[Debichem-devel] pdb2pqr

[Manuel Prinz]

Hi Olivier!

On Sat, May 19, 2012 at 12:00:05AM +0200, olivier.sallou at codeless.fr wrote:
> I tried to get pdb2pqr to build and upload it.  However, new version
> does not build at all (failure at install time). I think I will need
> Manuel help to get the package ready.

I'll have a look into it. Guess you now know why I said it's not
trivial to package! ;)

Could you send my a Debdiff so I can see what you did exactly? I did
not see any changes in the SVN. (And non-functional changes should not
be commited in the first place, IMHO.)

> As I have no idea of what propka is...

PROPKA is a tool that calculates pKa, the negative log of a
dissociation constant. It's measure for the the strength of an acid or
base.

PROPKA is a seperate software tool but distributed in the PDB2PQR
software package. It's different from an embedded code copy, as this
is the only channel of publication (meaning there is no download site
to get PROPKA, although it is standalone). There was a new upstream
release lately, so this might cause things to break.

> Additional stuff is needed as they had a web server, /var/www
> content should be moved, but this can be done easilly with a new
> directive in install file

I did not ship the web server previously (as documented in the
package) and I do not want to do that in the future. In order to get a
working web service the tool needs heavy patching and I do not see any
value in that. There are a lot of PDB2PQR servers around the web which
usually run on some SVN checkout, so that bugs are fixed soon. Given
the time that's needed to get a working web server in the Debian
package and the very low number of people who will run that, I think
this time can be better spent elsewhere.

If you want to do that, though, I'm not stopping you.

Best regards,
Manuel