Bio-Otto / rdkit-scripts

rdkit scripts making life easier

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:

1. There is a read_input.py script which contains the function read_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). I advise to use this function if you do not need other data from input files.
2. There is _template.py file 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.
3. Add help messages to your scripts.
4. Ideally scripts should be able to communicate with STDIN and STDOUT to combine them with pipes. I implemented this in gen_stereo_rdkit.py and gen_conf_rdkit.py.
5. 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.

Happy RDKiiting! :)