dwhswenson
Theoretical chemist. Lead developer of OpenPathSampling and Contact Map Explorer. Ecosystem Infrastructure Lead at OMSF.
Open Molecular Software FoundationChicago
Pinned Repositories
autorelease
Tools for keeping release behavior clean
codemodel
Advanced metaprogramming tools
conda-rc-check
A GitHub Action to check whether a conda package has a recent release candidate
contact_map
Contact map analysis for biomolecules; based on MDTraj
dotfiles
The dotfiles of David W.H. Swenson
openmm_scaled_md
Scaled MD implementation in OpenMM
OPSPiggybacker
Tools for converting path sampling simulations to OPS format
pyna
Python analysis for nucleic acids. Analysis scripts for Curves output.
openpathsampling
An open source Python framework for transition interface and path sampling calculations.
openpathsampling-cli
Command line tools for OpenPathSampling
dwhswenson's Repositories
dwhswenson/pyna
Python analysis for nucleic acids. Analysis scripts for Curves output.
dwhswenson/openmm_scaled_md
Scaled MD implementation in OpenMM
dwhswenson/openmm-mmst
Tools to use the Meyer-Miller-Stock-Thoss (mapped electron) Hamiltonian in OpenMM
dwhswenson/adaptivemd
A python framework to run adaptive Markov state model (MSM) simulation on HPC resources
dwhswenson/article_tools
A few scripts, etc., which make simplify the process of writing articles for academic journals.
dwhswenson/binding_md
Tools for studying (un)binding processes with molecular dynamics and path sampling
dwhswenson/dask-traj
This will be a parallel implementation of mdtraj, using dask
dwhswenson/dask-tutorial
Dask tutorial
dwhswenson/define_api
Script to help define the classes/objects in a Python API
dwhswenson/dwhs_profiling
Some wrappers and tools for profiling Python
dwhswenson/dynamiq_engine
MD Engine for dynamiq (engine as a separate package for reuse elsewhere)
dwhswenson/dynamiq_samplers
MC samplers for dynamiq-md projects
dwhswenson/gutis
Grand Unified Transition Interface Sampling
dwhswenson/nbsphinx-feedstock
A conda-smithy repository for nbsphinx.
dwhswenson/octomore
finding eight or more parameters we can try for applying openpathsampling to kinases
dwhswenson/OneWrapper
OneWrapper script for managing parallel replica exchange transition interface sampling
dwhswenson/onion
Find TIS layers from MSM in dynamical systems
dwhswenson/ops_parallel_committor
Parallelization of the OPS committor simulation
dwhswenson/parallelRETISgame
Developing strategies for parallel RETIS
dwhswenson/pyWigner
Python toolkit for LSC-IVR (classical Wigner) simulations
dwhswenson/repo-tools
Tools for repository setup, CI, etc. Single source for multiple repositories.
dwhswenson/spectral_density_discretization
dwhswenson/test_repo
testing for the behavior of autorelease
dwhswenson/vim-python-test-runner
A simple Django aware way of running python tests from within Vim