[WIP] Analysis tools for identifying ligand binding modes from MD or BLUES simulations.#113

Open

nathanmlim wants to merge 31 commits intomasterfrom

Commits on Jan 18, 2018

Add analysis tools for identifying ligand binding modes.
Nathan Lim
committed
Merge branch 'master' into id-ligandBM
Nathan Lim
authored
remove import analysis in __init__.py
Nathan Lim
committed
Break code into submodules
Nathan Lim
committed
Clean up files
Nathan Lim
committed

Commits on Jan 19, 2018

Update parameters and add unittest for msm.py
Nathan Lim
committed
Add test for clustering
Nathan Lim
committed
Add gitignore file
Nathan Lim
committed
Add more files to ignore
Nathan Lim
committed
Update tests
Nathan Lim
committed
Add analysis test data
Nathan Lim
committed
Add pyemma requirement
Nathan Lim
committed
Add scikit-learn requirement
Nathan Lim
committed
Remove Ipython requirement in tools.py
Nathan Lim
committed
Add pcca samples for tests
Nathan Lim
committed
Add other pcca sample file
Nathan Lim
committed
Add parameter to specify topfile with selecting leaders
Nathan Lim
committed
check matching silhouette scores up to 5 places
Nathan Lim
committed
Disable test for silhouette scoring.
Nathan Lim
committed

Commits on Jan 22, 2018

Add example notebook for analysis
Nathan Lim
committed
Clean up extra files
Nathan Lim
committed
Remove incompleted modules
Nathan Lim
committed
Add population module and example in notebook
Nathan Lim
committed

Commits on Jan 23, 2018

Switch to assigning trajectory frames by PCCA centers and generalized pose sampling plot.
Nathan Lim
committed

Commits on Jan 29, 2018

Update docstrings
Nathan Lim
committed

Commits on Jan 30, 2018

Correct some docstrings, add animation function and update example notebook
Nathan Lim
committed
Add VMD script for coloring ligand from analysis
Nathan Lim
committed

Commits on Jan 31, 2018

Add section on VMD viewpoint and frame conversion to GIF
Nathan Lim
committed

Commits on Feb 2, 2018

Fix output for saving cluster labels
Nathan Lim
committed

Commits on Feb 8, 2018

Add GIF to notebook
Nathan Lim
committed
Add GIF to notebook
Nathan Lim
committed