swamp.parsers.aleigenparser module

class AleigenParser(stdout, logger=None)

Bases: swamp.parsers.parser.Parser

Aleigen contact map alignment output parser

Parameters:

• stdout (str) – the stdout to be parsed (default None)
• logger (SwampLogger) – logging interface for the parser (default None)

Variables:

• con_sco (str) – the contact score obtained
• c1 (str) – number of contacts in the first input contact map
• c2 (str) – number of contacts in the second input contact map
• cmo (str) – contact maximum overlap between the two input contacr maps
• alignemnt (dict) – a dictionary with the residue sequence number equivalence across the two input maps

Example:

>>> from swamp.parsers import AleigenParser
>>> my_parser = AleigenParser('<stdout>')
>>> my_parser.parse()

alignment_length

Length of the alignment

parse()

Extract the figures of merit out of stdout

summary

A summary of the figures of merit