How to generate the 3D SDF from the output? #1

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1. alexgcsa

   changed the title [-]How to generate the SDF from the output?[/-] [+]How to generate the 3D SDF from the output?[/+] on Aug 1, 2021
2. federico-camerota commented on Aug 5, 2021

   

   federico-camerota

   on Aug 5, 2021

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   Hi @alexgcsa, I was able to modify the 'gen.py' script to output pdb files doing the following:

   from rdkit.Chem.rdmolfiles import  MolToPDBFile
   from rdkit.Chem.AllChem import EmbedMolecule
   
   out = solver.generate_samples_from_smiles(*args*)
   EmbedMolecule(out.rdmol, useRandomCoords=True)
   gen_mol = utils.set_rdmol_positions(out.rdmol, out.pos_gen[-1])
   MolToPDBFile(gen_mol, *output_filename*)
   

   where you should replace appropriately args and output_filename.
   If I understood properly the code, out.rdmol is the rdkit mol built from the smiles string.
   While out.pos_gen are the generated atom positions.

   According to the rdkit documentation, you should be able to write into sdf replacing the last line with:

   writer = SDWriter('out.sdf')
   writer.write(gen_mol)
   

   If you want to write the pkl into sdf, it should be enough to do:
   out = pickle.load(*pkl_file*)

   Hope you find this helpful :)

   P.S. If you find any error in my solution, please let me know

   👍React with 👍1Reacted by Chence Shi
3. alexgcsa commented on Aug 7, 2021

   

   alexgcsa

   on Aug 7, 2021

   Author

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   Thank you @federico-camerota , I will test your solution today.
4. shichence

   added

   enhancementNew feature or requestNew feature or request

   on Aug 16, 2021