Hi all, I opened an issue at rdkit-github for that matter.
https://github.com/rdkit/rdkit/issues/626 Thanks to your comments! If you want look at the code snippet I posted. At the moment, simply all stereo-isomers are generated. regards Soren On Fri, Sep 25, 2015 at 12:19 AM, Axel Pahl <axelp...@gmx.de> wrote: > Hi Soren, > > maybe this function which enumerates racemates with one stereocenter into > the corresponding enantiomers might help: > > def enum_racemates(sdf_list_or_file, find_only=True, mol_id="molid"): > """returns: result_sdf::list<mol>, racemic_molids::list<int> > find_only==True: return new sdf as list which contains all the > racemates of the input sdf. > find_only==False: return new sdf as list with ALL input structures, > where the racemates are > replaced by their two enantiomers. The returned sdf > is always > equal in size or larger as the input sdf. > Multiple stereo centers are not yet handled. > In the new sdf the molids are no longer unique and should be reassigned > (remove molid and run calc_props(sdf)).""" > > result_sdf = Mol_List() > racemic_molids = [] > > if not isinstance(sdf_list_or_file, list) and > sdf_list_or_file.atEnd(): # sdf is file > print(" * file object is at end, please reload.") > return None > > for mol in sdf_list_or_file: > first_undefined = False > chiral_centers = Chem.FindMolChiralCenters(mol, > includeUnassigned=True) > > if chiral_centers: > first_center = chiral_centers[0][0] > first_undefined = chiral_centers[0][1] == "?" > > if first_undefined: > racemic_molids.append(int(mol.GetProp(mol_id))) > if find_only: > result_sdf.append(mol) > continue > > else: > mol1 = Chem.Mol(mol) > mol2 = Chem.Mol(mol) > > mol1.GetAtomWithIdx(first_center).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW) > > mol2.GetAtomWithIdx(first_center).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW) > result_sdf.append(mol1) > result_sdf.append(mol2) > > else: > if not find_only: # return ALL mols > result_sdf.append(mol) > > return result_sdf, racemic_molids > > Please also have a look at this post > http://sourceforge.net/p/rdkit/mailman/message/32390126/ and Toby's > answer which pointed me in the right direction. > > Kind regards, > Axel > > > On 24.09.2015 23:17, Soren Wacker wrote: > > Hi, > > is it possible with RDKit to generate all stereoisomers of a given > compound? > > If not, is anyone working on it? > > If not, how difficult would it be / what would be the best way to > implement such a function. > > best regards > > Soren > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > Rdkit-discuss mailing > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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