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.
How do I get set up?
If you want to play with the examples, clone the repository and then run setup.py:
git clone https://bitbucket.org/extasy-project/wrappers.git cd wrappers python setup.py install --user
But if you are not bothered, just use pip:
pip install extasy.wrappers --user
Dependencies: ExTASY wrappers itself has no dependencies outside the standard python libraries. To run the examples though will require:
- An MD code: Amber (or Ambertools) and/or GROMACS
- A sampling analysis package: ExTASY CoCo and/or ExTASY-compliant LSDMap
How to run tests: See the README files in the folders under ./examples.
Who do I talk to?