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.
-
__init__
(jobname: str, cd_params: Dict[str, object], **kwargs)¶ Parameters: - jobname – The jobname.
- cd_params – A dictionary, with the keys
gpus
, set to True for GPU jobs, andcpus
, set to the number of cpus/gpus to use. - forcefield (str) – The name of the forcefield to use.
- sim_time (int) – The simulation time for the production stage in ps.
- sim_time_complex (int) – The simulation time for the complex leg in ps
- sim_time_solvent (int) – The simulation time for the solvent leg in ps
- rand_seed (int) – The random seed.
- ensemble (str) – The ensemble, NPT or NVT.
- buffer_width (float) – The buffer width in Angstrom determines how much solvent is added to the solute. This is only used if it is larger than the default buffer width.
- lambda_windows (int) – Number of lambda replicas to use for the FEP stages.
- custom_charge_mode (CUSTOM_CHARGE_MODE) – Set to CUSTOM_CHARGE_MODE.ASSIGN to assign custom charges. Set to CUSTOM_CHARGE_MODE.CLEAR to clear custom charges if present, without reassigning. Set to CUSTOM_CHARGE_MODE.KEEP to keep existing custom charges if present.
- h_mass (bool) – Set to True to enable hydrogen mass repartitioning and False to disable it. Default is True.
- concatenate (bool) – Set to True to concatenate the equilibration FEP stages. Default is True.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mapper_msj_generator', '__doc__': '\n Base class.\n\n ', '__init__': <function BaseMsjGenerator.__init__>, '_check_sim_params': <function BaseMsjGenerator._check_sim_params>, '_find_production_stages': <function BaseMsjGenerator._find_production_stages>, '_set_water_model': <function BaseMsjGenerator._set_water_model>, '_set_hmr': <function BaseMsjGenerator._set_hmr>, '_set_buffer_width': <function BaseMsjGenerator._set_buffer_width>, '_set_scale_solvent_vdw': <function BaseMsjGenerator._set_scale_solvent_vdw>, '_set_extract_structures': <function BaseMsjGenerator._set_extract_structures>, '_set_production_parameters': <function BaseMsjGenerator._set_production_parameters>, '_set_ff': <function BaseMsjGenerator._set_ff>, '_set_lambda_windows': <function BaseMsjGenerator._set_lambda_windows>, '_set_assign_custom_charge': <function BaseMsjGenerator._set_assign_custom_charge>, '_set_gpu': <function BaseMsjGenerator._set_gpu>, '_set_job_num_cpus': <function BaseMsjGenerator._set_job_num_cpus>, '__dict__': <attribute '__dict__' of 'BaseMsjGenerator' objects>, '__weakref__': <attribute '__weakref__' of 'BaseMsjGenerator' objects>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.mapper_msj_generator'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
-
class
schrodinger.application.desmond.mapper_msj_generator.
MapperMsjGenerator
(jobname, cd_params, **kwargs)¶ Bases:
schrodinger.application.desmond.mapper_msj_generator.BaseMsjGenerator
-
__init__
(jobname, cd_params, **kwargs)¶ In addition to the parameters passed to
BaseMsjGenerator
, theMapperMsjGenerator
supports the following.Parameters: - atom_mapping – The SMARTS string used to determine the core for atom mapping. Default is to determine the atom mapping automatically.
- align_core_only – Do not adjust the non-core atoms when aligning the core atoms. Default is False.
- ats – (deprecated) Set to True to enable automated torsion scaling. Default is False.
- charged_lambda_windows – Set the number of lambda windows used for charged perturbations. Default is 24.
- core_hopping_lambda_windows – Set the number of lambda windows used for core-hopping perturbations. Default is 16.
- fep_convergence – (deprecated) Adaptive sampling, tolerance value for statistical error on dG. Default is 0.0, which means no adaptive sampling.
- membrane – Set to the filename containing the membrane structures. Default is None, there is no membrane.
- salt_concentration – Concentration of ions to add in M. Default is 0.15 M.
- gcmc – Set to True to enable the GCMC production stage. Default is False.
- solvate – Set to True to enable the Solvate Pocket stage. Default is False.
- modify_dihe – Set to True to modify retained dihedral angle interactions for customized core. Default is False.
- minimize_volume – Set to True to turn on volume minimization during the system_builder or build_geometry stages. Default is False.
-
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, is_complex_leg=False, net_charge=False, ch=False, treat_solvent_like_complex=False)¶
-
write_master_msj
()¶
-
write_complex_msj
()¶
-
write_solvent_msj
()¶
-
modify_fep_launcher_stage
(raw)¶
-
modify_graph_stage
(raw)¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mapper_msj_generator', '__doc__': '\n ', '__init__': <function MapperMsjGenerator.__init__>, 'patch_ensemble': <function MapperMsjGenerator.patch_ensemble>, 'generate_master_msj': <function MapperMsjGenerator.generate_master_msj>, 'generate_complex_msj': <function MapperMsjGenerator.generate_complex_msj>, 'generate_solvent_msj': <function MapperMsjGenerator.generate_solvent_msj>, 'generate_subjob_msj': <function MapperMsjGenerator.generate_subjob_msj>, 'write_master_msj': <function MapperMsjGenerator.write_master_msj>, 'write_complex_msj': <function MapperMsjGenerator.write_complex_msj>, 'write_solvent_msj': <function MapperMsjGenerator.write_solvent_msj>, 'modify_fep_launcher_stage': <function MapperMsjGenerator.modify_fep_launcher_stage>, 'modify_graph_stage': <function MapperMsjGenerator.modify_graph_stage>, '_set_subjob_msj': <function MapperMsjGenerator._set_subjob_msj>, '_set_net_charge_box': <function MapperMsjGenerator._set_net_charge_box>, '_set_lambda_hopping': <function MapperMsjGenerator._set_lambda_hopping>, '_set_modify_dihedral': <function MapperMsjGenerator._set_modify_dihedral>, '_set_minimize_volume': <function MapperMsjGenerator._set_minimize_volume>, '_set_membrane_parameters': <function MapperMsjGenerator._set_membrane_parameters>, '_set_solvate': <function MapperMsjGenerator._set_solvate>, '_set_gcmc_stage_params': <function MapperMsjGenerator._set_gcmc_stage_params>, '_find_solvate_pocket_stage': <function MapperMsjGenerator._find_solvate_pocket_stage>, '_set_gcmc': <function MapperMsjGenerator._set_gcmc>, '_set_fep_type': <function MapperMsjGenerator._set_fep_type>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.mapper_msj_generator'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
-
class
schrodinger.application.desmond.mapper_msj_generator.
VacuumMsjGenerator
(jobname, cd_params, **kwargs)¶ Bases:
schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator
-
__init__
(jobname, cd_params, **kwargs)¶ See
MapperMsjGenerator
for a description of the input parameters.
-
generate_vacuum_msj
(net_charge=False, core_hopping=False)¶
-
write_vacuum_msj
(concatenate=False)¶
-
modify_fep_launcher_stage
(raw)¶
-
modify_graph_stage
(raw)¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mapper_msj_generator', '__doc__': '\n ', '__init__': <function VacuumMsjGenerator.__init__>, 'generate_vacuum_msj': <function VacuumMsjGenerator.generate_vacuum_msj>, 'write_vacuum_msj': <function VacuumMsjGenerator.write_vacuum_msj>, 'modify_fep_launcher_stage': <function VacuumMsjGenerator.modify_fep_launcher_stage>, 'modify_graph_stage': <function VacuumMsjGenerator.modify_graph_stage>, '_set_subjob_msj': <function VacuumMsjGenerator._set_subjob_msj>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.mapper_msj_generator'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
generate_complex_msj
(net_charge, ch=False)¶
-
generate_master_msj
()¶
-
generate_solvent_msj
(net_charge, ch=False)¶
-
generate_subjob_msj
(buffer_width, is_complex_leg=False, net_charge=False, ch=False, treat_solvent_like_complex=False)¶
-
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.
-
write_complex_msj
()¶
-
write_master_msj
()¶
-
write_solvent_msj
()¶
-
-
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
-
__init__
(jobname: str, cd_params: Dict[str, object], fmp_fname: str, **kwargs)¶ See
MapperMsjGenerator
for a description of the input parameters.In addition to these parameters, the following are supported.
Parameters: fmp_fname – Name of the fmp file to use for covalent fep.
-
generate_subjob_msj
(buffer_width, is_complex_leg=False, net_charge=False, ch=False, treat_solvent_like_complex=False)¶
-
modify_graph_stage
(raw)¶ Not support custom .pkl file for now
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mapper_msj_generator', '__doc__': '\n ', '__init__': <function CovalentMsjGenerator.__init__>, 'generate_subjob_msj': <function CovalentMsjGenerator.generate_subjob_msj>, 'modify_graph_stage': <function CovalentMsjGenerator.modify_graph_stage>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.mapper_msj_generator'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
generate_complex_msj
(net_charge, ch=False)¶
-
generate_master_msj
()¶
-
generate_solvent_msj
(net_charge, ch=False)¶
-
modify_fep_launcher_stage
(raw)¶
-
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.
-
write_complex_msj
()¶
-
write_master_msj
()¶
-
write_solvent_msj
()¶
-
-
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
-
__init__
(jobname: str, cd_params: Dict[str, object], mp: List[str], **kwargs)¶ See
MapperMsjGenerator
for a description of the input parameters.In addition to these parameters, the following are supported.
Parameters: mp – List of metalloprotein ct properties.
-
generate_subjob_msj
(buffer_width, is_complex_leg=False, net_charge=False, ch=False, treat_solvent_like_complex=False)¶
-
modify_graph_stage
(raw)¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mapper_msj_generator', '__doc__': '\n ', '__init__': <function MetalMsjGenerator.__init__>, 'generate_subjob_msj': <function MetalMsjGenerator.generate_subjob_msj>, 'modify_graph_stage': <function MetalMsjGenerator.modify_graph_stage>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.mapper_msj_generator'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
generate_complex_msj
(net_charge, ch=False)¶
-
generate_master_msj
()¶
-
generate_solvent_msj
(net_charge, ch=False)¶
-
modify_fep_launcher_stage
(raw)¶
-
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.
-
write_complex_msj
()¶
-
write_master_msj
()¶
-
write_solvent_msj
()¶
-
-
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 = '', neighbor: Union[int, NoneType] = None, **kwargs)¶ Bases:
schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator
-
__init__
(jobname: str, cd_params: Dict[str, object], fep_type: str, solvent_asl: Union[str, NoneType] = None, mutation_filename: str = 'mutations.txt', residue_file: str = '', neighbor: Union[int, NoneType] = None, **kwargs)¶ See
MapperMsjGenerator
for a description of the input parameters.In addition to these parameters, the following are supported.
Parameters: - fep_type – Type of protein fep.
- neighbor – Number of residues to flank the mutated residue when
creating the mutant peptides. Its default value will be
set based on
fep_type
. - solvent_asl – Specify ASL to put in solvent leg for protein residue mutation.
- mutation_filename – Filename containing the list of mutations.
- residue_file – Mae filename which contains the non-standard amino-acids structures.
-
generate_solvent_msj
(net_charge, ch=False)¶
-
generate_subjob_msj
(buffer_width, is_complex_leg=False, net_charge=False, ch=False)¶ For protein or ligand selectivity, 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__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mapper_msj_generator', '__doc__': '\n ', '__init__': <function ProteinMapperMsjGenerator.__init__>, 'generate_solvent_msj': <function ProteinMapperMsjGenerator.generate_solvent_msj>, 'generate_subjob_msj': <function ProteinMapperMsjGenerator.generate_subjob_msj>, 'modify_graph_stage': <function ProteinMapperMsjGenerator.modify_graph_stage>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.mapper_msj_generator'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
generate_complex_msj
(net_charge, ch=False)¶
-
generate_master_msj
()¶
-
modify_fep_launcher_stage
(raw)¶
-
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.
-
write_complex_msj
()¶
-
write_master_msj
()¶
-
write_solvent_msj
()¶
-
-
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.
-
__init__
(jobname: str, cd_params: Dict[str, object], **kwargs)¶ See
BaseMsjGenerator
for a description of the input parameters.In addition to these parameters, the following are supported.
Parameters: - hydration_fep_sim_time – The simulation time for the Hydration FEP production stage.
- sublimation_fep_sim_time – The simulation time for the Sublimation FEP production stage.
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generate_master_msj
() → schrodinger.utils.sea.Map¶ Generate the master msj.
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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.
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write_master_msj
() → str¶ Write out the master msj and return the filename.
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write_md_msj
() → str¶ Write out the md msj and return the filename.
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write_fep_msj
() → None¶ Write out the fep msj files.
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__class__
¶ alias of
builtins.type
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__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mapper_msj_generator', '__doc__': '\n Generates the msj files needed to run the Solubility FEP workflow.\n\n ', '__init__': <function SolubilityMsjGenerator.__init__>, 'generate_master_msj': <function SolubilityMsjGenerator.generate_master_msj>, 'generate_subjob_msj': <function SolubilityMsjGenerator.generate_subjob_msj>, 'write_master_msj': <function SolubilityMsjGenerator.write_master_msj>, 'write_md_msj': <function SolubilityMsjGenerator.write_md_msj>, 'write_fep_msj': <function SolubilityMsjGenerator.write_fep_msj>})¶
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__dir__
() → list¶ default dir() implementation
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__eq__
¶ Return self==value.
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__format__
()¶ default object formatter
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__ge__
¶ Return self>=value.
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__getattribute__
¶ Return getattr(self, name).
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__gt__
¶ Return self>value.
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__hash__
¶ Return hash(self).
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__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
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__le__
¶ Return self<=value.
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__lt__
¶ Return self<value.
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__module__
= 'schrodinger.application.desmond.mapper_msj_generator'¶
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__ne__
¶ Return self!=value.
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__new__
()¶ Create and return a new object. See help(type) for accurate signature.
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__reduce__
()¶ helper for pickle
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__reduce_ex__
()¶ helper for pickle
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__repr__
¶ Return repr(self).
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__setattr__
¶ Implement setattr(self, name, value).
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__sizeof__
() → int¶ size of object in memory, in bytes
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__str__
¶ Return str(self).
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__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
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__weakref__
¶ list of weak references to the object (if defined)
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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
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__init__
(jobname: str, cd_params: Dict[str, object], builder_params: Dict[str, object], **kwargs)¶ Parameters: - jobname – The jobname.
- cd_params – A dictionary, with the keys
gpus
, set to True for GPU jobs, andcpus
, set to the number of cpus/gpus to use. - forcefield (str) – The name of the forcefield to use.
- sim_time (int) – The simulation time for the production stage in ps.
- sim_time_complex (int) – The simulation time for the complex leg in ps
- sim_time_solvent (int) – The simulation time for the solvent leg in ps
- rand_seed (int) – The random seed.
- ensemble (str) – The ensemble, NPT or NVT.
- buffer_width (float) – The buffer width in Angstrom determines how much solvent is added to the solute. This is only used if it is larger than the default buffer width.
- lambda_windows (int) – Number of lambda replicas to use for the FEP stages.
- custom_charge_mode (CUSTOM_CHARGE_MODE) – Set to CUSTOM_CHARGE_MODE.ASSIGN to assign custom charges. Set to CUSTOM_CHARGE_MODE.CLEAR to clear custom charges if present, without reassigning. Set to CUSTOM_CHARGE_MODE.KEEP to keep existing custom charges if present.
- h_mass (bool) – Set to True to enable hydrogen mass repartitioning and False to disable it. Default is True.
- concatenate (bool) – Set to True to concatenate the equilibration FEP stages. Default is True.
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write_master_msj
() → str¶
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write_md_msj
() → str¶
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generate_master_msj
() → List[schrodinger.utils.sea.Map]¶
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generate_subjob_msj
() → List[schrodinger.utils.sea.Map]¶
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__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mapper_msj_generator', '__init__': <function MixedSolventMsjGenerator.__init__>, 'write_master_msj': <function MixedSolventMsjGenerator.write_master_msj>, 'write_md_msj': <function MixedSolventMsjGenerator.write_md_msj>, 'generate_master_msj': <function MixedSolventMsjGenerator.generate_master_msj>, 'generate_subjob_msj': <function MixedSolventMsjGenerator.generate_subjob_msj>, '_set_time': <function MixedSolventMsjGenerator._set_time>, '_set_system_builder_params': <function MixedSolventMsjGenerator._set_system_builder_params>, '__doc__': None})¶
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__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.desmond.mapper_msj_generator'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-