script_template_dtrj

Script template for scripts that process discrete trajectories.

Deprecated since version 1.6.0: Example deprecation warning. scripts.script_template_dtrj will be removed in MDTools 2.0.0. It is replaced by scripts.script_template_dtrj_new, because the latter has additional functionality xyz.

Todo

  • Example todo list.

  • Implement feature xyz.

Discrete trajectories must be stored in arrays. Arrays that serve as discrete trajectory must meet the requirements listed in mdtools.check.dtrj().

The following is a guide/template on how to write a docstring for a MDTools script. For more information see the Developer’s guide and the NumPy docstring convention.

The first part of the docstring should contain the following paragraphs (all separated by a blank line):

  1. One-sentence summary (preferably one line only).

  2. Potential deprecation warning.

  3. Potential todo list.

  4. Extended summary clarifying functionality, not implementation details or background theory (this goes in the Notes section).

Note that you will have to repeat parts of the docstring (especially the summary and a potentially abbreviated version of the Options section) when implementing the command-line interface with argparse.

Options

An reStructuredText option list listing all options with which the script can/must be called and their meaning.

-f

Name of the file containing the discrete trajectory. The discrete trajectory must be stored as numpy.ndarray either in a binary NumPy .npy file or in a (compressed) NumPy .npz archive. See mdtools.file_handler.load_dtrj() for more information about the requirements for the input file.

-o

Output filename.

-b

First frame to read from the discrete trajectory. Frame numbering starts at zero. Default: 0.

-e

Last frame to read from the discrete trajectory. This is exclusive, i.e. the last frame read is actually END - 1. A value of -1 means to read the very last frame. Default: -1.

--every

Read every n-th frame from the discrete trajectory. Default: 1.

--intermittency

Maximum number of frames a compound is allowed to leave its state whilst still being considered to be in this state provided that it returns to this state after the given number of frames. In other words, a compound is only considered to have left its state if it has left it for at least the given number of frames. Default: 0.

--debug

Run in debug mode.

Output

Optional section containing for example a list of files which are created by the script.

Outfile1 (-o).txt

A text file containing abc.

Outfile2 (--dtrj-out): .npy

A compressed .npz archive containing a binary NumPy .npy file called dtrj.npy that holds the discrete trajectory. The discrete trajectory is stored as numpy.ndarray of dtype numpy.uint32 and shape (n, f), where n is the number of reference compounds and f is the number of frames. The elements of the discrete trajectory are the states in which a given compound resides at a given frame.

See also

scripts.templates.script_template

Script template for scripts that process MD trajectories

scripts.templates.script_template_plot

Script template for scripts that create plots

some_function()

A function that is not defined in this script, but which helps understanding the script’s output or what the script does

Notes

Implementation details and background theory, i.e. a detailed description of the scientific problem which is solved by the script and particularly how it is solved.[1]

References

Examples

At least one particular use case of the script, optimally with a graph demonstrating how the generated data can be visualized.