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
togpus
or more genericslots
: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
togpus
or more genericslots
: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