schrodinger.application.desmond.stage.app.absolute_binding.stage module¶

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer(*args, **kwargs)¶

Bases: schrodinger.application.desmond.cmj.StructureStageBase

For the ligand with the matching ligand_hash_id, prepare the Absolute Binding structures for MD if the leg is not specified, otherwise prepare the structures for FEP. All other ligands will be ignored.

NAME = 'fep_absolute_binding_structure_primer'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

run(jobname: str, mae_fname: str) → Optional[str]¶

Parameters

jobname – Jobname for this stage.
input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer(*args, **kwargs)¶

Bases: schrodinger.application.desmond.cmj.StructureStageBase

NAME = 'fep_absolute_binding_fep_primer'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

run(jobname: str, cms_fname: str) → Optional[str]¶

Parameters

jobname – Jobname for this stage.
input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase(should_pack=True)¶

Bases: schrodinger.application.desmond.stage.launcher.FepLauncher

NAME = 'fep_absolute_binding_launcher_base'¶

get_edge_from_struct_file(struct_file: Union[str, pathlib.Path], g: graph.Graph)¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher(should_pack=True)¶

Bases: schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase

Launches the absolute binding FEP workflow.

NAME = 'fep_absolute_binding_md_launcher'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

crunch()¶: Don’t make output jobs since they will be created in poststage with the new Graph object.

check_param()¶

collect_inputfile(*args)¶

Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.

Parameters: jobs – List of jobs to include.
Returns: The filenames needed to run this stage.

poststage()¶: For any md jobs that showed a high RMSD for the ligand, mark the corresponding edge in the graph to skip FEP

get_md_jobs()¶

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher(should_pack=True)¶

Bases: schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase

Launches the absolute binding FEP workflow.

NAME = 'fep_absolute_binding_fep_launcher'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

check_param()¶

schrodinger.application.desmond.stage.app.absolute_binding.stage.get_csv_header() → str¶

class schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult(ligand_st: schrodinger.structure._structure.Structure = None, complex_st: schrodinger.structure._structure.Structure = None, complex_dg: schrodinger.application.desmond.measurement.Measurement = None, complex_dg_correction: float = None, solvent_dg: schrodinger.application.desmond.measurement.Measurement = None, high_rmsd: bool = False)¶

Bases: object

ligand_st: schrodinger.structure._structure.Structure = None¶

complex_st: schrodinger.structure._structure.Structure = None¶

complex_dg: schrodinger.application.desmond.measurement.Measurement = None¶

complex_dg_correction: float = None¶

solvent_dg: schrodinger.application.desmond.measurement.Measurement = None¶

high_rmsd: bool = False¶

property is_complete: bool¶

property final_dg: Optional[schrodinger.application.desmond.measurement.Measurement]¶

__init__(ligand_st: schrodinger.structure._structure.Structure = None, complex_st: schrodinger.structure._structure.Structure = None, complex_dg: schrodinger.application.desmond.measurement.Measurement = None, complex_dg_correction: float = None, solvent_dg: schrodinger.application.desmond.measurement.Measurement = None, high_rmsd: bool = False) → None¶

schrodinger.application.desmond.stage.app.absolute_binding.stage.get_results_by_ligand(sts_list: List[List[schrodinger.structure._structure.Structure]]) → DefaultDict[str, schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult]¶

Given a list of list of structures (each list corresponds to output structure from each FEP leg), return the result for each ligand.

Returns: dict with keys of [“complex_st”, “complex_dg”, “solvent_dg”, “complex_dg_correction”, “final_dg”]. final_dg is None if any values are missing.

schrodinger.application.desmond.stage.app.absolute_binding.stage.get_csv(results_by_ligand: dict) → str¶: Return the csv content report energies for each ligand. :param: results_by_ligand is got from get_results_by_ligand

schrodinger.application.desmond.stage.app.absolute_binding.stage.get_csv_row(ligand: str, smiles: str, complex_dg: Optional[schrodinger.application.desmond.measurement.Measurement] = None, solvent_dg: Optional[schrodinger.application.desmond.measurement.Measurement] = None, complex_dg_correction: Optional[float] = None, final_dg: Optional[schrodinger.application.desmond.measurement.Measurement] = None) → str¶: Given the results for a ligand, return a formatted row.

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis(should_pack=True)¶

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_absolute_binding_analysis'¶

TAG = 'FEP_ABSOLUTE_BINDING_ANALYSIS'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

check_param()¶

collect_inputfile()¶

crunch()¶: This is where jobs of this stage are created. This function should be overriden by the subclass.

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdPrimer¶: Bases: object

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingPrimer¶: Bases: object

class schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncher¶: Bases: object