Welcome to molgri’s documentation!
Molgri is a python package assisting you in studying approach vectors and orientations of two interacting molecules. Some of its main functions include:
generating uniform grids on 3- and 4-dimensional spheres (molgri.space)
generating pseudo-trajectories by positioning molecules at automatically generated distances and orientations (molgri.molecules)
performing analysis and visualisation of this data (molgri.plotting)
The package can be simply used as a command-line program. Users interesting in generating sphere grids, pseudo-trajoctories or corresponding visualistions are invited to read a quick introduction with many examples at our GitHub page .
Advanced users who may wish to import the package and extend it for their purposes are invited to read the following API.
Sub-packages
Interested in discretisation of 3D and 4D spheres, analysis of uniformity, generation of full rotational and translational grids independent of application?
-> read on in the sub-package
molgri.space
Interested in applying the grids to molecular structure files, generating pseudo-trajectories and analysing transitions based on the Markov state model (MSM) or Square-root approximation (SqRA)?
-> read on in the sub-package
molgri.molecules
Interested in visualising any of the above?
-> read on in the sub-package
molgri.plotting