def GetFragmentScore(mol):
score = 0.0
score += 2.0 * oechem.OECount(mol, oechem.OEAtomIsInRing())
score += 1.0 * oechem.OECount(mol, oechem.OENotAtom(oechem.OEAtomIsInRing()))
return score
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 RingSubSet(ifs, ofs, exo):
for mol in ifs.GetOEGraphMols():
submol = oechem.OEGraphMol()
adjustHcount = True
if exo:
isinring = oechem.OEAtomIsInRing()
isexo = oechem.OEIsNonRingAtomDoubleBondedToRing()
includeexo = oechem.OEOrAtom(isinring, isexo)
oechem.OESubsetMol(submol, mol, includeexo, adjustHcount)
else:
oechem.OESubsetMol(submol, mol, oechem.OEAtomIsInRing(),
adjustHcount)
submol.SetTitle(mol.GetTitle() + "_rings")
if submol.NumAtoms() != 0:
oechem.OEWriteMolecule(ofs, submol)
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 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 GetFuncGroups(mol):
'''
:param mol:
:return:
'''
funcGrps = []
for funcGrp in oemedchem.OEGetFuncGroupFragments(mol):
if oechem.OECount(funcGrp, oechem.OEIsHeavy()) > 5:
continue
if oechem.OECount(funcGrp, oechem.OEIsHetero()) == 0:
continue
if oechem.OECount(funcGrp, oechem.OEAtomIsInRing()) > 0:
continue
funcGrps.append(oechem.OEAtomBondSet(funcGrp))
return funcGrps
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <infile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
print("Title MolWt NumAtoms NumHeavyAtoms NumRingAtoms NumRotors NumConfs")
for mol in ifs.GetOEMols():
title = mol.GetTitle()
if not title:
title = "Untitled"
print("%s %.3f %d %d %d %d %d" %
(title, oechem.OECalculateMolecularWeight(mol), mol.NumAtoms(),
oechem.OECount(mol, oechem.OEIsHeavy()),
oechem.OECount(mol, oechem.OEAtomIsInRing()),
oechem.OECount(mol, oechem.OEIsRotor()), mol.NumConfs()))
# 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, "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(
# @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-PROP-LABEL-FONT-SCALE>
DepictMolecules(opts, smiles,
"OE2DMolDisplayOptions_SetAtomPropLabelFontScale")
# @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-STEREO-STYLE>
width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale
opts = oedepict.OE2DMolDisplayOptions(width, height, scale)
opts.SetAtomStereoStyle(oedepict.OEAtomStereoStyle_Display_All
| oedepict.OEAtomStereoStyle_HashWedgeStyle_Standard)
# @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-STEREO-STYLE>
DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetAtomStereoStyle")
# @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-VISIBILITY-FUNCTOR>
width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale
opts = oedepict.OE2DMolDisplayOptions(width, height, scale)
opts.SetAtomVisibilityFunctor(oechem.OEAtomIsInRing())
# @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-VISIBILITY-FUNCTOR>
DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetAtomVisibilityFunctor")
########################################################################
# BACKGROUND
########################################################################
# @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-BACKGROUND-COLOR>
width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale
opts = oedepict.OE2DMolDisplayOptions(width, height, scale)
opts.SetBackgroundColor(oechem.OEYellowTint)
# @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-BACKGROUND-COLOR>
DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetBackgroundColor")
########################################################################
#!/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, "c1cc[nH]c1CC2COCNC2")
submol = oechem.OEGraphMol()
oechem.OESubsetMol(submol, mol, oechem.OEAtomIsInRing(), True)
print(oechem.OEMolToSmiles(submol))
# @ </SNIPPET>
#!/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, "c1cc[nH]c1CC2COCNC2")
print("Number of heavy atoms =", oechem.OECount(mol, oechem.OEIsHeavy()))
print("Number of ring atoms =", oechem.OECount(mol, oechem.OEAtomIsInRing()))
# @ </SNIPPET>