wesbarnett / diffusion-mapLinks
Comparison of principal components analysis with diffusion maps on toy data sets and a molecular simulation trajectory
☆17Updated 8 years ago
Alternatives and similar repositories for diffusion-map
Users that are interested in diffusion-map are comparing it to the libraries listed below
Sorting:
- libdlfind is a C-API and Python interface to the DL-FIND geometry optimization library☆17Updated last year
- python simulation interface for molecular modeling. To cite this software publication: https://www.sciencedirect.com/science/article/pii/…☆13Updated 8 years ago
- Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run l…☆17Updated 2 months ago
- This plugin enables VMD to display data stored in h5 files that are structured according to the H5MD specifications (http://nongnu.org/h5…☆11Updated 6 years ago
- An Avogadro plugin with a gui to create packmol input files and run packmol from within Avogadro.☆11Updated 15 years ago
- A primer on statistical mechanics for biochemists☆46Updated 2 years ago
- Templates for use in preparing articles for the Living Journal of Computational Molecular Sciences (LiveCoMS)☆9Updated 2 years ago
- A lightweight C++11 Monte Carlo molecular simulation engine☆9Updated 7 years ago
- Library for calculating exact ligand cone angles☆13Updated 2 years ago
- kinetic isotope effect prediction with Gaussian☆15Updated 2 years ago
- Corrections to the text of the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford Un…☆31Updated 2 years ago
- a logistics and persistence engine for the analysis of molecular dynamics trajectories☆30Updated 5 years ago
- Sample code from Allen & Tildesley's Computer Simulation of Liquids, 1st Ed. See https://github.com/Allen-Tildesley/examples for moderni…☆16Updated 7 years ago
- Datasets for open forcefield parameterization and development☆11Updated 5 years ago
- Learning free energy landscapes using artificial neural networks☆14Updated 7 years ago
- Quantum Chemistry Laboratory package☆20Updated 2 years ago
- The new generation molecular viewer for IPython notebook☆82Updated 5 years ago
- Automated omics-scale protein modeling and simulation setup.☆53Updated 3 years ago
- Mapping from Coarse Grain Models to Atomistic (and Back)☆17Updated last year
- Introduction to Biophysics, requires one semester of calculus-based Physics.☆28Updated last year
- C++ Accelerated Python Diffusion Maps Library☆23Updated 6 years ago
- pyRMSD is a small Python package that aims to offer an integrative and efficient way of performing RMSD calculations of large sets of str…☆26Updated 4 years ago
- Python tools for VMD☆10Updated 7 years ago
- AstraZeneca add-ons to Orange.☆22Updated 4 years ago
- This is a short tutorial showing how to use both VMD and MDAnalysis to analyse a molecular dynamics simulation of a membrane protein.☆27Updated 4 years ago
- C++ implementation of the Diffusion Map, with Python bindings☆10Updated 7 years ago
- A novel approach to pose selection in protein-ligand docking based on graph theory.☆20Updated 8 years ago
- Data and analysis scripts for understanding molecular entropies, including conformer flexibility☆11Updated 4 years ago
- a toolbox for the manipulation, modelling and analysis of molecular structures☆27Updated 7 months ago
- A general-purpose, stochastic, biochemical reaction simulator for large reaction networks☆17Updated last year