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) → Optional[schrodinger.application.desmond.cmj.Engine]

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.
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.