compute neighborhood for efficient density-based geometric clustering
construct density network from landscape screening
Radii estimation for density-based clustering
Return data frame with population per frame
construct density network from landscape screening
Plot per-frame populations for given radii.
run screening (density-based geometric clustering)
generate cos/sin transformed dihedrals
returns normalized path for files in project
List names and paths to binaries called by prodyna
construct transition count matrix from trajectory
simulate state trajectory from Markov State Model
construct transtion matrix from trajectory
plot autocorrelation of observables
plot 2d-proj, 1d-proj and eigenvector content for given PCA
plot state geometries as Ramacolor plots
Compute RGB color code from sampling of Ramachandran plot
cumulative fluctuations for given PCA
run dPCA on cos/sin transformed angles
computes a cos/sin transform of angles on the fly
close the running VMD instance