I used the function to check if the fasta is smaller than 25 characters. If
it is then it is a peptide:
https://github.com/pslacerda/pymol-labimm/blob/master/scripts/peptbase/create.py#L186
There is another way to check for peptides using only selection?
Em seg., 6 de jul. de 2020 às 02:47, Thomas Holder <
thomas.hol...@schrodinger.com> escreveu:
> Hi Pedro,
>
> cmd.get_fastastr() always returned a FASTA formatted string. What changed
> in PyMOL 2.2 is that it now creates a record for every chain, not just for
> every object. There is a new "key" argument, you get the old behavior with
> key="model".
>
> print(cmd.get_fastastr(key="model"))
>
> If you actually want the plain sequence and not the fasta formatted
> string, then I suggest you use a function like this:
>
> def get_sequence(selection='all'):
> return ''.join(L.strip() for L in
> cmd.get_fastastr(selection).splitlines()
> if not L.startswith('>'))
>
>
> Cheers,
> Thomas
>
>
> > On Jul 4, 2020, at 5:17 PM, Pedro Lacerda <pslace...@gmail.com> wrote:
> >
> > Hi,
> >
> > The get_fastastr function changed. Before it returned the aminoacid
> sequence. Now it returns a FASTA formatted string.
> >
> > How can I get the old behaviour (ie. get the aminoacid sequence)?
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
Pedro Sousa Lacerda
Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA
@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907
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