rquiroga7 / sucos

easily accessible script to calculate SuCOS scores for pairs of molecules.

This Fork

This is a fork of the original SuCOS repository by Susan Leung. This fork contains a modified version of SuCOS, that has a normalized output, circumventing the issue of generating SuCOS scores of >1 in some circumstances. This is achieved by using the FeatMapScoreMode.Best scoring mode as default as opposed to the FeatMapScoreMode.All originally used in SuCOS. You can still use the other scoring modes when specified, however it is recommended to use the "Best" scoring mode for normalized SuCOS scores.

SuCOS

SuCOS is an RDKit-based overlap measure that combines volumetric shape and pharmacophoric features to give a combined overlap score similar to OpenEye's Tversky Combo and Malhotra and Karanicolas' COS measure.

For calculation of chemical feature overlap, most of the code is based on this RDKit blog post about using feature maps

If you use this code, please cite our ChemRxiv manuscript, where we show that SuCOS is better than RMSD and PLIF similarity for evaluating binding mode conservation in fragment-based drug discovery.

Getting Started

Prerequisites

• RDKit
• Numpy

Running the tests

You can run the unit tests by typing:

> python test_SuCOS.py

Command line help.

To list the options available in calc_SuCOS_normalized.py, type:

> python calc_SuCOS.py -h

usage: calc_SuCOS.py [-h] [--lig1 LIG1] [--lig2 LIG2] [--write] [--return_all]
                     [--score_mode {all,closest,best}]

run SuCOS

optional arguments:
  -h, --help            show this help message and exit
  --lig1 LIG1           the smaller/reference ligand, in sdf or mol2 file
                        format.
  --lig2 LIG2           the larger/query ligand(s), in sdf or .sdf.gz file
                        format.
  --write               writes the SuCOS score into a sdf file with suffix
                        _SuCOS_score.sdf
  --return_all
  --score_mode {all,closest,best}
                        choose the scoring mode for the feature map, default
                        is best.

Example

To find the overlap between 4e3g_lig.sdf and benzene.sdf in the test_data directory:

> python calc_SuCOS.py --lig1 test_data/4e3g_lig.sdf --lig2 test_data/benzene.sdf 

********************************
SuCOS score:	0.843867
********************************

License

SuCOS is licensed under the MIT license.