modify pymol startup script

[Arthur Zalevsky]

If you want alter CHEMPY_DATA or PYMOL_DATA variable you have to copy and modify startup script which is not very comfortable for non-expirienced users. But this operation is needed if you want use custom *.pkl fragments and you a user without write permissions on /usr/share/chempy

At the moment startup script looks like this:

#!/bin/sh
# debian wrapper script for pymol

export PYMOL_PATH=`python2.7 -c "from imp import find_module; print find_module('pymol')[1]"`
export PYMOL_DATA=/usr/share/pymol
export CHEMPY_DATA=/usr/share/chempy

python2.7 -m pymol.__init__ ${1+"$@"}

Better approach would be:

if [ ! -n "$PYMOL_DATA" ]
 then export PYMOL_DATA=/usr/share/pymol
fi

if [ ! -n "$CHEMPY_DATA" ]
 then export CHEMPY_DATA=/usr/share/chempy
fi

so user will have opportunity to start pymol like this:
$ CHEMPY_DATA=/home/$USER/chempy pymol

[Michael Banck (mbanck)]

Sounds reasonable.

Another more involved option would be to extend pymol to also check below ~/.pymol/, like ~/.pymol/chempy or whatever.

[Launchpad Janitor (janitor)]

This bug was fixed in the package pymol - 1.6.0.0-1

---------------
pymol (1.6.0.0-1) unstable; urgency=low

  * New upstream prelease.

  [ Michael Banck ]
  * debian/patches/11_fix__cmd_import.patch: Removed, no longer needed.
  * debian/patches/26_subversion_updates.patch: Likewise.
  * debian/pymol.install: Install data and scripts directories under
    /usr/share/pymol, as intended by upstream.
  * debian/pymol.launch.in: Updated for new data path location.
  * debian/patches/05_examples_data_path.patch: Removed, no longer needed.
  * debian/patches/09_chempy_data_path.patch: Likewise.
  * debian/patches/13_activate_vmd_plugin.patch: Likewise.
  * debian/patches/17_cmyk_png_data_path.patch: Likewise.
  * debian/patches/19_blosum_matrix_path.patch: Likewise.
  * debian/patches/20_output_license_terms.patch: Likewise.
  * debian/patches/25_ignore_setup_clean_errors.patch: Likewise.
  * debian/rules (override_dh_auto_clean): Do not abort on failure and remove
  * redundant call to setup.py.
  * debian/patches/22_fix_pymol_import.patch: Change the value of $PYMOL_PATH
    to the one found by find_module('pymol').
  * debian/patches/28_no_data_install_in_python_path.patch: New patch, skips
    installation of the data (and examples, test) directories into the pymol
    path.
  * debian/patches/29_fix_path_to_splash.patch: New patch, changes search path
    for splash image from $PYMOL_PATH to $PYMOL_DATA.
  * debian/patches/series: Disable 24_autodock_plugin.patch for now, as it does
    work currently.
  * debian/control (Standards-Version): Bumped to 3.9.4.

  [ Daniel Leidert ]
  * debian/control (Uploaders): Removed myself.
    (Depends): Added python-numpy (LP: #1076104).
    (Suggests): Added chemical-mime-data.
  * debian/gnome-pymol.desktop: Dropped unused file.
  * debian/pymol.desktop (MimeType, Exec): Additions (LP: #1087265).
  * debian/pymol.launch.in: Environmental path variables (LP: #925445).
  * debian/upstream: Minor additions.

 -- Debichem Team <email address hidden> Thu, 08 Aug 2013 20:32:10 +0200