If I convert some compounds to SMILES and back, sometimes they no longer match themselves with MCS if matchChiralTag=True, however the actual number of each type of chiral tag is still the same per Chem.FindMolChiralCenters(). Am I doing something wrong here?
This example uses the rapamycin structure from selleckchem: http://file.selleckchem.com/downloads/product-sdf/rapamycin-sirolimus-s1039.SDF ### BEGIN CODE EXAMPLE ### import rdkit.Chem as chem from rdkit.Chem.rdFMCS import FindMCS # read in the compound mymol = chem.MolFromMolFile('rapamycin-sirolimus-s1039.SDF', sanitize=True, removeHs=True, strictParsing=True) print(mymol.GetNumAtoms()) # convert to smiles and back mymol2 = chem.MolFromSmiles(chem.MolToSmiles(mymol, canonical=True, isomericSmiles=True)) print(mymol2.GetNumAtoms()) # compare the converted molecule to the original with chirality myMCS = FindMCS([mymol, mymol2], matchChiralTag=True, matchValences=True) print(myMCS.numAtoms) # compare the converted molecule to the original without chirality myMCSNotChiral = FindMCS([mymol, mymol2], matchChiralTag=False, matchValences=True) print(myMCSNotChiral.numAtoms) ### END CODE EXAMPLE ### All four of these should print 65, but the 3rd one comparing the molecule to itself after converting to SMILES and back matches only 19 atoms: ### BEGIN OUTPUT ### 65 65 19 65 ### END OUTPUT ### I generated this example w/ rdkit 2018.03.2.0 on python 3.6.5 installed via Anaconda on OSX 10.12.6. I also reproduced this with a version of Rapamycin I constructed de-novo using SMARTS reactions for each enzyme. This one also had an identical isomeric SMILES to the selleckchem one, but matched 39 out of 65 atoms with itself, vs 19 out of 65 for the selleckchem structure. Sincerely, Tyler Backman ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
