schrodinger.application.desmond.msj_generator.common module

class schrodinger.application.desmond.msj_generator.common.BaseMsjGenerator(jobname: str, cd_params: Dict[str, object], **kwargs)

Bases: object

Base class.

WorkflowParamsCls

alias of schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

__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.

class schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator(jobname, cd_params, **kwargs)

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

Class to generate the msj files for complex and solvent legs.

WorkflowParamsCls

alias of schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

__init__(jobname, cd_params, **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.

get_subjob_msj_template(leg_type: schrodinger.application.desmond.constants.FepLegTypes) → schrodinger.application.desmond.multisim.parser.Msj
property fep_type
generate_main_msj() → schrodinger.application.desmond.multisim.parser.Msj
generate_complex_msj(protocol, **kwargs)
generate_solvent_msj(protocol, **kwargs)
generate_subjob_msj(leg_type='solvent', protocol='default', **kwargs)
generate_membrane_msj()
write_main_msj() → str
write_subjob_msjs()

Write the msjs for each leg type. Subclasses which run additional legs should override and write the additional msjs

write_solvent_msj()
write_complex_msj()
write_membrane_msj()
modify_fep_launcher_stage(msj: schrodinger.application.desmond.multisim.parser.Msj, leg_types=None, protocols=None)

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)
schrodinger.application.desmond.msj_generator.common.MapperMsjGenerator

alias of schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator

schrodinger.application.desmond.msj_generator.common.BaseFepMsjGenerator

alias of schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator