PyPIC : Protein interactions calculator

PyPIC is a tool designed to calculate non-covalent interactions in a .pdb file.

Dependancies

• Python 3.9.6
• Biopython 1.77
• reduce 3.16
• tabulate 0.8.9

install Dependancies

git clone https://github.com/alihamraoui/PyPIC.git
conda env create -f requirements.yml

Example

python PyPIC -pdb test/data/pdb/1c8ca.pdb  -mmh -smh -ssh -tsv 

The above example computes the hydrogene bond in 1c8ca.pdb, displays the results, and writes them in the tsv files main_main_chain_1c8ca.tsv,main_side_chain_1c8ca.tsv and side_side_chain_1c8ca.tsv.

List of interactions available

• hydrophobic interactions
• disulphide bridges
• ionic interactions
• aromatic-aromatic interactions
• aromatic-sulphur interactions
• cation-pi interactions
• hydrogen bonds