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:

                    [--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 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```