swamp.search.searchjob module¶

class SearchJob(id, workdir, query, template_library, con_format='psicov', library_format='pdb', logger=None, query_pdb_benchmark=None, pdb_library=None, template_subset=None, algorithm='mapalign', python_interpreter='/empty/path/bin/ccp4-python')[source]¶

Bases: abc.ABC

Class that implements methods to search a library of templates using contact map alignment tools

The class is used to search a single query against the SWAMP library of templates. The CMO between the observed contacts for each member of the library and the predicted contacts of the query is computed.

Parameters:

Parameters:	id (str) – the id given to the MrRun and identifying this `SearchJob` instance workdir (str) – working directory where the search will be executed and temporary files will be created query (str) – file name of the query contact file template_library (str) – the directory containing all the templates to be used in the search con_format (str) – format of the contact prediction of the query (default ‘psicov’) library_format (str) – format of the contact maps contained in the library of templates query_pdb_benchmark (str) – file name of the pdb structure to be used for benchmarking (default None) pdb_library (str) – directory with the pdb files of the templates used for benchmarking (default None) template_subset (tuple) – a subset of templates to be used instead of the full library (default None) logger (SwampLogger) – logging interface for the search (default None) algorithm (str) – Indicate the alignment algorithm to be used in the search (default: ‘mapalign’)
Variables:	results (list) – a nested list with the results obtained in the search againts the library

id (str) – the id given to the MrRun and identifying this SearchJob instance
workdir (str) – working directory where the search will be executed and temporary files will be created
query (str) – file name of the query contact file
template_library (str) – the directory containing all the templates to be used in the search
con_format (str) – format of the contact prediction of the query (default ‘psicov’)
library_format (str) – format of the contact maps contained in the library of templates
query_pdb_benchmark (str) – file name of the pdb structure to be used for benchmarking (default None)
pdb_library (str) – directory with the pdb files of the templates used for benchmarking (default None)
template_subset (tuple) – a subset of templates to be used instead of the full library (default None)
logger (SwampLogger) – logging interface for the search (default None)
algorithm (str) – Indicate the alignment algorithm to be used in the search (default: ‘mapalign’)

Variables:

results (list) – a nested list with the results obtained in the search againts the library

eigen_template¶: A template for eigen vector file names

joblist¶: A list of Wrapper instances corresponding with the alignment between the query and each member of the template_list

pickle_fname¶: A pickle file where the results will be stored

run()[source]¶: Run each independent job contained at joblist

script¶: Instance of pyjob.Script that will be executed to complete the search

search_header¶: Header displayed when initiating SwampLogger

store_pickle()[source]¶: Store results into pickle_fname

template_list¶: The list of templates to be used in the search (considers template_subset)

tmp_eigen_query¶: A temporary file name to contain the eigen vectors of query