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.