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GROMACS Python API project

This project provides Python wrappers for Gromacs trajectory analysis framework.

You can find an example tool written with this framework in examples/example_pyapi.py.

We would be very grateful for any feedback at this very alpha stage of the project.

Building and installing

gromacs-pyapi has following dependencies:

  • Gromacs (tested with 2016.x branch)
  • CMake
  • SIP (confirmed to work with 4.19)

These should be present in repositories of any modern Linux distro.

To build do the following:

$ mkdir build
$ cd build
$ cmake .. -DCMAKE_INSTALL_PREFIX=~/.local
$ make
$ make install

Of course, you can choose any install location you like.

By default, the bindings will be built with currently active Python version. Both Python 2 and Python 3 are supported.

Usage

To use analysis framework, you need to subclass gromacs.TrajectoryAnalysis.TrajectoryAnalysisModule and override all virtual methods as stated in Gromacs documentation. To run the tool, provide an instance of your module to TrajectoryAnalysis.TrajectoryAnalysisCommandLineRunner.runAsMain function. All this boilerplate code can be copied from the example.

When run, the script will behave exactly like any other gmx tool, accepting the same set of command-line options. Module specific options can be provided in initOptions method with use of gromacs.Options.PyOptionsHolder class. This class is needed to overcome impossibilities to directly wrap gromacs Options framework in Python.

PyOptionHolder class has several static methods:

  • doubleOption
  • integerOption
  • stringOption
  • booleanOption
  • selectionOption
  • fileNameOption

All of these methods accept three arguments: name, count and default. Only name is mandatory, count is 1 by default. If count is zero, the option will accept an unlimited number of values. If count is greater than zero, the option will accept exactly count values.

You should store an instance of PyOptionsHolder class in your module's instance field and later access options values by name with [] operator. In other words, this class will behave as a dictionary.

This option framework may change in the future.

NumPy

All data sent from C++ side is not copied into Python memory. Instead, a memory view of some sort is returned. For topology, frames and selections all coordinate, velocity, etc. vectors are provided as NumPy arrays directly on top of C++ arrays allocated by Gromacs. This means that actual references to these arrays are only valid during current fuction call, e.g. analyzeFrame. If you try to store an array and use it later, you may get a segmentation fault or you may access not the array you were expecting, because of memory re-writing. If you need to store this data for later use, allocate your own array and make a copy.