetBond(atom, nbr).GetOrder() == 2:
ringNbrs.append(nbr)
continue
if TorsionGenerator.IsOrtho(nbr, torsion):
ringNbrs.append(nbr)
for nbr in ringNbrs:
if not torsionSet.HasAtom(nbr):
nbr.SetMapIdx(2)
torsionSet.AddAtom(nbr)
def MarkBridgingAtoms(BRIDGE_ATOM_IDX, mol, torsionSet):
NorOorS = oechem.OEOrAtom(
oechem.OEOrAtom(oechem.OEIsNitrogen(), oechem.OEIsOxygen()),
oechem.OEIsSulfur())
for atom in mol.GetAtoms(
oechem.OEAndAtom(oechem.OEHasMapIdx(2), NorOorS)):
for nbr in atom.GetAtoms(oechem.OEIsHeavy()):
if not torsionSet.HasAtom(nbr):
if nbr.GetMapIdx() == 0:
torsionSet.AddAtom(nbr)
if nbr.GetHvyDegree() == 1:
nbr.SetMapIdx(3)
continue
nbr.SetMapIdx(BRIDGE_ATOM_IDX)
def _OEFixConnectionNH(protein):
"""
Temporary fix, thanks to Jesper!
"""
for atom in protein.GetAtoms(
oechem.OEAndAtom(oespruce.OEIsModeledAtom(),
oechem.OEIsNitrogen())):
if oechem.OEGetPDBAtomIndex(atom) == oechem.OEPDBAtomName_N:
expected_h_count = 1
if oechem.OEGetResidueIndex(atom) == oechem.OEResidueIndex_PRO:
expected_h_count = 0
if atom.GetTotalHCount() != expected_h_count:
oechem.OESuppressHydrogens(atom)
atom.SetImplicitHCount(1)
oechem.OEAddExplicitHydrogens(protein, atom)
for nbr in atom.GetAtoms(oechem.OEIsHydrogen()):
oechem.OESet3DHydrogenGeom(protein, nbr)
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cnc(O)cc1CCCBr")
print("Number of chain atoms =", end=" ")
print(oechem.OECount(mol, oechem.OENotAtom(oechem.OEAtomIsInRing())))
print("Number of aromatic nitrogens =", end=" ")
print(
oechem.OECount(
mol, oechem.OEAndAtom(oechem.OEIsNitrogen(),
oechem.OEIsAromaticAtom())))
print("Number of non-carbons =", end=" ")
print(
oechem.OECount(mol,
oechem.OENotAtom(oechem.OEHasAtomicNum(oechem.OEElemNo_C))))
print("Number of nitrogen and oxygen atoms =", end=" ")
print(
oechem.OECount(
mol,
oechem.OEOrAtom(oechem.OEHasAtomicNum(oechem.OEElemNo_N),
oechem.OEHasAtomicNum(oechem.OEElemNo_O))))
# @ </SNIPPET>
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
# @ <SNIPPET-OEAtomMatchResidue>
resAla = oechem.OEAtomMatchResidueID()
resAla.SetName("ALA")
predAla = oechem.OEAtomMatchResidue(resAla)
print("Number of atoms matching residue name ALA = ", oechem.OECount(mol, predAla))
resChainA = oechem.OEAtomMatchResidueID()
resChainA.SetChainID("A")
predChainA = oechem.OEAtomMatchResidue(resChainA)
print("Number of atoms matching chain A = ", oechem.OECount(mol, predChainA))
resHis = oechem.OEAtomMatchResidueID()
resHis.SetName("HIS")
resHis.SetChainID("A")
resHis.SetResidueNumber("88")
predHis = oechem.OEAtomMatchResidue(resHis)
print("Number of atoms matching residue (HIS A 88) = ", oechem.OECount(mol, predHis))
# alternative way to initialize as regex
predHis2 = oechem.OEAtomMatchResidue("HIS:88:.*:A:.*:.*")
print("Number of atoms matching residue (HIS A 88) = ", oechem.OECount(mol, predHis2))
backbonepred = oechem.OEIsBackboneAtom()
print("Backbone atoms of residue (HIS A 88): ")
for atom in mol.GetAtoms(oechem.OEAndAtom(predHis, backbonepred)):
print(atom, oechem.OEAtomGetResidue(atom))
# @ </SNIPPET-OEAtomMatchResidue>
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