https://github.com/adicksonlab/wepy-analysis
Analysis tools for wepy simulations
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (11.7%) to scientific vocabulary
Repository
Analysis tools for wepy simulations
Basic Info
- Host: GitHub
- Owner: ADicksonLab
- License: mit
- Language: Python
- Default Branch: main
- Size: 59.6 KB
Statistics
- Stars: 1
- Watchers: 0
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
WepyAnalysis
WepyAnalysis is a modular toolkit for analyzing data generated from Weighted Ensemble (WE) simulations using the Wepy framework.
The codebase is organized into five main components:
- featurization/: Tools for extracting structural features from WE data
- dataset/: Code for generating datasets from WE data
- msm/: Building Markov State Models (MSMs) and performing kinetic analysis
- example/: Example scripts for running simulations with Wepy and building MSMs
This repository is under active development and intended for researchers working with WE data, especially those using the Wepy framework.
Installation
We recommend installing WepyAnalysis with a Python package manager such as conda or mamba. The package is tested and fully compatible with Python 3.12, and we strongly encourage using python>=3.10 for compatibility.
conda create -n wepy-analysis python=3.12
conda activate wepy-analysis
Once your python environment is ready, wepy-analysis can be installed with pip as follows:
pip install git+https://github.com/ADicksonLab/wepy-analysis
which will also install all dependencies. The installation procedure takes less than a minute to complete at a local desktop.
Dependencies:
Wepy (https://github.com/ADicksonLab/wepy) >= 1.2
geomm (https://github.com/ADicksonLab/geomm) >= 0.3
csnanalysis (https://github.com/ADicksonLab/CSNAnalysis) >= 0.6.0
numpy >= 2.3.1
scipy >= 1.16.0
h5py >= 3.14.0
mdtraj >= 1.11.0
scikit-learn >= 1.7.0
deeptime >= 0.4.5
More Information
- Example dataset files can be found at current Zenodo DOI
- This repository is a part of the preprint "Determinants of Improved CGRP Peptide Binding Kinetics Revealed by Enhanced Molecular Simulations" and can be used to build MSMs explained in the paper.
Owner
- Name: ADicksonLab
- Login: ADicksonLab
- Kind: organization
- Repositories: 25
- Profile: https://github.com/ADicksonLab
GitHub Events
Total
- Watch event: 1
- Member event: 1
- Push event: 19
- Create event: 2
Last Year
- Watch event: 1
- Member event: 1
- Push event: 19
- Create event: 2
Dependencies
- csnanalysis *
- deeptime *
- geomm *
- h5py *
- mdtraj *
- numpy *
- scikit-learn *
- scipy *
- wepy *