def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
smarts = itf.GetString("-smarts")
qmol = oechem.OEQMol()
if not oechem.OEParseSmarts(qmol, smarts):
oechem.OEThrow.Fatal("Invalid SMARTS: %s" % smarts)
oechem.OEGenerate2DCoordinates(qmol)
ss = oechem.OESubSearch(qmol)
if not ss.IsValid():
oechem.OEThrow.Fatal("Unable to initialize substructure search!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input molecule file!")
ofs = oechem.oemolostream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
if not oechem.OEIs2DFormat(ofs.GetFormat()):
oechem.OEThrow.Fatal("Invalid output format for 2D coordinates")
for mol in ifs.GetOEGraphMols():
oechem.OEPrepareSearch(mol, ss)
alignres = oedepict.OEPrepareAlignedDepiction(mol, ss)
if not alignres.IsValid():
oechem.OEThrow.Warning(
"Substructure is not found in input molecule!")
oedepict.OEPrepareDepiction(mol)
oechem.OEWriteMolecule(ofs, mol)
return 0
def align2d(file1, file2):
atomexpr = oechem.OEExprOpts_AtomicNumber | oechem.OEExprOpts_RingMember
bondexpr = oechem.OEExprOpts_RingMember
ifs1 = oechem.oemolistream(file1)
ifs2 = oechem.oemolistream(file2)
ifs1.SetConfTest(oechem.OEAbsCanonicalConfTest())
ifs2.SetConfTest(oechem.OEAbsCanonicalConfTest())
popts, dopts, report = prep_pdf_writer()
for mol1, mol2 in zip(ifs1.GetOEMols(), ifs2.GetOEMols()):
oechem.OESuppressHydrogens(mol1)
oechem.OESuppressHydrogens(mol2)
oechem.OEGenerate2DCoordinates(mol2)
ss = oechem.OESubSearch(mol2, atomexpr, bondexpr)
oechem.OEPrepareSearch(mol1, ss)
alignres = oedepict.OEPrepareAlignedDepiction(mol1, ss)
if not alignres.IsValid():
oechem.OEThrow.Error(
"Substructure is not found in input molecule!")
cell1 = report.NewCell()
cell2 = report.NewCell()
oedepict.OEPrepareDepiction(mol1, popts)
oedepict.OEPrepareDepiction(mol2, popts)
disp1 = oedepict.OE2DMolDisplay(mol1, dopts)
disp2 = oedepict.OE2DMolDisplay(mol2, dopts)
oedepict.OERenderMolecule(cell1, disp1)
oedepict.OERenderMolecule(cell2, disp2)
ofs = oechem.oeofstream()
if not ofs.open('output.pdf'):
oechem.OEThrow.Fatal("Cannot open output file!")
oedepict.OEWriteReport(ofs, "pdf", report)
def render_atom_mapping(filename, molecule1, molecule2, new_to_old_atom_map, width=1200, height=600):
"""
Render the atom mapping to a PDF file.
Parameters
----------
filename : str
The PDF filename to write to.
molecule1 : openeye.oechem.OEMol
Initial molecule
molecule2 : openeye.oechem.OEMol
Final molecule
new_to_old_atom_map : dict of int
new_to_old_atom_map[molecule2_atom_index] is the corresponding molecule1 atom index
width : int, optional, default=1200
Width in pixels
height : int, optional, default=1200
Height in pixels
"""
from openeye import oechem, oedepict
# Make copies of the input molecules
molecule1, molecule2 = oechem.OEGraphMol(molecule1), oechem.OEGraphMol(molecule2)
oechem.OEGenerate2DCoordinates(molecule1)
oechem.OEGenerate2DCoordinates(molecule2)
# Add both to an OEGraphMol reaction
rmol = oechem.OEGraphMol()
rmol.SetRxn(True)
def add_molecule(mol):
# Add atoms
new_atoms = list()
old_to_new_atoms = dict()
for old_atom in mol.GetAtoms():
new_atom = rmol.NewAtom(old_atom.GetAtomicNum())
new_atoms.append(new_atom)
old_to_new_atoms[old_atom] = new_atom
# Add bonds
for old_bond in mol.GetBonds():
rmol.NewBond(old_to_new_atoms[old_bond.GetBgn()], old_to_new_atoms[old_bond.GetEnd()], old_bond.GetOrder())
return new_atoms, old_to_new_atoms
[new_atoms_1, old_to_new_atoms_1] = add_molecule(molecule1)
[new_atoms_2, old_to_new_atoms_2] = add_molecule(molecule2)
# Label reactant and product
for atom in new_atoms_1:
atom.SetRxnRole(oechem.OERxnRole_Reactant)
for atom in new_atoms_2:
atom.SetRxnRole(oechem.OERxnRole_Product)
core1 = oechem.OEAtomBondSet()
core2 = oechem.OEAtomBondSet()
# add all atoms to the set
core1.AddAtoms(new_atoms_1)
core2.AddAtoms(new_atoms_2)
# Label mapped atoms
core_change = oechem.OEAtomBondSet()
index =1
for (index2, index1) in new_to_old_atom_map.items():
new_atoms_1[index1].SetMapIdx(index)
new_atoms_2[index2].SetMapIdx(index)
# now remove the atoms that are core, so only uniques are highlighted
core1.RemoveAtom(new_atoms_1[index1])
core2.RemoveAtom(new_atoms_2[index2])
if new_atoms_1[index1].GetAtomicNum() != new_atoms_2[index2].GetAtomicNum():
# this means the element type is changing
core_change.AddAtom(new_atoms_1[index1])
core_change.AddAtom(new_atoms_2[index2])
index += 1
# Set up image options
itf = oechem.OEInterface()
oedepict.OEConfigureImageOptions(itf)
ext = oechem.OEGetFileExtension(filename)
if not oedepict.OEIsRegisteredImageFile(ext):
raise Exception('Unknown image type for filename %s' % filename)
ofs = oechem.oeofstream()
if not ofs.open(filename):
raise Exception('Cannot open output file %s' % filename)
# Setup depiction options
oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetBondWidthScaling(True)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomMapIdx())
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
# Depict reaction with component highlights
oechem.OEGenerate2DCoordinates(rmol)
rdisp = oedepict.OE2DMolDisplay(rmol, opts)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEPink),oedepict.OEHighlightStyle_Stick, core1)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEPurple),oedepict.OEHighlightStyle_Stick, core2)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEGreen),oedepict.OEHighlightStyle_Stick, core_change)
oedepict.OERenderMolecule(ofs, ext, rdisp)
ofs.close()