Contact map plotting for predicted protein residue-residue contacts.
Project description
ContactVis
==========
Python package for simple protein residue-residue contact map plotting.
[Available also via the Python packaging index (PyPi)](https://pypi.python.org/pypi/ContactVis).
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 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```
==========
Python package for simple protein residue-residue contact map plotting.
[Available also via the Python packaging index (PyPi)](https://pypi.python.org/pypi/ContactVis).
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 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```
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