apallath/INDUSAnalysis

Python package to analyze molecular simulation data generated using GROMACS-INDUS.

INDUSAnalysis

Package to analyze simulation data generated using INDUS.

Installation

1. Install requirements

pip install -r requirements.txt

2. Build C extensions

python setup.py build_ext --inplace

2. Install package [in editable state]

pip install [-e] .

Tests

Run both unit tests and integration tests to make sure the package is installed and working correctly. All tests should pass.

Run ensemble tests (scientific tests) to make sure that selected ensemble methods generate the correct results.

Unit tests:

Run

pytest

inside the folder tests_unit/.

Integration tests:

Run

pytest

inside the folder tests_integration/.

Ensemble tests:

Run

pytest

inside the folder tests_ensemble/.

Usage

The package can be imported in any Python script using

import INDUSAnalysis

INDUSAnalysis library functions can be imported using

import INDUSAnalysis.lib

INDUSAnalysis ensemble scripts can be run directly using

python /path/to/INDUSAnalysis/ensemble/.../script.py

Scripts

scripts/ contains executable Python and VMD scripts.

Run

python /path/to/INDUSAnalysis/scripts/run_$analysis_name.py

with the required and optional arguments to run analysis on data generated from a single run [use the -h or --help flags for help with arguments].