Re: Package dssp does not contain /usr/bin/dssp and no information about the name change
Andreas, is manually creating a symlink a sufficient workaround for the
time being? I understand that this isn't ideal but I have other
priorities that will keep me occupied for the next couple of weeks.
As for the change Maarten made, I'm indifferent. I think the new name
(mkdssp) is more descriptive of what the executable is used for, and
since the fix in biopython is trivial, I'd prefer to stick to it rather
than change it back. What do you think?
Regards,
Jon
On Wed, 5 Mar 2014 16:54:53 +0100
Andreas Tille <andreas@an3as.eu> wrote:
> Hi Maarten,
>
> On Wed, Mar 05, 2014 at 03:46:12PM +0100, M.L. Hekkelman wrote:
> > >I'm currently busy with adjusting the tes suite for
> > >python-biopython (more information to come) and realised that the
> > >package dssp does not provide an executable with this name but
> > >rather only
> > >
> > > /usr/bin/mkdssp
> > >
> > >Is there any reason for this and if yes, why is this not
> > >documented?
> >
> > The reason was that DSSP is a databank and mkdssp (the application
> > formerly known as dssp) is the tool to create it.
>
> Hmmm, the BioPython folks do not seem to make a distinction about
> this at least their test suite checks for
>
> # Newer versions of DSSP
> dssp --version
>
> and
>
> # Older versions of DSSP
> dssp -h
>
> and if both fails you get
>
> Install dssp if you want to use it from Biopython.
>
> The actual test is then coded as follows:
>
> def test_DSSP(self):
> """Test DSSP generation from PDB"""
> p = PDBParser()
> pdbfile = "PDB/2BEG.pdb"
> model = p.get_structure("2BEG", pdbfile)[0]
> dssp = DSSP(model, pdbfile)
> self.assertEqual(len(dssp), 130)
>
>
> > But that was my
> > choice, when I found out people did not understand the difference
> > between the two. I guess it is not documented because I totally
> > forgot to do that, or perhaps I was too lame to do so. I'm sorry.
>
> I wonder whether it might make sense to at least provide a symlink
> with the old (original?) name since there are people out there (might
> be ignorant of the difference or not) who simply expect the name dssp.
>
> In addition this should be documented for sure.
>
> > I no longer work for the CMBI, and the maintenance of dssp should
> > probably be done by my successor there, Jon Black (I've cc'ed him).
> > Perhaps you two should decide what to do with this.
>
> Jon, I'd welcome if you would take over the maintenance of the package
> but for the moment it would be totally sufficient if you would comment
> on the issue above and I'll implement it as quick as possible.
>
> Kind regards
>
> Andreas.
>
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