htmd.metricdatagenerator module

class htmd.metricdatagenerator.MetricDataGenerator(fulldata, model=None, is_adaptive=False)

Bases: object

newMetricData(datasource, trajectories=None, olddata=None)

Converts trajectory indexes to a new MetricData object

newTrajectoriesClusterJumping(simlen, ntraj, startFrames=None, jumpprob=0.1)

clusterJumping only jumps one frame ahead and uses random chance to change the cluster from where to obtain new frames

newTrajectoriesFiller(simlen, ntraj, startFrames=None)
newTrajectoriesMSM(simlen, ntraj, startFrames=None)

Generates new synthetic (fake) trajectories sampled from the Markov State Model

newTrajectoriesSimple(simlen, ntraj, startFrames=None)

TrajectoriesSimple selects a random trajectory from the conformations in the cluster of the respawning conformations

parallelTest(simlen, ntraj, startFrames=None)
htmd.metricdatagenerator.abs2rel(absFrames, trajLengths)