Hi Pedro,
I would probably just count CA atoms. Something like this:
# Check nearby peptides
tmpsele = pm.get_unused_name("_tmp")
pm.select(tmpsele, f"({sim_pdb} and polymer) within 5 of "
f"({entry.pdb_id} and (bysegi resid {entry.ligand_resid} "
f"and chain {entry.ligand_chain}))")
for chain in pm.get_chains(tmpsele):
if pm.count_atoms(f"guide & bs. ({tmpsele} & chain {chain})") <= 25:
pm.delete(sim_pdb)
is_apo = False
break
pm.delete(tmpsele)
Cheers,
Thomas
> On Jul 6, 2020, at 10:59 PM, Pedro Lacerda <[email protected]> wrote:
>
> 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
> <[email protected]> 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 <[email protected]> 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/[email protected]
> > 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
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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