Thank you for this pearl. Em ter., 7 de jul. de 2020 às 11:23, Thomas Holder < thomas.hol...@schrodinger.com> escreveu:
> 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 <pslace...@gmail.com> 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 < > 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 > > -- > 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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