schrodinger.application.desmond.mapper_msj_generator module

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

Bases: object

Base class.

class schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator(jobname, cd_params, **kwargs)

Bases: schrodinger.application.desmond.mapper_msj_generator.BaseMsjGenerator

patch_ensemble()

A context manager to temporarily change the ensemble and subjob_msj template for this instance to ‘NVT’ if the ensemble is ‘NPT’ and this is a GCMC simulation. NOTE: This is useful to allow the complex and solvent legs to have different ensembles, but in the future this should be replaced with code that natively supports different ensembles for the complex and solvent leg.

generate_master_msj()
generate_complex_msj(net_charge, ch=False)
generate_solvent_msj(net_charge, ch=False)
generate_subjob_msj(buffer_width, complex=False, net_charge=False, ch=False)
write_master_msj()
write_complex_msj()
write_solvent_msj()
modify_fep_launcher_stage(raw)
modify_graph_stage(raw)
class schrodinger.application.desmond.mapper_msj_generator.VacuumMsjGenerator(jobname, cd_params, **kwargs)

Bases: schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator

generate_vacuum_msj(net_charge=False, core_hopping=False)
write_vacuum_msj(concatenate=False)
modify_fep_launcher_stage(raw)
modify_graph_stage(raw)
class schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator(jobname: str, cd_params: Dict[str, object], fmp_fname: str, **kwargs)

Bases: schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator

generate_subjob_msj(buffer_width, complex=False, net_charge=False, ch=False)
modify_graph_stage(raw)

Not support custom .pkl file for now

class schrodinger.application.desmond.mapper_msj_generator.MetalMsjGenerator(jobname: str, cd_params: Dict[str, object], mp: List[str], **kwargs)

Bases: schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator

generate_subjob_msj(buffer_width, complex=False, net_charge=False, ch=False)
modify_graph_stage(raw)
class schrodinger.application.desmond.mapper_msj_generator.ProteinMapperMsjGenerator(jobname: str, cd_params: Dict[str, object], fep_type: str, solvent_asl: Union[str, NoneType] = None, mutation_filename: str = 'mutations.txt', residue_file: str = '', **kwargs)

Bases: schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator

generate_solvent_msj(net_charge, ch=False)
generate_subjob_msj(buffer_width, complex=False, net_charge=False, ch=False)

For protein residue mutation, the subjob msj file will be the same as small molecule workflow; For protein stability, the subjob msj file will be the same as covalent bond workflow.

modify_graph_stage(raw)
class schrodinger.application.desmond.mapper_msj_generator.SolubilityMsjGenerator(jobname: str, cd_params: Dict[str, object], **kwargs)

Bases: schrodinger.application.desmond.mapper_msj_generator.BaseMsjGenerator

Generates the msj files needed to run the Solubility FEP workflow.

generate_master_msj() → schrodinger.utils.sea.Map

Generate the master msj.

generate_subjob_msj(is_fep: bool = True, hydration: bool = False) → schrodinger.utils.sea.Map

Generate the fep msj and return as a sea.Map.

Parameters:
  • is_fep – Set to True for FEP subjob, False for MD.
  • hydration – Set to True to for hydration FEP and False for sublimation FEP. Ignored if not FEP.
write_master_msj() → str

Write out the master msj and return the filename.

write_md_msj() → str

Write out the md msj and return the filename.

write_fep_msj() → None

Write out the fep msj files.

class schrodinger.application.desmond.mapper_msj_generator.MixedSolventMsjGenerator(jobname: str, cd_params: Dict[str, object], builder_params: Dict[str, object], **kwargs)

Bases: schrodinger.application.desmond.mapper_msj_generator.BaseMsjGenerator

write_master_msj() → str
write_md_msj() → str
generate_master_msj() → List[schrodinger.utils.sea.Map]
generate_subjob_msj() → List[schrodinger.utils.sea.Map]