[Debichem-devel] pdb2pqr

olivier.sallou at codeless.fr olivier.sallou at codeless.fr
Sat May 19 22:38:33 UTC 2012

Le 5/19/12 10:39 PM, Manuel Prinz a écrit :
> 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! ;)
I completly understand !!!! ;-)
> 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.)
I skipped install step with the following, just keeping configure and
make steps.
The install step was well done in debian/* files.

--- a/Makefile.in
+++ b/Makefile.in
@@ -644,7 +644,7 @@
-    @if test "$(PREFIX)" == "$(CWD)/" ; then \
+    @if test "1" == "1" ; then \
       echo Your current source directory is the install directory. 
to be done. ; \
     else \
       c=`pwd`; \

Install step tries to instal stuff in //usr, symlink web server etc....
and creates lots of errors.
Additionally, all propka stuff is missing regarding
debian/pdb2pqr.install and debian/proka.docs

>> 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.
In fact, it seems that in new upstream tarball, propka is not shipped
anymore, only wrappers.
Though, what is strange, is in DISTRIB files they include propkpa/*.py,
but they only have a directory named propka30.
propka wrappers are in propka30 instead of prokpa

So a basic configure/make/make install, besides Debian stuff, should not
work properly.

This certainly means that either provided tarball is not complete or
propka should be packaged separately.

> 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.
That's fine for me.
> If you want to do that, though, I'm not stopping you.
> Best regards, Manuel

Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE

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