Re: [Rdkit-discuss] Generation of stereo-isomers

[Axel P. <axe...@gm...>]

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
>
>
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