schrodinger.application.desmond.stage.fep_mapper module¶
- schrodinger.application.desmond.stage.fep_mapper.run_fep_mapper_cleanup(fmp_in_fname: str, main_jobname: str) Tuple[str, str] ¶
Run the fep_mapper_cleanup.py script and get the output. :param fmp_in_fname: The fmp file used to launch the FEP subjobs :param main_jobname: The main job’s jobname :return: The _out.fmp and _out.fmpdb created by fep_mapper_cleanup.py
- schrodinger.application.desmond.stage.fep_mapper.count_finished_compounds(fmp_in_fname: str, fmp_out_fname: str, count_skipped_compounds_reasons: Optional[list[schrodinger.application.desmond.constants.SkipFepReason]] = None) int ¶
Count how many compounds were finished by using fmp_in_fname as the reference.
- Parameters
fmp_in_fname – The fmp file used to launch the FEP subjobs
fmp_out_fname – The fmp file with data from the FEP subjobs added
count_skipped_compounds_reasons – If provided, a list of reasons why an edge might be skipped that should result in its nodes still being counted as complete
- Returns
The number of newly finished compounds, determined by comparing the number of edges with data on the out file to the in file
- schrodinger.application.desmond.stage.fep_mapper.find_most_recent_graph_output(prejobs: List[schrodinger.application.desmond.cmj.Job]) Optional[str] ¶
Get the filename of the fmp output from the most recent stage possible
- Parameters
prejobs – The prejobs to the current stage
- Returns
A graph fmp filename
- class schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper(*arg, **kwarg)¶
Bases:
schrodinger.application.desmond.cmj.StageBase
- NAME = 'covalent_fep_mapper'¶
- PARAM = <schrodinger.utils.sea.sea.Map object>¶
- __init__(*arg, **kwarg)¶
- crunch()¶
This is where jobs of this stage are created. This function should be overriden by the subclass.
- class schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper(*arg, **kwarg)¶
Bases:
schrodinger.application.desmond.cmj.StageBase
- NAME = 'protein_fep_mapper'¶
- PARAM = <schrodinger.utils.sea.sea.Map object>¶
- __init__(*arg, **kwarg)¶
- crunch()¶
This is where jobs of this stage are created. This function should be overriden by the subclass.
- class schrodinger.application.desmond.stage.fep_mapper.CombinedProteinFepMapper(*arg, **kwarg)¶
Bases:
schrodinger.application.desmond.cmj.StageBase
This class represents a combined protein FEP mapper.
- Variables
main_jobname (str) – The value of
-JOBNAME
flag set from the command line.
- NAME = 'combined_protein_fep_mapper'¶
- PARAM = <schrodinger.utils.sea.sea.Map object>¶
- __init__(*arg, **kwarg)¶
- crunch()¶
This is where jobs of this stage are created. This function should be overriden by the subclass.
- class schrodinger.application.desmond.stage.fep_mapper.FepMapper(*arg, **kwarg)¶
Bases:
schrodinger.application.desmond.cmj.StageBase
- NAME = 'fep_mapper'¶
- PARAM = <schrodinger.utils.sea.sea.Map object>¶
- __init__(*arg, **kwarg)¶
- crunch()¶
This is where jobs of this stage are created. This function should be overriden by the subclass.
- class schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup(*arg, **kwarg)¶
Bases:
schrodinger.application.desmond.cmj.StageBase
A stage to run the fep_mapper_cleanup.py script which collects results from FEP subjobs onto the input graph and writes it to new “_out.fmp”/”_out.fmpdb”
- NAME = 'fep_mapper_cleanup'¶
- PARAM = <schrodinger.utils.sea.sea.Map object>¶
- __init__(*arg, **kwarg)¶
- crunch()¶
This is where jobs of this stage are created. This function should be overriden by the subclass.
- class schrodinger.application.desmond.stage.fep_mapper.CalcDdg(should_pack=True)¶
Bases:
schrodinger.application.desmond.cmj.StageBase
- NAME = 'calc_ddg'¶
- CMD = ['run', '-FROM', 'desmond', 'calculate_ddg.py']¶
- PARAM = <schrodinger.utils.sea.sea.Map object>¶
- crunch()¶
This is where jobs of this stage are created. This function should be overriden by the subclass.