swamp.parsers.gesamtparser module

class GesamtErrorCodes

Bases: enum.Enum

An enumerator to handle the possible gesamt error codes

DISSIMILAR = 1

ERROR_2 = 2

NO_STDOUT = 3

READ_ERRORS = 4

class GesamtParser(mode, stdout=None, fname=None, logger=None)

Bases: swamp.parsers.parser.Parser

Gesamt output parser

Parameters:

• mode (str) – corresponds with mode used to create the output to be parsed
• stdout (str) – the stdout to be parsed (default None)
• fname (str) – the file name to be parsed (default None)
• logger (SwampLogger) – logging interface for the parser (default None)

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

Example:

>>> from swamp.parsers import GesamtParser
>>> my_parser = GesamtParser('<mode>', '<stdout>', '<fname>')
>>> my_parser.parse()

static get_pairwise_qscores(stdout)

Method to get the pairwise qscores of a given alignmnet between several models in an ensemble

Parameters:stdout (str) – gesamt stdout for the command Returns:qscores_dict: a dictionary with the pairwise qscores for each of the models in the alignment (dict)

parse()

Method to parse fname and store figures of merit

parse_hitfile()

Method to parse a gesamt .hit output file

Parameters:fname (str) – file name of the .hit output file Returns:a dataframe with the results contained in the hit file (pandas.Dataframe)

parse_stdout()

Method to retrieve qscore, rmsd, sequence identity and no. of aligned residues from stdout

Parameters:

• stdout (str) – gesamt stdout to be parsed
• n_models (int) – number of models that were used in the structural alignment to generate the provided stdout

Returns:

qscore, rmsd, sequence identity and no. of aligned residues (tuple)

summary

Dataframe with hits found in the archive if mode is ‘search-archive’ otherwise a tuple with all the parsed figures of merit