Package csb :: Package bio :: Package io :: Module hhpred |
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# Module hhpred

source code

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``'``