RDKit scripts
let's make life easier
The purpose of this repository is to collect useful scripts which mainly use RDKit. Contributions are welcome!
Comments and recommendations for contributors:
- There is a
read_input.pyscript which contains the functionread_input. It reads molecules from SMI, SDF, SDF.GZ and PKL (pickled molecules as tuples of mol and mol_title) files and STDIN (SMI and SDF formats are supported) and it returns tuples of (mol, mol_title). This is a generator and can be applied to process large collections of molecules. I advise to use this function if you do not need other data from input files. - There is
_template.pyfile which can be used as a template for new scripts. Please do not change names for input, output, ncpu and verbose arguments. This will help to make command line arguments consistent across scripts. - Add help messages to your scripts.
- Ideally scripts should be able to communicate with STDIN and STDOUT to combine them with pipes. I implemented this in
gen_stereo_rdkit.pyandgen_conf_rdkit.py. - All scripts can contain errors, so use them on your own risk. If you will find a mistake please create the issue and we will fix it. However, we constantly revise old scripts and fix errors because every found mistake is penultimate.
Particular scripts
vina_dock.py - performs parallel docking in fully automatic way: protonation of ligands, generation of 3D PDBQT representations, docking and storage of output in a single DB. It can run on a single machine as well as on distributed infrastructure using dask, interrupted computations can be easily resumed. It has several dependencies. See help for more details and examples.