MDSynthesis: a persistence engine for intermediate molecular dynamics data

Although the raw data for any study involving molecular dynamics simulations are the full trajectories themselves, often we are most interested in lower-dimensional measures of what is happening. These measures may be as simple as the distance between two specific atoms, or as complex as the percentage of contacts relative to some native structure. In any case, it may be time-consuming to obtain these lower-dimensional intermediate data, and so it is useful to store them.

Stay organized

MDSynthesis is designed to perform the logistics of medium-to-large-scale analysis of many trajectories, individually or as entire groups. It should allow the scientist to operate at a high level when working with the data, while MDSynthesis handles the details of storing and recalling this data.

Efficiently store intermediate data from individual simulations for easy recall

For a given simulation trajectory, MDSynthesis gives an interface (the Sim object) to the simulation data itself through MDAnalysis. Data structures generated from raw trajectories (pandas objects, numpy arrays, or any pure python structure) can then be stored and easily recalled later. Under the hood, datasets are stored in the efficient HDF5 format when possible.

Collect aggregated data and keep track of it, too

Sim objects can be gathered into arbitrary collections with Group objects. Groups can store datasets obtained from these collections, and can even contain other Groups as members.

Query for simulation results instead of manually hunting for them

Note: This feature is planned, but not yet present in the codebase.

Sim and Group objects persistently store their data to disk automatically, but it can be tedious to navigate around the filesystem to recall them later. The Coordinator object gives a single interface for querying all Sim and Group objects it is made aware of, allowing retrieval of specific datasets with a single line of code.

Documentation

A brief user guide is available on Read the Docs.

Dependencies

datreant: 0.6.0-dev
MDAnalysis: 0.9.1 up to 0.10.0
pandas: 0.16.1 or higher
PyTables: 3.2.0 or higher
h5py: 2.5.0 or higher
scandir: 1.0 or higher
PyYAML: 3.11 or higher

Contributing

This project is still under heavy development, and there are certainly rough edges and bugs. Issues and pull requests welcome!

sseyler / MDSynthesis