VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Thu Feb 06 2003 - 10:55:14 CST

Lars,

On Thu, Feb 06, 2003 at 01:15:02PM +0100, Lars Bruno Hansen wrote:
>
> dear all,
>
> I have a question about using VMD as a loadable python module.
> I think I need this in order to use the python scripts startvmd.py
> and the python class Molecule.

You actually don't need to run VMD as a python module (I've done it, sort of,
but it's highly experimental and unstable). The startvmd.py script is part
of that experiment, but it's not needed to use the Python features of VMD.
Sorry, guess I should have marked it as such in big letters.

>
> As I understand it I have to compile from the source code, as the loadable
> python module vmd is not included in the binary distribution
> vmd-1.8a29.bin.LINUX.opengl.tar.
>
> I use the options for the source distribution 1.8:
> LINUX OPENGL TCL PYTHON PTHREADS SWIG SHARED

Don't bother with swig; the python wrapper classes like Molecule use VMD's
built-in python API's, not the ones that would be generated by SWIG.

>
> I edited the configure script and changed python_include, python_library
> and the plugin_dir. I did not change any setting for SWIG, like
> swig_h and swig_ccpp (I am unsure if this is correct) . After this I ran
>
> make depend
>
> using an empty Makedata.depend (the Makedata.depend from the LINUX binary
> distribution is empty).
> After removing some extra '\' in Makedata.depend make did compile ok, until
> I got the error
>
> make: *** No rule to make target `vmd.i', needed by `vmd_python.C'.
>
> I was not able to locate vmd.i. I am unsure if I am doing something wrong
> or if this file is missing from the distribution?

vmd.i may well be missing from the source distribution, but as I mentioned
you won't need it to get full python functionality from VMD. You also
don't have to run make depend.

We're still in the process of writing up a README for building VMD from source,
since the process became more complex with the latest release, but here's an
outline of what should work:

 - Compile the plugins using "make LINUX" and
   "make distrib PLUGINDIR=/path/to/plugins".

 - Make a symlink from /path/to/plugins to the root vmd directory (the one
   that contains configure).

 - Put the following flags in configure.options:
   LINUX OPENGL FLTK TK IMD TCL PYTHON PTHREADS SILENT

 - Run ./configure; cd src; make

 - If you get errors about not finding Python.h, either edit the Makefile or
   make a symlink from /usr to vmd/lib/python/lib_LINUX. This is assuming
   that the Python include files are in /usr/include/python2.2; if they're
   in /usr/local/include/python2.2 then make the symlink from /usr/local.

 - When you've successfully compiled the binary, run "make install".

That should do it! Let us know if you have any more problems.

Cheers,
Justin

>
> My system is redhat linux 7.2.
>
> Any help on this is very much appreciated.
>
> with best regards
> Lars
>
> --
> Lars Bruno Hansen
> CAMP, Dept. of Physics, Building 307, DTU, DK-2800 Lyngby, Denmark
> Phone: +45 45 25 32 16 Fax: +45 45 93 23 99
> E-mail: lhansen_at_fysik.dtu.dk
> 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys