RepLikCompare

RepLikCompare is a Python package for working with Molecular Dynamics data, including dataset loading, clustering, dimensionality reduction, plotting, and ensemble comparison workflows.

Installation

Conda environment (recommended)

An environment.yml file is provided to create an environment with all dependencies, including hdbscan and umap-learn:

conda env create -f environment.yml
conda activate RepLikCompare

Installing the package

Once your environment is ready, you have two options:

Option A — without cloning (once published on PyPI)

pip install RepLikCompare

Option B — from source (works today)

git clone https://github.com/regueialaa/RepLikCompare.git
cd RepLikCompare
pip install .

Either way installs RepLikCompare together with all of its dependencies so it is available in both the terminal and Jupyter notebooks.

Quick start

You have two options for creating a dataset:

1. Use an existing pandas DataFrame.
2. Load the data directly from a CSV file.

The input dataset must contain two required columns:

• System: the system or condition being analyzed (e.g., WT or Mutant).
• Replica: the replicate identifier for each system (e.g., WT1, WT2, WT3, Mut1, Mut2, Mut3).

import RepLikCompare as rlc

# Create a dataset from an existing pandas DataFrame
dataset = rlc.Dataset.from_dataframe(df)

# Or load a dataset directly from a CSV file
dataset = rlc.Dataset.from_csv("df.csv")

Modules overview

See the Documentation for the full parameter reference of every function.

Documentation

For more details on the package, including installation, usage, and examples, check out the online documentation:

• 📖 Documentation

Authors

• Alaa REGUEI, PhD Student - Université Paris Cité, BFA.
• Samuel Murail, Associate Professor - Université Paris Cité, BFA.

License

Distributed under the MIT license -- see LICENSE for details.