renumber – Renumber entities¶

Renumber(seq_handle, sequence_number_with_attached_view=1, old_number_label=None)¶

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 first sequence of the alignment is considered the full-length sequence and it must match the model sequence wherever it is aligned (i.e. excluding gaps).

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")

Parameters:

• seq_handle (SequenceHandle / AlignmentHandle) – Sequence or alignment handle with attached view.

• sequence_number_with_attached_view (int) – Sequence number for the aln. handle (not used if seq. handle given)

Raises:

RuntimeError if unknown type of seq_handle or if attached view is missing or if the given alignment sequence is inconsistent.