conkit.applications.ccmpred module

Command line object for CCMpred contact prediction application

class CCMpredCommandline(cmd=’ccmpred’, **kwargs)[source]

Bases: Bio.Application.AbstractCommandline

Command line object for CCMpred [1] contact prediction application

The CCMpred program is a very fast pseudo-likelihood maximisation implementation of covariance detection in a Multiple Sequence Alignment. This wrapper allows for easy-to-use Python implementation.

[1]Seemayer S, Gruber M, Söding J (2014). CCMpred–fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics 30(21), 3128-3130.


To predict a contact map using a Multiple Sequence Alignment in JONES format, use:

>>> from conkit.applications import CCMpredCommandline
>>> ccmpred_cline = CCMpredCommandline(
...    alnfile="test.aln", matfile="output.mat"
... )
>>> print(ccmpred_cline)
ccmpred test.aln output.mat

You would typically run the command line with ccmpred_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).