[Chimera-users] Recursive structure matching and acquisition of descriptive numbers

Jaime Rodríguez-Guerra jaime.rogue at gmail.com
Thu Sep 8 05:38:15 PDT 2016


Such an honor to see my name listed here! Yes, with pychimera you should be
able to do it!

All you need to do is to patch the environment so that Chimera can find its
libraries and dependencies, and then initialize it. In practice, this means
importing pychimera and calling pychimera.patch_environ() and
pychimera.load_chimera() at module level. Then you can proceed as you'd do
with a standard Python distribution.

If you don't want (or are not able) to modify the script, pychimera also
installs a binary that will patch and load Chimera for you, so you can just
do "pychimera myscript.py" However, it's a bit buggy when it comes to
parsing additional arguments for your script. That said, the binary is very
useful to fiddle with Chimera internals from the command line, since it
provides a patched python in which you can import chimera, and also hooks
for ipython and jupyter notebook (with magic calls to render inline!).

pychimera will do its best to locate your Chimera installation, but if it
doesn't succeed, you can always provide it manually with the envvar
CHIMERADIR, which is what you would probably need to load the headless
edition of Chimera.

Additionally, it will load your current Python distribution sys.path, which
means it will be able to import already installed packages in such
distribution. As a result, you don't need to install the packages again for
Chimera. This is particularly useful if you are using virtual envs or conda

I think that's all. If further questions arise or something is not working
as you'd expect, please report that in the issues page of GH (
https://github.com/insilichem/pychimera), or write to me directly.

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