This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
Project Description

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
Release History

Release History

0.1.6

This version

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0.1.5

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0.1.4

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0.1.3

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0.1.2

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0.1.1

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0.1.0

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Download Files

Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
ContactVis-0.1.6.tar.gz (8.4 kB) Copy SHA256 Checksum SHA256 Source Jan 9, 2015

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