4.1.2. Dihedral Analysis

Analyzes selected dihedral angles over a multi-system simulation. Built using the framwework to run over a collection of systems contained in an Ensemble.

Added in version 0.8.0.

class mdpow.analysis.dihedral.DihedralAnalysis(dihedral_groups: List[EnsembleAtomGroup])[source]

Analyzes dihedral angles of selections from a single Ensemble .

Keywords:

dihedral_groups: list of EnsembleAtomGroup with four atoms selected on each. All selections must be from the same Ensemble .

Data is returned in a pandas.DataFrame with observations sorted by selection, solvent, interaction, lambda, time.

Example

Typical Workflow:

ens = Ensemble(dirname='Mol')

dihedral1 = Ens.select_atoms('name C1 or name C2 or name C3 or name C4')
dihedral2 = Ens.select_atoms('name C5 or name C8 or name C10 or name C12')

dih_run = DihedralAnalysis([dihedral1, dihedral2]).run(start=0, stop=10, step=1)

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

Runs _single_universe() on each system or _single_frame() on each frame in the system.

First iterates through keys of ensemble, then runs _single_universe() or _single_frame().