Re: [modeller_usage] residue selection by sequence

[Modeller Caretaker <modeller-care@salilab.org>]

On 3/9/18 1:31 AM, Shyam Saladi wrote:
> It is possible to specify a selection by the sequence of their residues? 
> Usually, I use model.residue_range(), but this can be tedious.
> Ideally, I'd like to do something like 
> model.residue_sequence('NNPLGTPGTS') to select all occurrences of that 
> sequence.
No, but it's pretty straightforward to write a little bit of Python to 
get what you want. Something like the following should work:
 def residue_sequence(model, search):
    one_letter = "".join(r.code for r in model.residues)
    start = 0
    ranges = []
    while True:
        f = one_letter.find(search, start)
        if f >= 0:
            ranges.append(model.residue_range(f, f+len(search)-1))
            start = f+len(search)
        else:
            return ranges
  return selection(residue_sequence(model, 'NNPLGTPGTS'))

	Ben Webb, Modeller Caretaker
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