ost.seq.alg.renumber Namespace Reference

Functions
def	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.

.. 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.GetSequence(sequence_number_with_attached_view))
  io.SavePDB(e, "renum.pdb")

Definition at line 41 of file renumber.py.