conkit.applications.bbcontacts module

Command line object for bbcontacts contact filtering application

class BbcontactsCommandline(cmd=’bbcontacts’, **kwargs)[source]

Bases: Bio.Application.AbstractCommandline

Command line object for bbcontacts [1] contact filtering application

The bbcontacts program is a Python program predicting residue-level contacts between beta-strands by detecting patterns in matrices of predicted couplings. bbcontacts can make use of a secondary structure assignment or a secondary structure prediction.

[1]Andreani J., Söding J. (2015). bbcontacts: prediction of beta-strand pairing from direct coupling patterns. Bioinformatics 31(11), 1729-1737.


In order to use bbcontacts, head over to the GitHub repository, download the latest version and install it using python install.


To filter a contact map using a Multiple Sequence Alignment in CCMpred format, use:

>>> from conkit.applications import BbcontactsCommandline
>>> bbcontacts_cline = BbcontactsCommandline(
...     matfile='test.mat', diversity_score=0.482, prefix='test'
... )
>>> print(bbcontacts_cline)

You would typically run the command line with bbcontacts_cline() or via the Python subprocess module.




__call__([stdin, stdout, stderr, cwd, env]) Execute command, wait for it to finish, return (stdout, stderr).
set_parameter(name[, value]) Set a commandline option for a program (OBSOLETE).