ost.bindings.hhblits3 Namespace Reference

Data Structures
class	HHblitsHit
class	HHblitsHeader
class	HHblits

Functions
def	ParseHeaderLine
def	ParseHHblitsOutput
def	ParseA3M
def	ParseHHM

Variables
list	__all__

Detailed Description

HHblits wrapper classes and functions.

Function Documentation

def ost.bindings.hhblits3.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.

def ost.bindings.hhblits3.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.

def ost.bindings.hhblits3.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.

def ost.bindings.hhblits3.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.

Variable Documentation

list __all__

Initial value:

= ['HHblits', 'HHblitsHit', 'HHblitsHeader',
           'ParseHHblitsOutput', 'ParseA3M', 'ParseHHM',
           'ParseHeaderLine']

Definition at line 831 of file hhblits3.py.