ContactVis 0.1.6

Contact map plotting for predicted protein residue-residue contacts.

Python package for simple protein residue-residue contact map plotting. The tool can be used from python like this:

#!/usr/bin/env python

from contactvis import plot_contact_map

plot_contact_map.plot_map(fasta_filename, contact_filename, factor,
c2_filename='', psipred_horiz_fname='', psipred_vert_fname='',
pdb_filename='', is_heavy=False, chain='', sep=',', outfilename='')

Or from command line:

plot_contact_map.py [-h] [-o OUTFILE] [-f FACTOR] [--c2 C2] [--psipred_horiz PSIPRED_HORIZ]
[--psipred_vert PSIPRED_VERT] [--pdb PDB] [--heavy] [--chain CHAIN] fasta_file contact_file

To reproduce the different examples in the test folder 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.pdf

Comparison to contacts from the native PDB structure (pairwise CB-atom distance with 8Å 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