schrodinger.protein.renumber_residues module

Module to rename the residues in a given protein sequence either incrementally or based on a given template protein sequence.

schrodinger.protein.renumber_residues.renumber_residues(seq, start=1, increment=1, preserve_icode=False)

Renumbers the residues so that the first residue gets the ‘start’ number and the next gets an increment by ‘increment’ and so on.

Parameters:
  • seq (schrodinger.protein.sequence.ProteinSequence) – The sequence to renumber
  • start (int) – Residue number for the starting residue
  • increment (int) – Increase in residue number
  • preserve_icode (bool) – Whether to preserve insertion code in the sequence or not

Gaps in the sequence will also be counted during the numbering.

schrodinger.protein.renumber_residues.renumber_residues_by_template(seq, template_seq)

Renumbers the residues of a sequence based on the residue numbers of the template sequence.

Parameters:

Before renumbering, the sequence and template are aligned in such a way that the alignment gets maximum identity using schrodinger.protein.align.MaxIdentityAligner.

Insertion codes are used when the sequence residue is aligned to a gap in the template.

Insertion code in the template sequence is always preserved.