6.2.1. Ensemble Analysis base class

New in version 0.8.0.

The Analysis modules help in the implementation analyses of MDPOW simulations. To simplify the process of analyzing a collection of systems generated by a free energy simulation the objects in Ensemble Objects allow for a molecule directory’s systems to be loaded into MDAnalysis Universes and be analyzed as a group.

EnsembleAnalysis is a class inspired by the AnalysisBase from MDAnalysis which iterates over the systems in the ensemble and the frames in the systems. It sets up both iterations between universes and universe frames allowing for analysis to be run on both whole systems and the frames of those systems. This allows for users to easily run analyses on MDPOW simulations.

class mdpow.analysis.ensemble.EnsembleAnalysis(ensemble=None)

Base class for running multi-system analyses

The class is designed based on the AnalysisBase class in MDAnalysis and is a template for creating multi-universe multi-frame analyses using the Ensemble object

Keywords:

ensemble

The Ensemble being analyzed in the class

Example Analysis

Dihedral Analysis Demonstration:

class DihedralAnalysis(mdpow.ensemble.EnsembleAnalysis):
    def __init__(self, DihedralEnsembleGroup):
        super(DihedralAnalysis, self).__init__(DihedralEnsembleGroup.ensemble)

        self._sel = DihedralEnsembleGroup

    def _prepare_ensemble(self):
        self.result_dict = {}
        for s in ['water', 'octanol']:
            self.result_dict[s] = {'Coulomb': {},
                                   'VDW': {}}
        for key in self._sel.group_keys():
            self.result_dict[key[0]][key[1]][key[2]] = None

    def _prepare_universe(self):
        self.angle_dict = {'angle': None,
                           'time': None}
        self.angles = []

    def _single_frame(self):
        angle = calc_dihedrals(self._sel[self._key].positions[0], self._sel[self._key].positions[1],
                               self._sel[self._key].positions[2], self._sel[self._key].positions[3])
        self.angles.append(angle)

    def _conclude_universe(self):
        self.angle_dict['time'] = self.times
        self.angle_dict['angle'] = self.angles
        self.result_dict[self._key[0]][self._key[1]][self._key[2]] = self.angle_dict

    def _conclude_ensemble(self):
        self.results = pd.DataFrame(data=self.result_dict)

D = DihedralAnalysis.run(start=0 stop=10, step=1)

_prepare_ensemble()

For establishing data structures used in running analysis on the entire ensemble.

Data structures will not be overwritten upon moving to next system in ensemble.

_prepare_universe()

For establishing data structures used in running analysis on each trajectory in ensemble

Data structures will be overwritten between upon after each trajectory has been run

_single_universe()

Calculations on a single Universe object.

Run on each universe in the ensemble during when self.run in called.

_single_frame()

Calculate data from a single frame of trajectory

Called on each frame for universes in the Ensemble.

_conclude_ensemble()

Run after all trajectories in ensemble are finished

_conclude_universe()

Run after each trajectory is finished

static check_groups_from_common_ensemble(groups: List[mdpow.analysis.ensemble.EnsembleAtomGroup])

Checks if inputted list of EnsembleAtomGroup originate from the same Ensemble

Checks every EnsembleAtomGroup in list to determine if their ensemble() references the same object in memory. If two EnsembleAtomGroup object don’t have a common Ensemble ValueError is raised.

run(start=None, stop=None, step=None)

Runs _single_universe on each system and _single_frame on each frame in the system.

First iterates through keys of ensemble, then runs _setup_system which defines the system and trajectory. Then iterates over trajectory frames.