[Debichem-devel] [Outreachy] pymol

merlettaia merlettaia at gmail.com
Wed Jul 27 16:44:51 UTC 2016

Hi Andreas,

For now I wrote simple test which runs over all .py and .pml scripts inside
specific directory and tries to run them with pymol with -c flag (for now
this script doesn't care if python errors appear during run - it only
checks that pymol closes as expected). This is made because some of these
scripts (located in `data` and `examples` directories in upstream source
tree) use data from other directories in relative paths and write to the
folder where they are located in. I symlink them to temporary directory. I
haven't solved usage of files from relative paths yet, that's why this
leads to python exceptions, but pymol still closes as expected.
Incorrect paths are present in installed example scripts, for example, in
/usr/share/doc/pymol/examples/generate_amber.py there is a line:

    model= io.pdb.fromFile("../../test/dat/pept.pdb")

Since in installation this path is incorrect, this script also raises
python exception (but pymol command line closes as expected). I don't know
how to deal with these relative files. I can fix as many examples as I
could to make them find input parameters correctly when they are installed,
or write several examples by myself. What is a better solution?

I've updated patches 22 and 31 and fixed several lintian warnings.

Is this bug in the same state as it was?
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=506202 - I can fix it
too, if no one fixed it yet.

For now I'll add a testsuite for apbs (it will be very simple, but probably
it would help make it work with pdb2pqr).

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