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ExTASY Wrappers

A library to simplify the construction of ExTASY simulation-analysis workflows.

What is this repository for?

  • ExTASY wrappers provide a consistent API for launching command line applications (such as MD simulations or simulation analysis jobs) from python scripts. Though designed originally with ExTASY simulation-analysis workflows in mind, they are extensible to many other possible applications.

In a nutshell, the construction and execution of a complete simulation or analysis job is reduced to a python function call of the form:

results = kernel.run(inputs)

where "kernel" might be pmemd, grompp, pyCoCo, LSDMap, etc.

See the Wiki for more details.

  • Version 0.0.1

How do I get set up?

  • Clone the repository and then run setup.py:
git clone https://bitbucket.org/extasy-project/wrappers.git
cd wrappers
python setup.py install --user
  • Dependencies: ExTASY wrappers itself has no dependencies outside the standard python libraries. To run the examples though will require:
  1. An MD code: Amber (or Ambertools) and/or GROMACS
  2. A sampling analysis package: ExTASY CoCo and/or ExTASY-compliant LSDMap

Running the parallel examples will additionally require: Dask and/or mpipool

  • How to run tests: See the README files in the folders under ./examples.

Who do I talk to?

  • Charlie Laughton