PDB plugin for PyMOL

This repository is based on PDBe’s PDB plugin for
PyMOL. The
original documentation
for the plugin is found on the
PyMOL Wiki.

Versions

The plugin has been updated to newer versions of PyMOL and Python. Here is
an overview of the download URLs for various versions:

• PyMOL 2.x and Python 2 or Python 3:
  • https://github.com/ArturKlauser/pymol-pdb-plugin/raw/master/PDB_plugin.py
• PyMOL 1.x and Python 3:
  • https://github.com/ArturKlauser/pymol-pdb-plugin/raw/v1.x-python3/PDB_plugin.py
  • The original plugin doesn’t work for Python 3 based installations due to
    changed locations of tk imports.
• PyMOL 1.x and Python 2 (original plugin from PDBe):
  • This repository: https://github.com/ArturKlauser/pymol-pdb-plugin/raw/v1.x/PDB_plugin.py
  • Original URL: http://www.ebi.ac.uk/pdbe/pdb-component-library/pymol_plugin/PDB_plugin.py

Installation

To install the plugin for PyMOL 1.7 or later use the PyMOL menu:

• Plugin -> Plugin Manager
• select the Install New Plugin tab
• fill in the URL field with one of the URLs above
• click Fetch

For earlier versions of PyMOL install the plugin manually from the above URL.

Contributing

If you find a bug feel free to open an issue for it. Please describe in as
much detail as possible how to reproduce what you see, e.g. which version of
PyMOL and Python you are using and all the steps you performed to lead to
your result. Also describe the output you are getting as well what you had
expected to get, i.e. why do you consider the current behavior an error.

If you want to help fix an issue in the code, feel free to send a pull request.

Programming Style

Please conform to the
Google Python style guide.
The code in this repository is auto-formatted with
yapf —style google and linted with
flake8.

Before starting to work on changes install required packages.

pip install -r requirements.txt
pre-commit install

Before committing or sending a pull request run the pre-commit checks and tests.

pre-commit run --all-files
tools/test