4.1.1. Solvation Shell Analysis

Analyzes the number of solvent molecules within given distances of the solute. The solvation tool is built with the framwework.

Added in version 0.8.0.

class mdpow.analysis.solvation.SolvationAnalysis(solute: EnsembleAtomGroup, solvent: EnsembleAtomGroup, distances: List[float])[source]

Measures the number of solvent molecules withing the given distances in an Ensemble .

Parameters:

solute: An EnsembleAtom containing the solute used to measure distance.
solvent: An EnsembleAtom containing the solvents counted in by the distance measurement. Each solvent atom is counted by the distance calculation.
distances: Array like of the cutoff distances around the solute measured in Angstroms.

The data is returned in a pandas.DataFrame with observations sorted by distance, solvent, interaction, lambda, time.

Example

Typical Workflow:

ens = Ensemble(dirname='Mol')
solvent = ens.select_atoms('resname SOL and name OW')
solute = ens.select_atoms('resname UNK')

solv_dist = SolvationAnalysis(solute, solvent, [1.2, 2.4]).run(stop=10)

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().