Data Structures
class	HHblits

class	HHblitsHeader

class	HHblitsHit

Functions
	ParseHeaderLine (line)

	ParseHHblitsOutput (output)

	ParseA3M (a3m_file)

	ParseHHM (profile)

	_ParseOptions (opts)

Detailed Description

HHblits wrapper classes and functions.

Function Documentation

◆ _ParseOptions()

_ParseOptions ( opts )

protected

:return: Tuple of strings (opt_cmd, opt_str), where opt_cmd can be
         passed to command ("-" added in front of keys, options
         separated by space) and opt_str (options separated by "_")
         can be used for filenames.
:param opts: Dictionary of options, one "-" is added in front of every
             key. Boolean True values add flag without value.

Definition at line 807 of file hhblits3.py.

◆ ParseA3M()

ParseA3M ( a3m_file )

Parse secondary structure information and the multiple sequence alignment 
out of an A3M file as produced by :meth:`HHblits.BuildQueryMSA`.

:param a3m_file: Iterable containing the lines of the A3M file
:type a3m_file: iterable (e.g. an open file handle)

:return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
         (:class:`list`) and "msa" (:class:`~ost.seq.AlignmentHandle`).
         If not available, "ss_pred" and "ss_conf" entries are set to None.

Definition at line 295 of file hhblits3.py.

◆ ParseHeaderLine()

ParseHeaderLine ( line )

Fetch header content.

First, we seek the start of the identifier, that is, the first whitespace
after the hit number + 1. Since the identifier may contain whitespaces
itself, we cannot split the whole line

:param line: Line from the output header.
:type line: :class:`str`

:return: Hit information and query/template offsets
:rtype: (:class:`HHblitsHit`, (:class:`int`, :class:`int`))

Definition at line 117 of file hhblits3.py.

◆ ParseHHblitsOutput()

ParseHHblitsOutput ( output )

Parses the HHblits output as produced by :meth:`HHblits.Search` and returns
the header of the search results and a list of hits.

:param output: Iterable containing the lines of the HHblits output file
:type output: iterable (e.g. an open file handle)

:return: a tuple of the header of the search results and the hits
:rtype: (:class:`HHblitsHeader`, :class:`list` of :class:`HHblitsHit`)

Definition at line 148 of file hhblits3.py.

◆ ParseHHM()

ParseHHM ( profile )

Parse secondary structure information and the MSA out of an HHM profile as
produced by :meth:`HHblits.A3MToProfile`.

:param profile: Opened file handle holding the profile.
:type profile: :class:`file`

:return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
         (:class:`list`), "msa" (:class:`~ost.seq.AlignmentHandle`) and
         "consensus" (:class:`~ost.seq.SequenceHandle`).
         If not available, "ss_pred" and "ss_conf" entries are set to None.

Definition at line 371 of file hhblits3.py.

Data Structures