Python interface for the pocket detection method of the NanoShaper software with volume ranking (not native in NanoShaper)
-
A locally installed version of NanoShaper https://gitlab.iit.it/SDecherchi/nanoshaper
-
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
Run: python3 NS_pocketVol.py <structureName>.pqr
A "results" folder will be created containing the structure name as a subfolder. In this folder there will be (default output, check options below):
- <structureName>_infoPockets.txt : Information on the volume of each extracted pocket.
- 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.
- --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.
Modify the temp/template.prm file for finer control over NanoShaper pocket output
The structure must be in PQR format