DynamicAnalysisBase¶

class mdhelper.analysis.base.DynamicAnalysisBase(trajectory: ReaderBase, parallel: bool, verbose: bool = False, **kwargs)[source]¶

A dynamic analysis base object.

Parameters:

trajectoryMDAnalysis.coordinates.base.ReaderBase: Simulation trajectory.
parallelbool: Determines whether the analysis is performed in parallel.
verbosebool, default: True: Determines whether detailed progress is shown.
**kwargs: Additional keyword arguments to pass to MDAnalysis.analysis.base.AnalysisBase.

Methods

`run`	Performs the calculation.
`save`	Saves results to a binary or archive file in NumPy format.

run(start: int = None, stop: int = None, step: int = None, frames: slice | ndarray[int] = None, verbose: bool = None, **kwargs) → SerialAnalysisBase | ParallelAnalysisBase[source]¶

Performs the calculation.

See also

For parallel-specific keyword arguments, see ParallelAnalysisBase.run().

Parameters:

startint, optional: Starting frame for analysis.
stopint, optional: Ending frame for analysis.
stepint, optional: Number of frames to skip between each analyzed frame.
framesslice or array-like, optional: Index or logical array of the desired trajectory frames.
verbosebool, optional: Determines whether detailed progress is shown.
**kwargs: Additional keyword arguments to pass to MDAnalysis.lib.log.ProgressBar.

Returns:

selfSerialAnalysisBase or ParallelAnalysisBase: Analysis object with results.

save(file: str | TextIO, archive: bool = True, compress: bool = True, **kwargs) → None¶

Saves results to a binary or archive file in NumPy format.

Parameters:

filestr or file: Filename or file-like object where the data will be saved. If file is a str, the .npy or .npz extension will be appended automatically if not already present.
archivebool, default: True: Determines whether the results are saved to a single archive file. If True, the data is stored in a .npz file. Otherwise, the data is saved to multiple .npy files.
compressbool, default: True: Determines whether the .npz file is compressed. Has no effect when archive=False.
**kwargs: Additional keyword arguments to pass to numpy.save(), numpy.savez(), or numpy.savez_compressed(), depending on the values of archive and compress.