pywindow.PDB

class pywindow.PDB(filepath)[source]

Bases: Trajectory

Methods

Parameters:

filepath (pathlib.Path | str)

analysis(frames='all', ncpus=1, ncpus_analysis=1, override=False, modular=False, rebuild=False, swap_atoms=None, forcefield=None)

Perform structural analysis on a frame/ set of frames.

Depending on the passed parameters a frame, a list of particular frames, a range of frames (from, to), or all frames can be analysed with this function.

The analysis is performed on each frame and each discrete molecule in that frame separately. The steps are as follows:

  1. A frame is extracted and returned as a MolecularSystem.

  2. If swap_atoms is set the atom ids are swapped.

  3. If forcefield is set the atom ids are deciphered.

  4. If rebuild is set the molecules in the system are rebuild.

  5. Each discrete molecule is extracted as Molecule

  6. Each molecule is analysed with Molecule.full_analysis()

  7. Analysis output populates the analysis_output dictionary.

As the analysis of trajectories often have to be unique, many options are conditional.

A side effect of this function is that the analysed frames are also returned to the frames mimicking the behaviour of the get_frames().

Parameters:

  • frames (int | list | tuple | str) – int or list or tuple or str Specified frame (int), or frames (list), or range (touple), or all/everything (str). (default=’all’)

  • override (bool) – bool If True, an output already storred in analysis_output can be override. (default=False)

  • swap_atoms (dict | None) – dict, optional If this kwarg is passed with an appropriate dictionary a pywindow.MolecularSystem.swap_atom_keys() will be applied to the extracted frame.

  • forcefield (str | None) – str, optional If this kwarg is passed with appropriate forcefield keyword a pywindow.MolecularSystem.decipher_atom_keys() will be applied to the extracted frame.

  • modular (bool) – bool, optional If this kwarg is passed a pywindow.MolecularSystem.make_modular() will be applied to the extracted frame. (default=False)

  • rebuild (bool) – bool, optional If this kwarg is passed a rebuild=True is passed to pywindow.MolecularSystem.make_modular() that will be applied to the extracted frame. (default=False)

  • ncpus (int) – int, optional If ncpus > 1, then the analysis is performed in parallel for the specified number of parallel jobs. Otherwise, it runs in serial. (default=1)

  • ncpus_analysis (int) – int, optional If ncpus > 1, then the analysis is performed in parallel for the specified number of parallel jobs. Otherwise, it runs in serial. (default=1)

Returns:

NoneType

The function returns None, the analysis output is returned to analysis_output dictionary.

Return type:

None

get_frames(frames='all', override=False, swap_atoms=None, forcefield=None, extract_data=True)

Extract frames from the trajectory file.

Depending on the passed parameters a frame, a list of particular frames, a range of frames (from, to), or all frames can be extracted with this function.

Parameters:
Returns:

Dictionary of frames.

Return type:

dict[int, MolecularSystem]

save_analysis(filepath=None, override=False)

Dump the content of analysis_output as JSON dictionary.

Parameters:
Return type:

None

save_frames(frames='all', filepath=None, decipher=True, swap_atoms=None, forcefield=None)
Parameters:
Return type:

None