https://github.com/concept-lab/ns_pocket
Python interface for the pocket detection method of the NanoShaper software with volume ranking
Science Score: 23.0%
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Low similarity (8.9%) to scientific vocabulary
Repository
Python interface for the pocket detection method of the NanoShaper software with volume ranking
Basic Info
- Host: GitHub
- Owner: concept-lab
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Size: 3.19 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
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):
- <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.
### 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
Owner
- Name: CONCEPT Lab @ IIT
- Login: concept-lab
- Kind: organization
- Location: Genova, Italy
- Website: https://concept.iit.it/
- Repositories: 5
- Profile: https://github.com/concept-lab