swamp.wrappers.gesamt module

class Gesamt(workdir, mode, pdbin=None, gesamt_archive=None, pdbout=None, nthreads=1, hits_out=None, min1=0.1, min2=0.1, pdb_archive=None, logger=None)

Bases: swamp.wrappers.wrapper.Wrapper

Wrapper around gesamt

This class can be used to perform structural alignments using gesamt and parse the obtained results.

Parameters:

• workdir (str, None) – working directory Gesamt instance
• mode (str) – specify the type of task to be done with gesamt
• pdbin (str, tuple, list) – input pdb file name. If an iterable is given, assumes multiple structure alignment
• gesamt_archive (str, None) – location of the gesamt archive to be scanned (default None)
• pdbout (str, None) – output pdb file name (default None)
• nthreads (int) – number of threads to be used by gesamt (default 1)
• hits_out (str, None) – file name of the .hits output file (default None)
• min1 (float) – argument to be passed to gesamt as -min1 (default 0.1)
• min2 (float) – argument to be passed to gesamt as -min2 (default 0.1)
• pdb_archive (str, None) – location of the pdb archive to be used in gesamt (default None)
• logger (swamp.logger.swamplogger.SwampLogger) – logging interface for the wrapper

Variables:

• error (bool) – if True an error has occurred along the process
• qscore (float) – qscore as reported by gesamt
• rmsd (float) – the obtained rmsd as reported by gesamt
• seq_id (float) – sequence identity between the input structures
• n_align (int) – number of aligned residues

allowed_modes

A list with the allowed values for mode

cmd

Command to be executed on run()

static get_optimum_alignment(pdbfiles, nthreads=1, logger=None)

Method to get the optimum alignment between a set given pdb files.

This method considers all the structure arrangements: it screens for all the possible sets of reference structures and inverted structures possible). This can be computationally demanding so multi-threading is possible.

Parameters:

• pdbfiles (tuple, list) – the set of pdb files to be aligned
• nthreads (int) – number of threads to be used when screening all possible arrangements (default 1)
• logger (None, SwampLogger) – logging interface to be used (default None)

Returns:

the Gesamt instance instance for the optimal alignment and a gemmi.Structure hierarchy with the aligned structuresas an ensemble (tuple)

get_scores(logfile=None)

Use a GesamtParser instance to extract the scores and figures of merit out of the logcontents and hits_out

Parameters:logfile – Not in use

keywords

No keywords are used in gesamt through stdin

pdbout

Setter for pdbout

summary_results

A summary of the figures of merit obtained through the structural alignment

wrapper_name

The name of this ~swamp.wrapper.wrapper.Wrapper child class (gesamt)