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molecule-viewer's Introduction

Molecule Viewer

Visualise proteins from PDB and molecules from ChEMBL using PyMOL.

Dependencies

Installation

  1. (optional) Install dependencies using conda:
    • conda env create -f environment.yml
    • conda activate molecule-viewer.
  2. pip install .

Usage

If you've installed dependencies with conda, you'll need to run conda activate molecule-viewer first.

molecule-viewer [-h] [--working-directory DIRECTORY] [--MMFF94] [--UFF]
                       [--ETKDG]
                       [scripts [scripts ...]]

positional arguments:
  scripts               Scripts to execute before entering interactive mode.

optional arguments:
  -h, --help            show this help message and exit
  --working-directory DIRECTORY, -w DIRECTORY
                        Working directory where molecule files are stored.
  --MMFF94              Use the MMFF94 method for 3D conformer generation. (default)
  --UFF                 Use the UFF method for 3D conformer generation.
  --ETKDG               Use the ETKDG method for 3D conformer generation.

The molecule-viewer command will load PyMOL, optionally run some scripts, and enter an interactive Python console. The ChemicalMolecule and Protein classes, as well as the ConformationMethod enum are available in this environment (rather than the PyMOL console). To exit, the quit() at the interactive prompt, rather than exiting the PyMOL window.

See molecule_viewer/methods.py for documentation on 3D conformer generation methods for ChemicalMolecules. This method can also be supplied in the call to ChemicalMolecule.show

To run the demo, run:

molecule-viewer scripts/demo.py

(click 'Zoom' and 'Orient' in PyMOL to see both molecules)

molecule-viewer's People

Contributors

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Watchers

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