Pinned Repositories
AGDIFF
Implementation of AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction
ClassicalGSG
A new logP predictor method using GSG and NNs
CSNAnalysis
Tools for creating, analyzing and visualizing Conformation Space Networks
flexibletopology
ML-based molecular representation models using PyTorch
geomm
Mirror of main geomm repository. Simple and stupid library for strictly geometric operations (zero-knowledge of topology) common to computational biology and chemistry. https://adicksonlab.github.io/geomm/
mastic
Multi-Atom Structure/Selection Toolkit with Interaction Capabilities
ml4md-jb
Jupyter book and content for "Machine Learning for Molecular Dynamics" course
mlforce
A PyTorch OpenMM plugin to generate forces for Flexible Topology simulations
OpenRXN
A free, open-source tool for modeling chemical reaction networks in Python
wepy
Weighted Ensemble simulation framework in Python
ADicksonLab's Repositories
ADicksonLab/wepy
Weighted Ensemble simulation framework in Python
ADicksonLab/CSNAnalysis
Tools for creating, analyzing and visualizing Conformation Space Networks
ADicksonLab/OpenRXN
A free, open-source tool for modeling chemical reaction networks in Python
ADicksonLab/flexibletopology
ML-based molecular representation models using PyTorch
ADicksonLab/mastic
Multi-Atom Structure/Selection Toolkit with Interaction Capabilities
ADicksonLab/ml4md-jb
Jupyter book and content for "Machine Learning for Molecular Dynamics" course
ADicksonLab/ClassicalGSG
A new logP predictor method using GSG and NNs
ADicksonLab/AGDIFF
Implementation of AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction
ADicksonLab/geomm
Mirror of main geomm repository. Simple and stupid library for strictly geometric operations (zero-knowledge of topology) common to computational biology and chemistry. https://adicksonlab.github.io/geomm/
ADicksonLab/mlforce
A PyTorch OpenMM plugin to generate forces for Flexible Topology simulations
ADicksonLab/openmm_systems
Collection of premade molecular systems for use with OpenMM
ADicksonLab/mlforce_ft
ADicksonLab/WESTPA-WExplore
A plugin to run the WExplore algorithm in the WESTPA toolkit
ADicksonLab/conda-recipes
conda build recipes for the Omnia project
ADicksonLab/jekyll-ion-site
Code to build lab website using jekyll with the "ion" theme
ADicksonLab/LaTeX-Glossary
A collection of some glossary and acronym entries for the glossaries LaTeX package
ADicksonLab/openmmexampleplugin
An example of how to write a plugin for OpenMM
ADicksonLab/pbvs_schrodinger
ADicksonLab/preprints
ADicksonLab/scoop
SCOOP (Scalable COncurrent Operations in Python)
ADicksonLab/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
ADicksonLab/vmd_inxplot
Collection of scripts for visualizing interactions in VMD
ADicksonLab/wepy-activity
This package is for use with Wepy. It can be used to calculate (un)binding free energies from pulling trajectories of Lennard-Jones Pairs. This also serves as an example use of 'activities' with Wepy.
ADicksonLab/wepy-developer-resources
Resources to support users and developers in the wepy ecosystem
ADicksonLab/wepy-tests
ADicksonLab/westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis