Package csb :: Package bio :: Package io :: Module hhpred :: Class HHProfileParser

Class HHProfileParser

object --+
         |
        HHProfileParser

A class that is HHpred HMM format aware. Produces a ProfileHMM object representation of a given HHpred profile HMM.

Note: This is NOT a regular PDB file! It must be specifically formatted for use with HHpred.

Instance Methods

__init__(self, hhm_file, pdb_file=None)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

format_structure(self, input_pdb, chain_id, output_file)
Format input_pdb as an HHpred pre-parsed structure file for the current HMM.

source code

ProfileHMM

parse(self, units=LogScales)
Parse the HMM profile.

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties
Inherited from `object`: `__class__`

Method Details

init(self, hhm_file, pdb_file=None)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

hhm_file (str) - *.hhm file name to parse
pdb_file (str) - an optional hhm structure file, containing the structural data, associated with the HMM.

Raises:

IOError - if any of the files does not exist

Overrides: object.__init__

(inherited documentation)

format_structure(self, input_pdb, chain_id, output_file)

source code

Format input_pdb as an HHpred pre-parsed structure file for the current HMM. Formatting means: only chain_id left in the PDB file, residue sequence numbers strictly corresponding to the HMM states' ranks.

Parameters:

input_pdb (str) - source PDB file name
chain_id (str) - source chain ID (which chain to pick from the structure)
output_file (str) - save the output PDB file here

Raises:

StructureFormatError - when the specified PDB chain does not correspond to the HMM.

parse(self, units=LogScales)

source code

Parse the HMM profile.

Parameters:

units (csb.core.EnumItem) - also convert the profile score units to the specified csb.bio.hmm.ScoreUnits kind

Returns: ProfileHMM

a ProfileHMM instance

Raises:

HHProfileFormatError - when the hhm file is invalid/corrupt

Class HHProfileParser

__init__(self, hhm_file, pdb_file=None) (Constructor)

format_structure(self, input_pdb, chain_id, output_file)

parse(self, units=LogScales)

init(self, hhm_file, pdb_file=None)
(Constructor)