schrodinger.application.desmond.msj_generator.fep.protein module¶

class schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator(jobname: str, cd_params: Dict[str, object], **kwargs)¶

Bases: schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator

WorkflowParamsCls¶: alias of schrodinger.application.desmond.msj_generator.workflow_params.ProteinWorkflowParams

__init__(jobname: str, cd_params: Dict[str, object], **kwargs)¶

# TODO consider renaming cpus to gpus or more generic slots :param jobname: The jobname.

Parameters: cd_params – A dictionary with cpus set to the number of gpu slots to use, and ‘mps_factor` set to the number of processes per GPU.

property fep_type¶

generate_solvent_msj(protocol='default')¶

modify_graph_stage(msj: schrodinger.application.desmond.multisim.parser.Msj)¶: Modify parameters of two stages that are relevant to generate a protein fep graph.

modify_params_protein_mutation_generation(mut_gen_stage: schrodinger.application.desmond.arkdb.ArkDb)¶: Modify stage parameters relevant to the protein mutation generation.

modify_params_protein_mapper(pmapper_stage: schrodinger.application.desmond.arkdb.ArkDb)¶: Modify stage parameters relevant to the protein fep mapper.

modify_graph_fname(stg: schrodinger.application.desmond.arkdb.ArkDb)¶: Modify the fmp filename for stages that support graph_file parameter.

class schrodinger.application.desmond.msj_generator.fep.protein.CombinedProteinMsjGenerator(jobname: str, cd_params: Dict[str, object], **kwargs)¶

Bases: schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator

Msj generator for the combined protein fep workflows (FEP_TYPES.PRM_PROTEIN_BINDING and FEP_TYPES.PRM_LIGAND_BINDING). Extends the capability of ProteinMapperMsjGenerator to add the fragment leg that is needed for the combined workflows.

WorkflowParamsCls¶: alias of schrodinger.application.desmond.msj_generator.workflow_params.ProteinWorkflowParams

__init__(jobname: str, cd_params: Dict[str, object], **kwargs)¶

# TODO consider renaming cpus to gpus or more generic slots :param jobname: The jobname.

Parameters: cd_params – A dictionary with cpus set to the number of gpu slots to use, and ‘mps_factor` set to the number of processes per GPU.

write_fragment_msj()¶: Write the fragment subjob msjs.

write_subjob_msjs()¶: Write the msjs for each leg type. Subclasses which run additional legs should override and write the additional msjs

modify_fep_launcher_stage(msj: schrodinger.application.desmond.multisim.parser.Msj)¶

Modifies the FEP launcher stage in the given MSJ object.

Parameters

msj – The MSJ object to modify.
leg_types – The types of legs to modify. If None, defaults to [FepLegTypes.COMPLEX, FepLegTypes.SOLVENT].

Raises

ValueError – If no FEP launcher stage is found in the MSJ object.

modify_graph_stage(msj: schrodinger.application.desmond.multisim.parser.Msj)¶: If using one stage to generate protein graphs, use`CombinedProteinFepMapper` stage in the corresponding template msj; modify parameters of CombinedProteinFepMapper stage. This overrides the parent method in ProteinMapperMsjGenerator.