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README.md
contactplot.py
setup.py

README.md

contactplot.py: Solvent Accessible Surface Area plot software.

contactplot.py is a python script used to plot the dr-sasa's Solvent Accessible Surface Area results.

dr-sasa

dr-sasa is a solvent accessible surface area calculation software for biological molecules, that supports proteins, DNA and RNA inputs. The input files can be in the PDB or MOL2 format. PDB format files will use a NACCESS compatible VdW radii lookup table, while MOL2 formats will use the same VdW radii used in Chimera.

If you use this software in your research, please acknowledge it by citing the following:

Ribeiro, J., Ríos-Vera, C., Melo, F. and Schüller, A. (2018) 
“Calculation of accurate contact surface areas between atoms for the 
quantitative analysis of non-bonded molecular interactions”. 
Bioinformatics (submitted).

Install

Requeriments

  • Python >= 2.7
  • Matplotlib >= 2.1
  • Pandas
  • Seaborn
  • Doctopt
  • Git (Optional, only if you are installing via pip)

how to install

Using PIP:

Open your terminal (cmd in Windows) and run the following command:

pip install git+https://github.com/crosvera/contactplot.git

Usage

coontactplot.py has three operational modes:

  • residue: Plots the Buried Surface Area (BSA or Delta SASA) matrix files calculated for residues (*.by_res.tsv) as a heatmap.
  • atom: Plots the Buried Surface Area matrix file calculated for atoms (*._by_atom.tsv) as a heatmap.
  • protein-ligand: Plots the Buried Surface Area produced between a protein-ligand interface using the BSA file calculated for atoms (*._by_atom.tsv) as heatmap.

Usage:

contactplot.py residue <tablefile> <atmasafile> [--skip-non-contact <outputfile>]
contactplot.py atom  <tablefile> <atmasafile> [--skip-non-contact <outputfile>]
contactplot.py protein-ligand  <tablefile> <atmasafile> [--skip-non-contact <outputfile>]

Where:

  • --skip-non-contact option is used to avoid ploting atoms or residues with none contact information.
  • <outputfile> parameter if you want to change the output filename.

Example:

#Plot using residue mode
contactplot.py residue 3f3e_complex.LIGAND_vs_PROTEIN.by_res.tsv 3f3e_complex.atmasa --skip-non-contact

#Plot using atom mode
contactplot.py atom 3f3e_complex.LIGAND_vs_PROTEIN.by_atom.tsv 3f3e_complex.atmasa --skip-non-contact

#Plot using protein-ligand mode
contactplot.py atom 3f3e_complex.LIGAND_vs_PROTEIN.by_atom.tsv 3f3e_complex.atmasa --skip-non-contact
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