ost::seq::alg::renumber Namespace Reference

Functions
def	Renumber
Variables
tuple	__all__ = ('Renumber', )

---

Function Documentation

def ost::seq::alg::renumber::Renumber	(		seq_handle,
			sequence_number_with_attached_view = 1
	)

Function to renumber an entity according to an alignment between the model
sequence and the full-length target sequence. The aligned model sequence or
the alignment itself with an attached view needs to be provided. Upon
succcess, the renumbered entity is returned.
If an alignment is given, the sequence must 

.. code-block:: python

  from ost.seq.alg import renumber
  from ost.bindings.clustalw import *
  ent = io.LoadPDB("path_to_model")
  s = io.LoadSequence("path_to_full_length_fasta_seqeunce")
  pdb_seq = seq.SequenceFromChain("model", ent.chains[0])
  aln = ClustalW(s, pdb_seq)
  aln.AttachView(1, ent.chains[0].Select(""))
  e = Renumber(aln.sequences[1])
  io.SavePDB(e, "renum.pdb")
 
:param seq_handle: Sequence or alignment handle with attached view.
:type seq_handle:  :class:`SequenceHandle` / :class:`AlignmentHandle`
:param sequence_number_with_attached_view: Sequence number for the aln. handle
                                           (not used if seq. handle given)
:type sequence_number_with_attached_view:  :class:`int`
:raises: :exc:`RuntimeError` if unknown type of *seq_handle* or if attached
         view is missing or if the given alignment sequence is inconsistent.

Definition at line 41 of file renumber.py.

---

Variable Documentation

tuple __all__ = ('Renumber', )

Definition at line 83 of file renumber.py.