NS_pocket

Python interface for the pocket detection method of the NanoShaper software with volume ranking (not native in NanoShaper)

Requirements

• A locally installed version of NanoShaper https://gitlab.iit.it/SDecherchi/nanoshaper

OR

• Install patchelf:

    e.g. sudo apt install patchelf (Ubuntu)

    Use the provided NanoShaper executable by running the install_script within install binaries folder.

If using the first option, make sure to copy NanoShaper executable in the temp folder

Instructions

Run: python3 NS_pocketVol.py <structureName>.pqr

Output

A "results" folder will be created containing the structure name as a subfolder. In this folder there will be (default output, check options below):

1. <structureName>_infoPockets.txt : Information on the volume of each extracted pocket.
2. p<number>_atm.pqr: Structure atoms which contact the pocket (a subset of the original provided PQR).

The pocket number reflects a ranking by volume.

Options:

• --off : produces also: 3. p<number>.off : Triangulated pocket as generated by NanoShaper; 4. <structureName>.off file: SES triangulation of the structure as generated by NanoShaper.
• --boolMap: compact result representation--> 2., 3., 4. are not produced. Instead, all information on putative pocket is contained in a single "<structureName>_labelled.pqr" file with dummy integers in the Charge field of the original PQR:0=not associated to any binding site; 1-->n belonging to pocket with rank given by the integer.

Advanced:

Modify the temp/template.prm file for finer control over NanoShaper pocket output

Attention:

The structure must be in PQR format