Hi Tyler,
This one is "non-trivial". It's going to take me a while to look though it
and figure out what's going on.
-greg
On Fri, Jun 8, 2018 at 12:02 AM Tyler Backman <tback...@lbl.gov> wrote:
> 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
>
>
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