RDKitter knows that Schrodinger contributes RDKit I think.
https://www.schrodinger.com/news/schr%C3%B6dinger-contributes-rdkit
Schrodinger provides many computational tools for drug discovery, that is not only GUI tool but also python API. Many tool can call from python and also RDKit. And RDKit can read maestro file vise versa.
It is easy to do it like reading SDFiles.
I am writing the blog post on my personal PC and I do not have schrodinger software’s license. So I got test files from schrodingers github repository.
https://github.com/schrodinger
On ipython notebook
!wget https://raw.githubusercontent.com/schrodinger/maeparser/master/test/test.mae !wget https://github.com/schrodinger/maeparser/raw/master/test/test2.maegz from rdkit import Chem from rdkit.Chem import Draw from rdkit.Chem import rdmolfiles from rdkit.Chem.Draw import rdDepictor from rdkit.Chem.Draw import IPythonConsole from rdkit import rdBase import gzip rdDepictor.SetPreferCoordGen(True) rdBase.rdkitVersion >'2018.09.1'
Read mols from mae format.
maemols = rdmolfiles.MaeMolSupplier("test.mae") mols = [m for m in maemols] Draw.MolsToGridImage(mols)
Read mols form maegz
maemols2 = rdmolfiles.MaeMolSupplier(gzip.open("test2.maegz")) mols2 = [m for m in maemols2] Draw.MolsToGridImage(mols2)
Both cases work fine.
If user want to integrate rdkit and schrodinger tools, the method will be useful.
Note book uploaded my github repo.
https://nbviewer.jupyter.org/github/iwatobipen/playground/blob/master/maeparser.ipynb