#!/usr/bin/env python3 # (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. ############################################################################# # Calculates XLogP of a molecule and depict the contribution of # fragments to the total XLogP ############################################################################# import sys from openeye import oechem from openeye import oedepict from openeye import oegrapheme from openeye import oemolprop from openeye import oemedchem from openeye import oequacpac def main(argv=[__name__]): itf = oechem.OEInterface(InterfaceData) oedepict.OEConfigureImageWidth(itf, 400.0) oedepict.OEConfigureImageHeight(itf, 300.0) oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle) if not oechem.OEParseCommandLine(itf, argv): return 1 iname = itf.GetString("-in") oname = itf.GetString("-out") # check input/output files ifs = oechem.oemolistream() if not ifs.open(iname): oechem.OEThrow.Fatal("Cannot open input file!") 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!") # read a molecule mol = oechem.OEGraphMol() if not oechem.OEReadMolecule(ifs, mol): oechem.OEThrow.Fatal("Cannot read input file!") # initialize fragmentation function fragfunc = get_fragmentation_function(itf) # create image width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf) image = oedepict.OEImage(width, height) # setup depiction options opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) oedepict.OESetup2DMolDisplayOptions(opts, itf) opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome) # depict molecule with XLogP atom contributions oedepict.OEPrepareDepiction(mol) depict_molecule_fragment_xlogp(image, mol, fragfunc, opts) oedepict.OEWriteImage(ofs, ext, image) return 0 def set_atom_properties(mol, datatag): """ Attaches the XLogP atom contribution to each atom with the given tag. :type mol: oechem.OEMolBase :type datatag: string """ oequacpac.OERemoveFormalCharge(mol) avals = oechem.OEFloatArray(mol.GetMaxAtomIdx()) logp = oemolprop.OEGetXLogP(mol, avals) mol.SetTitle(mol.GetTitle() + " -- OEXLogP = %.2f" % logp) for atom in mol.GetAtoms(): val = avals[atom.GetIdx()] atom.SetData(datatag, val) def fragment_molecule(mol, fragfunc, grouptag): """ Fragments the molecule and stores each fragment as a group on the molecule. :type mol: oechem.OEMolBase :type fragfunc: function() :type grouptag: string """ for frag in fragfunc(mol): atoms = oechem.OEAtomVector() for atom in frag.GetAtoms(): atoms.append(atom) bonds = oechem.OEBondVector() for bond in frag.GetBonds(): bonds.append(bond) mol.NewGroup(grouptag, atoms, bonds) def set_fragment_properties(mol, datatag, grouptag): """ Calculates the fragment contribution based on attached atom properties for pre-generated fragments. :type mol: oechem.OEMolBase :type datatag: string :type grouptag: string """ minvalue = float("inf") maxvalue = float("-inf") for group in mol.GetGroups(oechem.OEHasGroupType(grouptag)): sumprop = 0.0 for atom in group.GetAtoms(): sumprop += atom.GetData(datatag) group.SetData(datatag, sumprop) minvalue = min(minvalue, sumprop) maxvalue = max(maxvalue, sumprop) return minvalue, maxvalue def depict_molecule_fragment_xlogp(image, mol, fragfunc, opts): """ Generates an image of a molecule depicting the fragment contribution of XLogP. :type image: oedepict.OEImageBase :type mol: oechem.OEMolBase :type fragfunc: function() :type opts: oedepict.OE2DMolDiplayOptions """ # calculate atom contributions of XLogP sdatatag = "XLogP" idatatag = oechem.OEGetTag(sdatatag) set_atom_properties(mol, idatatag) # fragment molecule sgrouptag = "fragment" igrouptag = oechem.OEGetTag(sgrouptag) fragment_molecule(mol, fragfunc, igrouptag) # calculate fragment contributions minvalue, maxvalue = set_fragment_properties(mol, idatatag, igrouptag) # initialize color gradient lightgrey = oechem.OEColor(240, 240, 240) colorg = oechem.OELinearColorGradient(oechem.OEColorStop(0.0, lightgrey)) colorg.AddStop(oechem.OEColorStop(minvalue, oechem.OEDarkGreen)) colorg.AddStop(oechem.OEColorStop(maxvalue, oechem.OEDarkPurple)) # generate image frames iwidth, iheight = image.GetWidth(), image.GetHeight() mframe = oedepict.OEImageFrame(image, iwidth, iheight * 0.8, oedepict.OE2DPoint(0.0, 0.0)) cframe = oedepict.OEImageFrame(image, iwidth, iheight * 0.2, oedepict.OE2DPoint(0.0, iheight * 0.8)) # initialize molecule display opts.SetDimensions(mframe.GetWidth(), mframe.GetHeight(), oedepict.OEScale_AutoScale) disp = oedepict.OE2DMolDisplay(mol, opts) # initialize highlighting style highlight = oedepict.OEHighlightByLasso(oechem.OEWhite) highlight.SetConsiderAtomLabelBoundingBox(True) colorgopts = oegrapheme.OEColorGradientDisplayOptions() for group in mol.GetGroups(oechem.OEHasGroupType(igrouptag)): groupvalue = group.GetData(idatatag) colorgopts.AddMarkedValue(groupvalue) # depict fragment contribution color = colorg.GetColorAt(groupvalue) highlight.SetColor(color) abset = oechem.OEAtomBondSet(group.GetAtoms(), group.GetBonds()) oedepict.OEAddHighlighting(disp, highlight, abset) # render molecule and color gradient oedepict.OERenderMolecule(mframe, disp) oegrapheme.OEDrawColorGradient(cframe, colorg, colorgopts) def get_fragmentation_function(itf): fstring = itf.GetString("-fragtype") if fstring == "funcgroup": return oemedchem.OEGetFuncGroupFragments if fstring == "ring-chain": return oemedchem.OEGetRingChainFragments return oemedchem.OEGetRingLinkerSideChainFragments ############################################################################# # INTERFACE ############################################################################# InterfaceData = """ !CATEGORY "input/output options" 1 !PARAMETER -in !ALIAS -i !TYPE string !REQUIRED true !KEYLESS 1 !VISIBILITY simple !BRIEF Input molecule filename !END !PARAMETER -out !ALIAS -o !TYPE string !REQUIRED true !KEYLESS 2 !VISIBILITY simple !BRIEF Output filename of the generated image !END !END !CATEGORY "fragmentation options" 2 !PARAMETER -fragtype !ALIAS -ftype !TYPE string !REQUIRED false !KEYLESS 3 !DEFAULT funcgroup !LEGAL_VALUE funcgroup !LEGAL_VALUE ring-chain !LEGAL_VALUE ring-linker-sidechain !VISIBILITY simple !BRIEF Fragmentation type !END !END """ if __name__ == "__main__": sys.exit(main(sys.argv))