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.