PisaPy

Python PDBePISA Wrapper

Python code to automatically interact with PDBePISA (Proteins, Interfaces, Structures and Assemblies) web server.

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Description :

Allows to automatically run PISA interfaces web server and downloading the generated xml files by giving pdb files or a pdb id.

Updates 2024

The script files Pisa_xml_parser.py and Parse_Interfacetable.py now look for respective .xml files in the specified pdb_folder performing a limited-depth search in its immediate subdirectories. In addition, the new script file Residue_xml_parser.xml generates a ResidueTable.csv results table from the residue0.xml and saves a ResiduePlot.pdf plot. Updates currently only work when providing files and not PDB ids.

Requirements :

System :

• Linux : The code has only been tested on Ubuntu.

Browser :

The code has only been tested with firefox.

Python packages :

In order to be able to run this code of course you need to have python3 but also some python packages :

• selenium
• halo
• argparse
• pandas
• networkx
• matplotlib
• Biopython

PyPi installation :

$pip install selenium
$pip install halo
$pip install argparse
$pip install pandas
$pip install networkx
$pip install matplotlib
$pip install biopython

Conda installation :

$conda create -n pisapy python
$source activate pisapy
$conda install -c conda-forge selenium
$conda install -c conda-forge halo
$conda install -c conda-forge argparse
$conda install pandas
$conda install -c anaconda networkx
$conda install -c conda-forge matplotlib
$conda install -c conda-forge biopython

Others :

selenium requires geckodriver for firefox, check this link for the other browsers. Naccess is also needed if you want to get the accessibility (note that this part is not required as the accessibility files given by pisa are also being downloaded)

Script files :

RunPisaPy.py PisaAuto_id.py PisaAuto_file.py Pisa_xml_parser.py Parse_Interfacetable.py Residue_xml_parser.py Auto_Naccess.py Download_pdbfasta.py

Usage :

1. First clone this repository :

$git clone https://github.com/hocinebib/PisaPy.git

or download it.

Exemple of usage :

With 1 pdb id :

$cd PisaPy/
$python src/PisaAuto_id.py 6ta5

with pdb files :

$python3 src/PisaAuto_file.py pdb_folder/

Exemple of pipeline usage :

With 1 pdb id :

$cd PisaPy/
$python src/RunPisaPy.py 6ta5 naccess_bin_path

With many pdb ids :

$cd PisaPy/
$python src/RunPisaPy.py "6ta5 6iol 6iok" naccess_bin_path

with pdb files :

$python3 src/RunPisaPy.py pdb_folder/ --d 1 naccess_bin_path

Graphical User Interface Version : PisaPyUI