Multiprocessing SasMol

Multiprocessing SasMol

class multiprocessing_sasmol.Multiprocessing_SasMol

Class containing methods to manage the creation and combination of sasmol.system objects and to manage multiprocessing jobs using these objects.

Examples

First example shows how to use class methods from system object:

>>> import sasmol.system as system
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule.read_dcd('hiv1_gag_200_frames.dcd')
>>> number_of_batches = 10
>>> test = Multiprocessing_SasMol()
>>> molecules = test.divide_molecule(number_of_batches)
>>> test.submit_jobs(molecules, test.example_worker, number_of_batches)

>>> molecules = molecule.divide_molecule(number_of_batches)
>>> test = Multiprocessing_SasMol()
>>> test.submit_jobs(molecules, test.example_worker, number_of_batches)

Note

THIS CLASS IS NEW AND IS UNDER ACTIVE DEVELOPMENT AND MAY CHANGE DRAMATICALLY

### LAST THREE LINES OF EXAMPLE ARE FOR CONSIDERATION FOR POTENTIAL

WOULD REQUIRE CLASS TO INHERIT FROM SASMOL.SYSTEM.ATOM

self parameter is not shown in the Parameters section in the documentation

divide_molecule(molecule, number_of_batches, **kwargs)

Method makes a deep copy of frame 0 of the input molecule into a set of new molecules indicated by the number_of_batches input variable.

After duplicating the molecule, the coordinates are assigned to the duplicate molecules.

The number of frames per duplicate is the same, except perhaps when the number of frames is not an equal divisor of number_of_batches which leads to the remainder frames assigned to the last duplicate molecule.

Parameters:

• molecule – system object :
• number_of_batches – integer : number of duplicate molecules to generate
• kwargs – optional future arguments

Returns:

updated self._coor

Return type:

None

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule.read_dcd('hiv1_gag_200_frames.dcd')
>>> number_of_batches = 10
>>> test = Multiprocessing_SasMol()
>>> molecules = test.divide_molecule(number_of_batches)

>>> molecules = molecule.divide_molecule(number_of_batches)

Note

Last line in the examples is an alternative use case to explore yet not implemented.

example_worker(i, molecule, **kwargs)

Example method to execute in parallel using multiprocessing

Parameters:

• i – integer : job number
• molecule – sasmol object
• kwargs – optional future arguments

Returns:

list of float center_of_mass values

Return type:

com

get_frame_lists(number_of_frames, number_of_batches, **kwargs)

Utility method to determine individual frame lists for each of the total number_of_frames divided into number_of_batches

Parameters:

• number_of_frames – integer : number of frames in complete molecule
• number_of_batches – integer : number of frame groups to create
• kwargs – optional future arguments

Returns:

integer list of frame lists

Return type:

frames

Examples

>>> frames = self.get_frame_lists(molecule.number_of_frames(), number_of_batches)

submit_jobs(molecules, target_method, number_of_jobs, **kwargs)

Utility method to start a set of multiprocessing jobs

Parameters:

• molecules – list : system objects
• target_method – string : name of method to call
• number_of_jobs – int : number of job / processes to run
• kwargs – optional future arguments

Returns:

Return type:

None

Examples

>>> test.submit_jobs(molecules, test.example_worker, number_of_batches)