Package csb :: Package bio :: Package io :: Module hhpred

Module hhpred

HHpred-related format parsers.

This module defines two HHpred format parsers: HHProfileParser and HHOutputParser. The first one is used to read HMM (*.hhm) files:

>>> HHProfileParser("profile.hhm", "profile.pdb").parse()
<ProfileHMM>            # ProfileHMM object

while the latter parses HHsearch results files (*.hhr):

>>> HHOutputParser().parse_file("hits.hhr"):
<HHpredHitList>        # collection of HHpredHit-s

See ProfileHMM, HHpredHitList and HHpredHit from csb.bio.hmm for details. For text serialization of HMM profiles, see HHMFileBuilder in this module.

Classes
	HHMFileBuilder Builder for HHpred's hhm files.
	HHOutputFormatError
	HHOutputParser Parser for HHsearch result (*.hhr) files.
	HHProfileFormatError
	HHProfileParser A class that is HHpred HMM format aware.
	HHpredOutputParser Parser for HHsearch result (*.hhr) files.
	HHpredProfileParser A class that is HHpred HMM format aware.
	StructureFormatError

Variables
	__package__ = `'csb.bio.io'`