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 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)
def has_undesirable_elements(mol):
'''
returns True if molecule contains any element other than
H, C, N, O, F, S, Cl, or P
@param mol:
@type mol: OEGraphMol
@return: bool
'''
atomsHC = oechem.OEOrAtom(oechem.OEIsHydrogen(), oechem.OEIsCarbon())
atomsNO = oechem.OEOrAtom(oechem.OEIsNitrogen(), oechem.OEIsOxygen())
atomsFS = oechem.OEOrAtom(oechem.OEHasAtomicNum(9), oechem.OEIsSulfur())
atomsHCNO = oechem.OEOrAtom(atomsHC, atomsNO)
atomsHCNOFS = oechem.OEOrAtom(atomsHCNO, atomsFS)
atomsHCNOFSCl = oechem.OEOrAtom(atomsHCNOFS, oechem.OEHasAtomicNum(17))
atomsHCNOFSClP = oechem.OEOrAtom(atomsHCNOFSCl, oechem.OEIsPhosphorus())
undesirable_atom = mol.GetAtom(oechem.OENotAtom(atomsHCNOFSClP))
if undesirable_atom is not None:
return True
return False
# 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>
def has_nitrogen_with_negative_formal_charge(mol):
for atom in mol.GetAtoms(oechem.OEIsNitrogen()):
if atom.GetFormalCharge() < 0:
return True
return False
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
# @ <SNIPPET-OESHORTESTPATH>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1ccc2c(c1)cccn2")
atomA = mol.GetAtom(oechem.OEHasAtomIdx(2))
atomB = mol.GetAtom(oechem.OEHasAtomIdx(8))
print("shortest path =", end=" ")
for atom in oechem.OEShortestPath(atomA, atomB):
print(str(atom), end=" ")
print("\n")
# @ </SNIPPET-OESHORTESTPATH>
# @ <SNIPPET-OESHORTESTPATH-EXCLUDE>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1ccc2c(c1)cccn2")
atomA = mol.GetAtom(oechem.OEHasAtomIdx(2))
atomB = mol.GetAtom(oechem.OEHasAtomIdx(8))
print("shortest path =", end=" ")
for atom in oechem.OEShortestPath(atomA, atomB, oechem.OEIsNitrogen()):
print(str(atom), end=" ")
print("\n")
# @ </SNIPPET-OESHORTESTPATH-EXCLUDE>
# @ </SNIPPET>