OpenStructure
|
Data Structures | |
class | HHblitsHit |
class | HHblitsHeader |
class | HHblits |
Functions | |
def | ParseHeaderLine |
def | ParseHHblitsOutput |
def | ParseA3M |
def | ParseHHM |
Variables | |
list | __all__ |
HHblits wrapper classes and functions.
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.
list __all__ |
Definition at line 831 of file hhblits3.py.