I posted a memo about how to read maestro file format from RDKit. It means that rdkitter can use “mae” format from RDKit. ;-)
BTW, schrodinger’s site provides API for python. I would like to know the way to communicate rdkit from schrodinger python API.
I read the API in lunch break and tested some methods. Fortunately it worked well.
Example is below.
“rdkit_adapter” method provides a tool to connect rdkit-schrodinger’s python.
At first read sample sdf from rdkit.
from schrodinger.thirdparty import rdkit_adapter from rdkit import Chem mols = [ mol for mol in Chem.SDMolSupplier("solubility.sdf") if mol != None]
Then sanitize mol and convert rdkit mol object to schrodinger mol object. It can do with rdkit_adapter.from_rdkit method like this.
for mol in mols: Chem.SanitizeMol(mol) schromols =  for mol in mols: try: shmol = rdkit_adapter.from_rdkit(mol) schromols.append(shmol) except: pass
Now I could convert rdkit mol objects to schrodinger mol objects. Next I tried conversion from schrodinger mol objects to rdkit mol objects. I used rdkit_adapter.to_rdkit method.
rdmols =  for mol in schromols: try: rdmol = rdkit_adapter.to_rdkit(mol) rdmols.append(rdmol) except: pass
I could not show output because I wrote this blog post from my personal computer. But above code worked.
And there are many methods are provided to schrodinger mol obj. Hmm it seems exciting for me. I check the API more deeply!