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.
- htmd.adaptive.adaptive.getEpochFromName(name)#
Given a adaptive simulation name, tells you which epoch it belongs to.
- htmd.adaptive.adaptive.reconstructAdaptiveTraj(simlist, trajID)#
Reconstructs a long trajectory out of short adaptive runs.
- Parameters:
- Returns:
mol (
Molecule
object) – A Molecule object containing the reconstructed trajectorychain (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)