ContactVis
Python package for simple protein residue-residue contact map plotting. Available also via the Python packaging index (PyPi).
Installation
ContactVis can be installed from PyPi with:
pip -U ContactVis
or
easy_install -U ContactVis
Usage
Within python:
from contactvis import plot_contact_map
plot_contact_map.plot_map(fasta_filename, contact_filename, factor, c2_filename='', psipred_filename='', pdb_filename='', is_heavy=False, chain='', sep=',', outfilename='')
Terminal:
plot_contact_map [-h] [-i] [-o OUTFILE] [-f FACTOR] [--c2 C2]
[--psipred_horiz PSIPRED_HORIZ] [--pdb PDB]
[--heavy] [--chain CHAIN]
fasta_file contact_file
To reproduce the examples in test run the following commands:
Simple map of the given contact file with coloring according to contact probability:
python ../plot_contact_map.py sequence.fasta predicted.contacts -o cm_simple
Comparison to contacts from the native PDB structure (pairwise CB-atom distance with 8Ã… cutoff):
python ../plot_contact_map.py sequence.fasta predicted.contacts -o cm_pdb.pdf --pdb native_structure.pdb
Compare two different predicted contact maps to each other and to a native PDB structure and include secondary structure information along the diagonal (red: helix, blue: sheet):
python ../plot_contact_map.py sequence.fasta predicted.contacts -o cm_compare_pdb.pdf --pdb native_structure.pdb --c2 predicted.contacts2 --psipred_horiz psipred.horiz
