swamp.parsers.topconsparser module

class TopconsParser(fname, logger=None)[source]

Bases: swamp.parsers.parser.Parser

Topcons file parser

Parameters:
  • fname (str) – the file name to be parsed (default None)
  • logger (SwampLogger) – logging interface for the parser (default None)
Variables:
  • tmhelices (Dataframe) – Dataframe with the mappings for the TM helices predicted by topcons
  • residue_topology (Dataframe) – Dataframe with the residue topology as predicted by topcons
Example: 
>>> from swamp.parsers import TopconsParser
>>> my_parser = TopconsParser('<fname>')
>>> my_parser.parse()
parse()[source]

Parse the fname prediction file and retrieve the TM topology

summary

Abstract property to store a summary of the parsed figures of merit