htmd.adaptive.adaptive module

class htmd.adaptive.adaptive.AdaptiveBase

Bases: ABC, ProtocolInterface

run()

Runs the adaptive

Use this command to start the adaptive.

Example

>>> adapt = Adaptive()
>>> adapt.run()

htmd.adaptive.adaptive.epochSimIndexes(simlist)

Finds the simulation indexes for each epoch.

Creates a dictionary with the epoch number as key and values the simlist indexes of the simulations corresponding to the given epoch.

Parameters:

simlist (list) – A simulation list created using the simlist function

htmd.adaptive.adaptive.getEpochFromName(name)

Given a adaptive simulation name, tells you which epoch it belongs to.

Parameters:

name (str) – Simulation name

Returns:

epoch – The epoch

Return type:

int

htmd.adaptive.adaptive.reconstructAdaptiveTraj(simlist, trajID)

Reconstructs a long trajectory out of short adaptive runs.

Parameters:

• simlist (numpy.ndarray of Sim objects) – A simulation list generated by the simlist function

• trajID (int) – The id of the trajectory from which to start going back.

Returns:

• mol (Molecule object) – A Molecule object containing the reconstructed trajectory

• chain (np.ndarray) – The simulation IDs of all simulations involved

• pathlist (np.ndarray of str) – The names of all simulations involved.

Examples

>>> mol, chain, pathlist = reconstructAdaptiveTraj(data.simlist, 52)