Hi Stefano, This is documented in the "0D structures" section: "if you wish to identify additional stereocenters whose stereo configuration is unspecified, ...then you may wish to trigger perception." The reason we don't do this by default is simply for speed.
Regards, Noel On Mon, 12 Oct 2020 at 19:40, Stefano Forli <fo...@scripps.edu> wrote: > Hi, > > I've found a solution that works, so I'm posting it here for posterity. > By forcing mol.SetChiralityPerceived(False) right after reading the > molecule I can get the proper behavior restored: > > (3.1.0) > 0 True IsChiral() > 0 True HasTetrahedralStereo() > > I think I can see why this can make sense, in the perspective of forcing > to keep the information in the input. > An interesting behavior worth reporting in the docs. > > Thanks, > > S > > > On 10/10/20 11:27 PM, Stefano Forli wrote: > > Hi all, > > > > we've been looking at migrating our OB2 code to OB3 and we have found > differences in how to deal with chirality, which I don't know how to sort > out. I wrote the test code below, which returns different results for > "C(Br)(Cl)F" depending on the version. In particular, with v2, the first > carbon atom is: > > > > 0 True IsChiral() > > 0 True HasTetrahedralStereo() > > > > while for v3: > > > > 0 False IsChiral() > > 0 False HasTetrahedralStereo() > > > > While it would make more sense that no tetrahedral configuration is > defined, I would expect the atom to be perceived as chiral. I've read the > latest documentation I could find from Noel ( > https://open-babel.readthedocs.io/en/latest/Stereochemistry/stereo.html) > with no success. > > Since it seems that the OBMol.IsChiral() method does not exist anymore, > I have no clues on how to detect if a molecule is chiral, and if so, which > atoms are chiral. > > > > Any suggestions? > > > > Thanks, > > > > S > > > > > > ---------- > > import sys > > try: # 3 > > from openbabel import openbabel as ob > > except: # 2 > > import openbabel as ob > > print(ob.OBReleaseVersion()) > > conv = ob.OBConversion() > > conv.SetInFormat("smi") > > mol = ob.OBMol() > > conv.ReadString(mol, "C(Br)(Cl)F") > > try: > > # not available anymore in OB3 > > print(mol.IsChiral(), "IsChiral()") > > except: > > pass > > facade = ob.OBStereoFacade(mol, True) > > for a in ob.OBMolAtomIter(mol): > > idx = a.GetId() > > print(idx, a.IsChiral(), "IsChiral()") > > print(idx, facade.HasTetrahedralStereo(idx), > "HasTetrahedralStereo()") > > ---------- > > > > > > > > > > > > > > > > -- > > Stefano Forli, PhD > > Assistant Professor > Dept. of Integrative Structural > and Computational Biology, MB-112A > Scripps Research > 10550 North Torrey Pines Road > La Jolla, CA 92037-1000, USA. > > tel: +1 (858)784-2055 > email: fo...@scripps.edu > http://www.scripps.edu/faculty/forli/ > > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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