def isRotatableBond(bond):
inRing = oechem.OEBondIsInRing()
return (not inRing(bond)) and (
isAmideRotor(bond) or \
isMethylRotor(bond) or \
isEtherRotor(bond)
)
def ring_connectivity(self):
"""
Returns
-------
ring_connectivity: int
number of bonds on the atom that are a part of a ring
"""
return len([b for b in self.atom.GetBonds(oechem.OEBondIsInRing())])
def OEAddLabel_Predicate(disp):
ringhighlight = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, ringhighlight,
oechem.OEAtomIsInRing(), oechem.OEBondIsInRing())
ringlabel = oedepict.OEHighlightLabel("ring", oechem.OELightGreen)
oedepict.OEAddLabel(disp, ringlabel, oechem.OEAtomIsInRing())
chainhighlight = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oedepict.OEAddHighlighting(disp, chainhighlight,
oechem.OEAtomIsInChain(), oechem.OEBondIsInChain())
chainlabel = oedepict.OEHighlightLabel("chain", oechem.OEBlueTint)
oedepict.OEAddLabel(disp, chainlabel, oechem.OEAtomIsInChain())
def OEAddLabel_OEAtomBondSet(disp):
mol = disp.GetMolecule()
ringset = oechem.OEAtomBondSet(mol.GetAtoms(oechem.OEAtomIsInRing()),
mol.GetBonds(oechem.OEBondIsInRing()))
ringhighlight = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, ringhighlight, ringset)
ringlabel = oedepict.OEHighlightLabel("ring", oechem.OELightGreen)
oedepict.OEAddLabel(disp, ringlabel, ringset)
chainset = oechem.OEAtomBondSet(mol.GetAtoms(oechem.OEAtomIsInChain()),
mol.GetBonds(oechem.OEBondIsInChain()))
chainhighlight = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oedepict.OEAddHighlighting(disp, chainhighlight, chainset)
chainlabel = oedepict.OEHighlightLabel("chain", oechem.OEBlueTint)
oedepict.OEAddLabel(disp, chainlabel, chainset)
def GetAdjacentTorsions(mol, refTorsion):
'''
Returns all torsions that are 0 or 1 path length away from
the reference torsion
@param mol: OEGraphMol
@param refTorsion: OETorsion
@return: int
'''
adjTorsions = []
PATH_LENGTH_THRESHOLD = 1
torset = {
str(refTorsion.b.GetIdx()) + "_" + str(refTorsion.c.GetIdx()): True
}
torset[str(refTorsion.c.GetIdx()) + "_" +
str(refTorsion.b.GetIdx())] = True
pred = oechem.OEAndBond(oechem.OEHasOrder(1),
oechem.OENotBond(oechem.OEBondIsInRing()))
for adjTorsion in oechem.OEGetTorsions(mol, pred):
# skip nitrile
order_ab = adjTorsion.a.GetBond(adjTorsion.b).GetOrder()
order_cd = adjTorsion.c.GetBond(adjTorsion.d).GetOrder()
if order_ab == 3 or order_cd == 3:
continue
# skip torsions involving terminal -N-H
if adjTorsion.a.IsHydrogen() and adjTorsion.b.IsNitrogen():
continue
if adjTorsion.d.IsHydrogen() and adjTorsion.c.IsNitrogen():
continue
key1 = str(adjTorsion.b.GetIdx()) + "_" + str(
adjTorsion.c.GetIdx())
key2 = str(adjTorsion.c.GetIdx()) + "_" + str(
adjTorsion.b.GetIdx())
if key1 in torset or key2 in torset:
continue
pathLen = TorsionGenerator.GetMinPathLength(refTorsion, adjTorsion)
if pathLen <= PATH_LENGTH_THRESHOLD:
adjTorsions.append(adjTorsion)
torset[key1] = True
torset[key2] = True
return adjTorsions
def ring_connectivity(self):
return len([b for b in self.atom.GetBonds(oechem.OEBondIsInRing())])
#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# 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
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "CC(=O)Nc1c[nH]cc1")
print("Number of ring bonds =", oechem.OECount(mol, oechem.OEBondIsInRing()))
print("Number of rotor bonds =", oechem.OECount(mol, oechem.OEIsRotor()))
# @ </SNIPPET>
# 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#CCC1CCNC=C1")
print("Number of non-rotatable bonds =", end=" ")
print(oechem.OECount(mol, oechem.OENotBond(oechem.OEIsRotor())))
print("Number of ring double bonds =", end=" ")
print(
oechem.OECount(
mol, oechem.OEAndBond(oechem.OEBondIsInRing(), oechem.OEHasOrder(2))))
print("Number of double or triple bonds =", end=" ")
print(
oechem.OECount(mol,
oechem.OEOrBond(oechem.OEHasOrder(2),
oechem.OEHasOrder(3))))
# @ </SNIPPET>