Convert list of smiles strings ['x', 'y', 'z'] to mol files or MDL mol blocks using RDKit










0














I have generated a list of smiles strings and defined them as 'result'



I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this:



m = Chem.MolFromSmiles('result')
print(Chem.MolToMolBlock(m))


This script does not work and returns:




ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToMolBlock(NoneType) did not match C++ signature:
MolToMolBlock(RDKit::ROMol mol, bool includeStereo=True, int confId=-1, bool kekulize=True, bool forceV3000=False)




How would I go about correcting this?



Thanks!










share|improve this question




























    0














    I have generated a list of smiles strings and defined them as 'result'



    I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this:



    m = Chem.MolFromSmiles('result')
    print(Chem.MolToMolBlock(m))


    This script does not work and returns:




    ArgumentError: Python argument types in
    rdkit.Chem.rdmolfiles.MolToMolBlock(NoneType) did not match C++ signature:
    MolToMolBlock(RDKit::ROMol mol, bool includeStereo=True, int confId=-1, bool kekulize=True, bool forceV3000=False)




    How would I go about correcting this?



    Thanks!










    share|improve this question


























      0












      0








      0







      I have generated a list of smiles strings and defined them as 'result'



      I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this:



      m = Chem.MolFromSmiles('result')
      print(Chem.MolToMolBlock(m))


      This script does not work and returns:




      ArgumentError: Python argument types in
      rdkit.Chem.rdmolfiles.MolToMolBlock(NoneType) did not match C++ signature:
      MolToMolBlock(RDKit::ROMol mol, bool includeStereo=True, int confId=-1, bool kekulize=True, bool forceV3000=False)




      How would I go about correcting this?



      Thanks!










      share|improve this question















      I have generated a list of smiles strings and defined them as 'result'



      I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this:



      m = Chem.MolFromSmiles('result')
      print(Chem.MolToMolBlock(m))


      This script does not work and returns:




      ArgumentError: Python argument types in
      rdkit.Chem.rdmolfiles.MolToMolBlock(NoneType) did not match C++ signature:
      MolToMolBlock(RDKit::ROMol mol, bool includeStereo=True, int confId=-1, bool kekulize=True, bool forceV3000=False)




      How would I go about correcting this?



      Thanks!







      python-3.x spyder rdkit






      share|improve this question















      share|improve this question













      share|improve this question




      share|improve this question








      edited Nov 12 '18 at 3:05









      Graham

      3,533123559




      3,533123559










      asked Nov 12 '18 at 0:50









      Matt Hostetler

      62




      62






















          1 Answer
          1






          active

          oldest

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          0














          You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
          Variable names are not strings, so don't use them with quotes.



          First you have to convert the SMILES one by one to mol objects.



          from rdkit import Chem
          result = ['C', 'CC', 'CCC']
          mo = [Chem.MolFromSmiles(r) for r in result]


          Then you can print the Molblocks one by one.



          for m in mo:
          print(Chem.MolToMolBlock(m))


          That will give you this:



           RDKit 2D

          1 0 0 0 0 0 0 0 0 0999 V2000
          0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
          M END


          RDKit 2D

          2 1 0 0 0 0 0 0 0 0999 V2000
          0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
          1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
          1 2 1 0
          M END


          RDKit 2D

          3 2 0 0 0 0 0 0 0 0999 V2000
          0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
          1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
          2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
          1 2 1 0
          2 3 1 0
          M END





          share|improve this answer




















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            1 Answer
            1






            active

            oldest

            votes








            1 Answer
            1






            active

            oldest

            votes









            active

            oldest

            votes






            active

            oldest

            votes









            0














            You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
            Variable names are not strings, so don't use them with quotes.



            First you have to convert the SMILES one by one to mol objects.



            from rdkit import Chem
            result = ['C', 'CC', 'CCC']
            mo = [Chem.MolFromSmiles(r) for r in result]


            Then you can print the Molblocks one by one.



            for m in mo:
            print(Chem.MolToMolBlock(m))


            That will give you this:



             RDKit 2D

            1 0 0 0 0 0 0 0 0 0999 V2000
            0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
            M END


            RDKit 2D

            2 1 0 0 0 0 0 0 0 0999 V2000
            0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
            1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
            1 2 1 0
            M END


            RDKit 2D

            3 2 0 0 0 0 0 0 0 0999 V2000
            0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
            1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
            2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
            1 2 1 0
            2 3 1 0
            M END





            share|improve this answer

























              0














              You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
              Variable names are not strings, so don't use them with quotes.



              First you have to convert the SMILES one by one to mol objects.



              from rdkit import Chem
              result = ['C', 'CC', 'CCC']
              mo = [Chem.MolFromSmiles(r) for r in result]


              Then you can print the Molblocks one by one.



              for m in mo:
              print(Chem.MolToMolBlock(m))


              That will give you this:



               RDKit 2D

              1 0 0 0 0 0 0 0 0 0999 V2000
              0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
              M END


              RDKit 2D

              2 1 0 0 0 0 0 0 0 0999 V2000
              0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
              1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
              1 2 1 0
              M END


              RDKit 2D

              3 2 0 0 0 0 0 0 0 0999 V2000
              0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
              1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
              2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
              1 2 1 0
              2 3 1 0
              M END





              share|improve this answer























                0












                0








                0






                You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
                Variable names are not strings, so don't use them with quotes.



                First you have to convert the SMILES one by one to mol objects.



                from rdkit import Chem
                result = ['C', 'CC', 'CCC']
                mo = [Chem.MolFromSmiles(r) for r in result]


                Then you can print the Molblocks one by one.



                for m in mo:
                print(Chem.MolToMolBlock(m))


                That will give you this:



                 RDKit 2D

                1 0 0 0 0 0 0 0 0 0999 V2000
                0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                M END


                RDKit 2D

                2 1 0 0 0 0 0 0 0 0999 V2000
                0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                1 2 1 0
                M END


                RDKit 2D

                3 2 0 0 0 0 0 0 0 0999 V2000
                0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                1 2 1 0
                2 3 1 0
                M END





                share|improve this answer












                You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
                Variable names are not strings, so don't use them with quotes.



                First you have to convert the SMILES one by one to mol objects.



                from rdkit import Chem
                result = ['C', 'CC', 'CCC']
                mo = [Chem.MolFromSmiles(r) for r in result]


                Then you can print the Molblocks one by one.



                for m in mo:
                print(Chem.MolToMolBlock(m))


                That will give you this:



                 RDKit 2D

                1 0 0 0 0 0 0 0 0 0999 V2000
                0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                M END


                RDKit 2D

                2 1 0 0 0 0 0 0 0 0999 V2000
                0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                1 2 1 0
                M END


                RDKit 2D

                3 2 0 0 0 0 0 0 0 0999 V2000
                0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
                1 2 1 0
                2 3 1 0
                M END






                share|improve this answer












                share|improve this answer



                share|improve this answer










                answered Nov 12 '18 at 17:37









                rapelpy

                146115




                146115



























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