Dear Oriol, At the moment there is no way to do this. I think it should be fixable, but I need to do a bit more investigation.
-greg On Mon, Dec 7, 2015 at 7:05 PM, Oriol Senan Campos <[email protected]> wrote: > Dear RDKit community > > I am trying to compare structurally several molecules using ecfp > fingerprints. I would like to distinguish between cis/trans isomers, but > after looking at the documentation and previous threads I am not able to > include stereochemical information from the sdf files. > > > Here is my example, which corresponds to 9-cis-retinal: > > https://pubchem.ncbi.nlm.nih.gov/compound/6436082#section=Top > <https://pubchem.ncbi.nlm.nih.gov/compound/6436082#section=Top> > 9-cis-Retinal | C20H28O - PubChem > 9-cis-Retinal | C20H28O | CID 6436082 - structure, chemical names, > physical and chemical properties, classification, patents, literature, > biological activities, safety/hazards/toxicity information, supplier lists, > and more. > Més informació... > <https://pubchem.ncbi.nlm.nih.gov/compound/6436082#section=Top> > > and retinal (trans-retinal): > > https://pubchem.ncbi.nlm.nih.gov/compound/638015#section=Top > > > The sdf files are attached > > > file1 = "Structure2D_CID_6436082.sdf" > > file2 = "Structure2D_CID_638015.sdf" > > > mol1 = > Chem.MolFromMolFile(file1) > > Chem.AssignAtomChiralTagsFromStructure(mol1) > Chem.AssignStereochemistry(mol1cis,force=True, cleanIt = True, > flagPossibleStereoCenters = True) > fps1 = AllChem.GetMorganFingerprint(mol1,2, useChirality = True) > > > file2 = "Structure2D_CID_638015.sdf" > mol2 = > Chem.MolFromMolFile(file2) > > Chem.AssignAtomChiralTagsFromStructure(mol2) > Chem.AssignStereochemistry(mol2, force = True, cleanIt = True, > flagPossibleStereoCenters = True) > fps2 = AllChem.GetMorganFingerprint(mol21,2, useChirality = True) > > DataStructs.DiceSimilarity(fps1,fps2) > > Out[250]: 1.0 > > Is there a possibility to obtain a structural similarity < 1 in cases like > my example? > > Thank you very much > Best Regards > > > > Oriol Senan > PhD Student Universitat Rovira i Virgili > > http://seeslab.info/researchers/senan/ > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple > OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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