molgri.molecules

The sub-package molgri.molecules is largely based on MDAnalysis handling of molecular structure and trajectory files. However, the parsers are wrapped in own objects and passed to Pseudotrajectory generators that write out a sequence of structures according to FullGrid prescription. Analysis of (pseudo)trajectories is possible with the module transitions.

Modules

molgri.molecules.parsers	Parse files and energies - wrap MDAnalysis functions.
molgri.molecules.pts	Apply a FullGrid to a ParsedMolecule in a specific sequence.
molgri.molecules.transitions	Combine a ParsedTrajectory and a FullGrid to generate a MSM or SqRA model.
molgri.molecules.writers	Write pseudo-trajectories to files.