Trajectory analysis
===================

A MD simulation performed with the :mod:`metafalcon` package produces a `dynamics-0.log` file that
contains the main results. Every restart will increase the fileindex by one, so that previous
results won't get overwritten. For every dynamics step, coordinates, velocities, energies and other
metadata are saved that can be analyzed afterwards.

Run

::

    metaFALCON log2xyz

to extract a file `dynamics.xyz` that contains the coordinates along the trajectory in a format
able to be opened in most molecular visualization programs. You can change start and end points as
well as specify the step size. For details, use the `--help` option.

Bond lengths, bond angles, torsion angles, coordination numbers and energetic properties can be
extracted using the :class:`analyze_trajectory <metafalcon.analysis.analyze.analyze_trajectory>`
class::

    from metafalcon.analysis.analyze import analyze_trajectory
    anl = analyze_trajectory()

In order to analyze the two bond lengths between the first and the second \/ third atom, run::

    anl.add_property("bond", atoms=[0, 1])
    anl.add_property("bond", atoms=[0, 2])

A full description of all possible properties to be analyzed can be found in the documentation of
the :meth:`add_property() <metafalcon.analysis.analyze.analyze_trajectory.add_property>` method
documentation. All added properties will be saved in the `meta-config.json` file and you can
review the list of current analysis properties with::

    print(anl.get_properties())

If you want to remove an element from the list, do

::

    anl.remove_property("bond", atoms=[0, 1])

or

::

    anl.remove_property("bond")

for removing all bond lengths. The whole list can be resetted with :meth:`reset_properties()
<metafalcon.analysis.analyze.analyze_trajectory.reset_properties>`. If not the whole dynamics
trajectory should be analyzed to save computation time, the :attr:`start`, :attr:`end` and
:attr:`stride` attributes can be set by the respective setter functions.

::

    anl.set_start(200)
    anl.set_end(500)
    anl.set_stride(20)

will analyze every 20th time step from step 200 to step 500.

Finally, you can run the analysis with::

    anl.analyze()

This run will producte a `analyze_\*.dat` file for every analyzed property.

If you only want to analyze the properties that are already specified in the `meta-config.json`
file, use the command line tool::

    metaFALCON analyze