Hi!
We have developed a Chimera extension for this (PLIPGUI), within our Tangram Project. It should be usable separate of the full suite, but the dependencies must be installed manually:
- PLIP: The code itself, with no dependencies
- Openbabel: Plip needs it.
- In some cases, I had to install lxml and future, as well.
I normally create a conda environment with Python 2.7 and install the dependencies there, but you can also use a normal directory and use
pip install -t <location> <packages> to install them there. Then, make sure to point to that location in the Chimera> Favorites> Add to Favorites/Tools> Locations dialog. More information here:
https://tangram-suite.readthedocs.io/en/latest/install.html#install-only-one-specific-extension. Make sure that PLIP does not install numpy, because it will be incompatible with Chimera's. To sum up:
2. Create a new environment: conda create -n plip -c openbabel python=2.7 lxml openbabel
3. Activate the environment: conda activate plip
6. Obtain extensions path: echo ${CONDA_PREFIX}/lib/python2.7/site-packages
7. Copy that path and paste it in Chimera> Favorites> Add to Favorites/Tools> Locations. Click Save. A new InsiliChem submenu will be available under Tools.
Documentation will be updated here (
https://tangram-suite.readthedocs.io/en/latest/tangram_plip.html) at some point, but the usage is straight-forward once it is installed.
Just go to Tools> Insilichem> Tangram PLIP, select your opened compound, and voilà. I reckon the install process is not very intuitive because of the added dependencies, so in some future I might port PLIP to be Chimera only (no openbabel deps), thus simplifying
the process.
Let me know if you need something else.
Cheers,
Jaime.