def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-in")
ifs = oechem.oemolistream()
ifs.SetConfTest(oechem.OEAbsoluteConfTest()) # VTL
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if ext != "pdf":
oechem.OEThrow.Fatal("Output must be PDF format.")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
report = oedepict.OEReport(ropts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(),
oedepict.OEScale_AutoScale)
for mol in ifs.GetOEMols(): # VTL ignore confs; dont use GetOEGraphMols
print(mol.GetTitle()) # VTL
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(cell, disp)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, 12,
oedepict.OEAlignment_Center, oechem.OEBlack)
for pagenum, footer in enumerate(report.GetFooters()):
text = "Page %d of %d" % (pagenum + 1, report.NumPages())
oedepict.OEDrawTextToCenter(footer, text, font)
oedepict.OEWriteReport(ofs, ext, report)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 400.0)
oedepict.OEConfigureImageHeight(itf, 400.0)
oedepict.OEConfigureImageGridParams(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
rows = oedepict.OEGetImageGridNumRows(itf)
cols = oedepict.OEGetImageGridNumColumns(itf)
grid = oedepict.OEImageGrid(image, rows, cols)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(grid.GetCellWidth(), grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
celliter = grid.GetCells()
for iname in itf.GetStringList("-in"):
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Warning("Cannot open %s input file!" % iname)
continue
for mol in ifs.GetOEGraphMols():
if not celliter.IsValid():
break
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(celliter.Target(), disp)
celliter.Next()
oedepict.OEWriteImage(ofs, ext, image)
return 0
def depict(mol, width=500, height=200):
from IPython.display import Image
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetDepictOrientation(oedepict.OEDepictOrientation_Horizontal)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
ofs = oechem.oeosstream()
oedepict.OERenderMolecule(ofs, 'png', disp)
ofs.flush()
return Image(data="".join(ofs.str()))
def genHBIndexGuide(inpmol):
"""
For each mol, generate depiction of molecule with labeled
indices as read in by oechem. Saved as _____
"""
mol = oechem.OEGraphMol(inpmol)
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetDepictOrientation(oedepict.OEDepictOrientation_Horizontal)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
oedepict.OERenderMolecule(outfn, mol)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Cannot read input file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
oedepict.OEPrepareDepiction(mol, popts)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
dopts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def depictMatch(mol, match, width=500, height=200):
from IPython.display import Image
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetDepictOrientation(oedepict.OEDepictOrientation_Horizontal)
dopt.SetSuppressHydrogens(True)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
hstyle = oedepict.OEHighlightStyle_Color
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, match)
ofs = oechem.oeosstream()
oedepict.OERenderMolecule(ofs, 'png', disp)
ofs.flush()
return Image(data="".join(ofs.str()))
def prep_pdf_writer():
itf = oechem.OEInterface()
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
report = oedepict.OEReport(ropts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(), oedepict.OEScale_AutoScale)
return popts, dopts, report
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigurePrepareDepictionOptions(
itf, oedepict.OEPrepareDepictionSetup_SuppressHydrogens
| oedepict.OEPrepareDepictionSetup_DepictOrientation)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oemolostream(".sdf")
if itf.HasString("-out"):
oname = itf.GetString("-out")
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")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
popts.SetClearCoords(True)
for mol in ifs.GetOEGraphMols():
oedepict.OEPrepareDepiction(mol, popts)
oechem.OEWriteMolecule(ofs, mol)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
oedepict.OEConfigureHighlightParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Cannot read input file!")
smarts = itf.GetString("-smarts")
ss = oechem.OESubSearch()
if not ss.Init(smarts):
oechem.OEThrow.Fatal("Cannot parse smarts: %s" % smarts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
oedepict.OEPrepareDepiction(mol, popts)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
dopts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetMargins(10.0)
disp = oedepict.OE2DMolDisplay(mol, dopts)
hstyle = oedepict.OEGetHighlightStyle(itf)
hcolor = oedepict.OEGetHighlightColor(itf)
oechem.OEPrepareSearch(mol, ss)
unique = True
for match in ss.Match(mol, unique):
oedepict.OEAddHighlighting(disp, hcolor, hstyle, match)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
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)
