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ContactVis 0.1.5

Contact map plotting for predicted protein residue-residue contacts.


Python package for simple protein residue-residue contact map plotting.


    #!/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='')


`` [-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 ../ sequence.fasta predicted.contacts -o cm_simple``

Comparison to contacts from the native PDB structure (pairwise CB-atom distance with 8Å cutoff):
``python ../ 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 ../ sequence.fasta predicted.contacts -o cm_compare_pdb.pdf --pdb native_structure.pdb --c2 predicted.contacts2 --psipred_horiz psipred.horiz``
File Type Py Version Uploaded on Size
ContactVis-0.1.5.tar.gz (md5) Source 2014-02-01 7KB
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