Just a quick FYI that a fix for this is now fixed and checked in:
In [4]: fp1 =
rdMolDescriptors.GetMorganFingerprint(Chem.MolFromSmiles('C/C=C/C'),2,useChirality=True)
In [5]: fp2 =
rdMolDescriptors.GetMorganFingerprint(Chem.MolFromSmiles('C/C=C\\C'),2,useChirality=True)
In [6]: DataStructs.DiceSimilarity(fp1,fp2)
Out[6]: 0.6666666666666666
Best,
-greg
On Thu, Dec 10, 2015 at 1:38 PM, Greg Landrum <[email protected]>
wrote:
> 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/
>>
>>
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