solventExposed

A script based on NanoShaper protein surface software returning the list of atoms and residues solvent exposed (or according to a user defined probe radius)

Requirements

• Install NanoShaper https://gitlab.iit.it/SDecherchi/nanoshaper
• or directly use executable provided in the "NS" folder:
  • To correctly link the libraries install patchelf (sudo apt get install patchelf or https://gist.github.com/ruario/80fefd174b3395d34c14) then run the "install_script"

Usage

Important:

1. in the working folder the provided temp folder must be present with a working NanoShaper executable inside (run the install_script before, see above)
2. The input file must be in PQR format

python3 expRes.py <structure_name> For help type python3 expRes.py -h

Default parameters: Probe_radius=1.4 (water), Thread_number=1 (for NanoShaper triangulation)

Note: The probe radius can be changed.

Example:

Hen Egg-White Lisozyme 1hew.pqr:

python3 expRes.py --savePQR --saveRES 1hew

--> 1hew_exposed.pqr file containing the subset of exposed atoms of the original PQR

--> 1hew_resList.txt file containing the list of exposed residues