swamp.wrappers.aleigen module¶

class AlEigen(workdir, map_a, map_b, format_a='aleigen', format_b='aleigen', get_matrix=False, pdb_a=None, pdb_b=None, n_eigen='10', logger=None, eigenvectors=None)[source]¶

Bases: swamp.wrappers.mapalign.MapAlign

Wrapper around al-eigen.

This class can be used to perform contact map alignments using al-eigen and parse the obtained results. The class extends methods and datastructures from MapAlign and can be used in the same manner.

Parameters:	workdir (str) – working directory for this `AlEigen` instance map_a (str) – file name of the map A to be used in the alignment pdb_a (str) – file name of the pdb A to be used for benchmarking of the alignment format_a (str) – contact prediction file format of map A (default ‘aleigen’) map_b (str) – file name of the map B to be used in the alignment pdb_b (str) – file name of the pdb B to be used for benchmarking of the alignment format_b (str) – contact prediction file format of map B (default ‘aleigen’) n_eigen (str) – number of eigen vectors to be used in the alignment (default ‘10’) get_matrix (bool) – if True an alignment matrix is retrieved (default False) logger (SwampLogger) – logging interface for the wrapper (default None) eigenvectors (tuple) – tuple with the file names of both pre-computed eigenvectors (default None)
Variables:	c1 (str) – number of contacts in map_a c2 (str) – number of contacts in map_b cmo (str) – contact maximum overlap obtained in this alignment
Example:

>>> from swamp.wrappers import AlEigen
>>> aleigen = AlEigen('<workdir>', '<map_a>', '<map_b>')
>>> aleigen.run()

static create_eigen_vectors(cmap, vector_output, map_format='aleigen')[source]¶

Create an eigen vector file from a given contact map

Parameters:	cmap (str) – file name of the input contact map vector_output (str) – file name to store the output eigen vectors map_format (str) – file format of the input contact map file (default ‘aleigen’)

get_scores(logfile=None)[source]¶

Method to extract the figures of merit out the stdout

Parameters:	logfile – Not in use

keywords¶: Keywords passed through the command line to aleigen

summary_results¶: A list with a summary of the obtained figures of merit

wrapper_name¶: The name of this ~swamp.wrapper.wrapper.Wrapper child class (aleigen)