# 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>
#
# 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()
if not oechem.OEParseSmiles(mol, "C1=CC=CC=C1"):
print("SMILES string was invalid!")
print("Number of aromatic atoms =",
oechem.OECount(mol, oechem.OEIsAromaticAtom()))
oechem.OEAssignAromaticFlags(mol)
print("Number of aromatic atoms =",
oechem.OECount(mol, oechem.OEIsAromaticAtom()))
# @ </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
# @ <SNIPPET-AROM-PERCEIVE>
mol = oechem.OEGraphMol()
oechem.OEParseSmiles(mol, "C1[NH]C=CC=1CO")
oechem.OEAssignAromaticFlags(mol)
# @ </SNIPPET-AROM-PERCEIVE>
# @ <SNIPPET-AROM-LOOP1>
for atom in mol.GetAtoms(oechem.OEIsAromaticAtom()):
print(atom.GetIdx(), oechem.OEGetAtomicSymbol(atom.GetAtomicNum()))
# @ </SNIPPET-AROM-LOOP1>
# @ <SNIPPET-AROM-LOOP2>
for atom in mol.GetAtoms():
if atom.IsAromatic():
print(atom.GetIdx(), oechem.OEGetAtomicSymbol(atom.GetAtomicNum()))
# @ </SNIPPET-AROM-LOOP2>
# @ </SNIPPET>
def highltigh_torsion_by_cluster(mapped_molecule,
clustered_dihedrals,
fname,
width=600,
height=400):
"""
Highlight torsion by cluster. This is used to visualize clustering output.
Parameters
----------
mapped_molecule: oemol with map indices
clustered_dihedrals
fname
width
height
Returns
-------
"""
mol = oechem.OEMol(mapped_molecule)
atom_bond_sets = []
for cluster in clustered_dihedrals:
atom_bond_set = oechem.OEAtomBondSet()
for dihedral in clustered_dihedrals[cluster]:
a = mol.GetAtom(oechem.OEHasMapIdx(dihedral[0] + 1))
atom_bond_set.AddAtom(a)
for idx in dihedral[1:]:
a2 = mol.GetAtom(oechem.OEHasMapIdx(idx + 1))
atom_bond_set.AddAtom(a2)
bond = mol.GetBond(a, a2)
atom_bond_set.AddBond(bond)
a = a2
atom_bond_sets.append(atom_bond_set)
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetSuppressHydrogens(False)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
disp = oedepict.OE2DMolDisplay(mol, opts)
aroStyle = oedepict.OEHighlightStyle_Color
aroColor = oechem.OEColor(oechem.OEBlack)
oedepict.OEAddHighlighting(disp, aroColor, aroStyle,
oechem.OEIsAromaticAtom(),
oechem.OEIsAromaticBond())
hstyle = oedepict.OEHighlightStyle_BallAndStick
# if color:
# highlight = oechem.OEColor(color)
# # combine all atom_bond_sets
# atom_bond_set = oechem.OEAtomBondSet()
# for ab_set in atom_bond_sets:
# for a in ab_set.GetAtoms():
# atom_bond_set.AddAtom(a)
# for b in ab_set.GetBonds():
# atom_bond_set.AddBond(b)
# oedepict.OEAddHighlighting(disp, highlight, hstyle, atom_bond_set)
# else:
highlight = oedepict.OEHighlightOverlayByBallAndStick(
oechem.OEGetContrastColors())
oedepict.OEAddHighlightOverlay(disp, highlight, atom_bond_sets)
#hcolor = oechem.OEColor(oechem.OELightBlue)
#oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_sets)
return oedepict.OERenderMolecule(fname, disp)
def highlight_torsion(mapped_molecule,
dihedrals,
fname,
width=600,
height=400,
combine_central_bond=True,
color=None):
mol = oechem.OEMol(mapped_molecule)
atom_bond_sets = []
if combine_central_bond:
central_bonds = [(tor[1], tor[2]) for tor in dihedrals]
eq_torsions = {
cb: [
tor for tor in dihedrals
if cb == (tor[1], tor[2]) or cb == (tor[2], tor[1])
]
for cb in central_bonds
}
for cb in eq_torsions:
atom_bond_set = oechem.OEAtomBondSet()
for dihedral in eq_torsions[cb]:
a = mol.GetAtom(oechem.OEHasMapIdx(dihedral[0] + 1))
atom_bond_set.AddAtom(a)
for idx in dihedral[1:]:
a2 = mol.GetAtom(oechem.OEHasMapIdx(idx + 1))
atom_bond_set.AddAtom((a2))
bond = mol.GetBond(a, a2)
atom_bond_set.AddBond(bond)
a = a2
atom_bond_sets.append(atom_bond_set)
if not combine_central_bond:
for dihedral in dihedrals:
atom_bond_set = oechem.OEAtomBondSet()
a = mol.GetAtom(oechem.OEHasMapIdx(dihedral[0] + 1))
atom_bond_set.AddAtom(a)
for idx in dihedral[1:]:
a2 = mol.GetAtom(oechem.OEHasMapIdx(idx + 1))
atom_bond_set.AddAtom((a2))
bond = mol.GetBond(a, a2)
atom_bond_set.AddBond(bond)
a = a2
atom_bond_sets.append(atom_bond_set)
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetSuppressHydrogens(False)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
disp = oedepict.OE2DMolDisplay(mol, opts)
aroStyle = oedepict.OEHighlightStyle_Color
aroColor = oechem.OEColor(oechem.OEBlack)
oedepict.OEAddHighlighting(disp, aroColor, aroStyle,
oechem.OEIsAromaticAtom(),
oechem.OEIsAromaticBond())
hstyle = oedepict.OEHighlightStyle_BallAndStick
if color:
highlight = oechem.OEColor(color)
# combine all atom_bond_sets
atom_bond_set = oechem.OEAtomBondSet()
for ab_set in atom_bond_sets:
for a in ab_set.GetAtoms():
atom_bond_set.AddAtom(a)
for b in ab_set.GetBonds():
atom_bond_set.AddBond(b)
oedepict.OEAddHighlighting(disp, highlight, hstyle, atom_bond_set)
else:
highlight = oedepict.OEHighlightOverlayByBallAndStick(
oechem.OEGetContrastColors())
oedepict.OEAddHighlightOverlay(disp, highlight, atom_bond_sets)
#hcolor = oechem.OEColor(oechem.OELightBlue)
#oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_sets)
return oedepict.OERenderMolecule(fname, disp)
def highlight_bonds(mol_copy,
fname,
conjugation=True,
rotor=False,
width=600,
height=400,
label=None):
"""
Generate image of molecule with highlighted bonds. The bonds can either be highlighted with a conjugation tag
or if it is rotatable.
Parameters
----------
mol_copy: OEMol
fname: str
Name of image file
conjugation: Bool, optional, Default is True
If True, the bonds with conjugation tag set to True will be highlighted
rotor: Bool, optional, Default is False
If True, the rotatable bonds will be highlighted.
width: int
height: int
label: string. Optional, Default is None
The bond order label. The options are WibergBondOrder, Wiberg_psi4, Mayer_psi4.
"""
mol = oechem.OEMol(mol_copy)
bond_index_list = []
for bond in mol.GetBonds():
if conjugation:
try:
if bond.GetData('conjugated'):
bond_index_list.append(bond.GetIdx())
except ValueError:
pass
if rotor:
if bond.IsRotor():
bond_index_list.append(bond.GetIdx())
atomBondSet = oechem.OEAtomBondSet()
for bond in mol.GetBonds():
if bond.GetIdx() in bond_index_list:
atomBondSet.AddBond(bond)
atomBondSet.AddAtom(bond.GetBgn())
atomBondSet.AddAtom(bond.GetEnd())
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetSuppressHydrogens(True)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
if label is not None:
bond_label = {
'WibergBondOrder': LabelWibergBondOrder,
'Wiberg_psi4': LabelWibergPsiBondOrder,
'Mayer_psi4': LabelMayerPsiBondOrder
}
bondlabel = bond_label[label]
opts.SetBondPropertyFunctor(bondlabel())
disp = oedepict.OE2DMolDisplay(mol, opts)
aroStyle = oedepict.OEHighlightStyle_Color
aroColor = oechem.OEColor(oechem.OEBlack)
oedepict.OEAddHighlighting(disp, aroColor, aroStyle,
oechem.OEIsAromaticAtom(),
oechem.OEIsAromaticBond())
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atomBondSet)
return oedepict.OERenderMolecule(fname, disp)