6.1.1. Solvation Shell Analysis¶
Analyzes the number of solvent molecules within given distances of the solute. The solvation tool is built with the framwework.
New in version 0.8.0.
-
class
mdpow.analysis.solvation.
SolvationAnalysis
(solute: mdpow.analysis.ensemble.EnsembleAtomGroup, solvent: mdpow.analysis.ensemble.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 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.