Modifications

AmberTools' sqm executable is required for parameter generation and depends on libgfortran5. Install them after setting up the repository:

conda install -c conda-forge ambertools libgfortran5

PyMOL is required but not installed automatically because no pip wheel is available. Install PyMOL separately from pymol.org or build from the open-source GitHub repository. There's also a conda package package available:

conda install -c conda-forge pymol-open-source

Ensure the pymol executable is on your PATH.

The default installation covers the core features of PCC-FECalc. Depending on your workflow, you may wish to install optional extras or adjust configuration files:

  • Documentation build: pip install .[docs] installs mkdocs and related plugins for building the documentation.
  • Testing: pip install .[test] installs pytest for running the test suite.
  • Scheduler settings: edit the system_settings.JSON example to match your cluster's scheduler (e.g., slurm, pbs, or lsf).

These adjustments allow the package to integrate with different environments and use cases.