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 [http://pubchem.ncbi.nlm.nih.gov/images/pclogo_220.gif]<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/
Structure2D_CID_638015.sdf
Description: Structure2D_CID_638015.sdf
Structure2D_CID_6436082.sdf
Description: Structure2D_CID_6436082.sdf
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