Contact map plotting for predicted protein residue-residue contacts.
Project description
==========
ContactVis
==========
Python package for simple protein residue-residue contact map plotting.
Usage::
=======
#!/usr/bin/env 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='')
Or::
``plot_contact_map.py [-h] [-o OUTFILE] [-f FACTOR] [--c2 C2]
[--psipred_horiz PSIPRED_HORIZ] [--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``
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``
ContactVis
==========
Python package for simple protein residue-residue contact map plotting.
Usage::
=======
#!/usr/bin/env 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='')
Or::
``plot_contact_map.py [-h] [-o OUTFILE] [-f FACTOR] [--c2 C2]
[--psipred_horiz PSIPRED_HORIZ] [--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``
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``
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
ContactVis-0.1.1.tar.gz
(7.8 kB
view hashes)