schrodinger.application.desmond.mxmd.mxmd_cleanup module

A post-simulation clean-up script that for Mixed Solvent workflow. This script extracts the occupancy data for each cosolvent subjob and combines them into a single occupancy map. The script writes a Maestro Project file (.prjzip) and a ‘results’ directory which contains CNS maps for each cosolvent and a a Maestro structure of the last snapshots for each cosovlent subjob.

The command should be run from the base directory of the mixed solvent job.

schrodinger.application.desmond.mxmd.mxmd_cleanup.read_checkpoint_file(chkpt_file: str) → Union[schrodinger.application.desmond.cmj.Engine, NoneType]

Read multisim checkpoint file. :param chkpt_file: Checkpoint file name.

Returns:Engine object: Raise:ValueError if the checkpoint file could not be read.

schrodinger.application.desmond.mxmd.mxmd_cleanup.get_stage(job: schrodinger.application.desmond.cmj.Engine, stage_name: str) -> (typing.Union[int, NoneType], typing.Union[str, NoneType])

Return the index of stage with name stage_name.

Parameters:job – The checkpoint file object.

:param stage_name : The name of the stage.

Returns:Index of stage_name or None if not found. Job directory or None if not found.

class schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp(chkpt_file: str, sigma: float = 20.0)

Bases: object

Class for cleaning up mixed solvent subjobs.

__init__(chkpt_file: str, sigma: float = 20.0) → None

Initialize self. See help(type(self)) for accurate signature.

run() → None

Run the cleanup workflow.

get_subjob_names() → List[str]

Returns:A list of subjob names.

create_results_directory()

Create directory in which all data results will be written to.

read_archive_data() → None

Copy cns and raw file from the subjob analysis’ stage.

write_cns_mae_files() → List[str]

Write CNS and Maestro files for each probe type.

Returns:List of cns files for each probe.

set_ref_ct() → None

Read one of the output structures and extract the original input coordinates.

write_maestro_project(cns_files: List[str], pt_name: str) → None

Write a maestro prj table containing a summary of the results.

Parameters:

• cns_files – List of cns files.
• pt_name – Filename for the output project.

prepare_ct(ct: schrodinger.structure.Structure, probe: str = '') → None

Change structure title and remove trajectory info.

Parameters:

• ct – Structure to modify.
• probe – If specified, the name of the probe. Otherwise use the jobname. This is the default.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.mxmd.mxmd_cleanup', '__doc__': '\n Class for cleaning up mixed solvent subjobs.\n ', '__init__': <function CleanUp.__init__>, 'run': <function CleanUp.run>, 'get_subjob_names': <function CleanUp.get_subjob_names>, 'create_results_directory': <function CleanUp.create_results_directory>, 'read_archive_data': <function CleanUp.read_archive_data>, 'write_cns_mae_files': <function CleanUp.write_cns_mae_files>, 'set_ref_ct': <function CleanUp.set_ref_ct>, 'write_maestro_project': <function CleanUp.write_maestro_project>, 'prepare_ct': <function CleanUp.prepare_ct>, '__dict__': <attribute '__dict__' of 'CleanUp' objects>, '__weakref__': <attribute '__weakref__' of 'CleanUp' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.mxmd.mxmd_cleanup'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.desmond.mxmd.mxmd_cleanup.parse_cmd(cmdline: List[str]) → argparse.Namespace

Parse the command line and return a namespace objcet.

Parameters:cmdline – Command line arguments. Returns:An initalized Namespace object.

schrodinger.application.desmond.mxmd.mxmd_cleanup.main(cmdline=None) → None

Main function to launch jobs.