schrodinger.application.desmond.mxmd.mxmd_stage module¶
Multisim stages that relate to Mixed solvent MD.
-
class
schrodinger.application.desmond.mxmd.mxmd_stage.
MixedSolventSetup
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
Multisim stage that builds a cosolvent system. Setting acetonitrile, isopropanol and pyrimidine as default probes as they are water-miscible.
-
NAME
= 'mixed_solvent_setup'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
__class__
¶ alias of
schrodinger.application.desmond.cmj._StageBaseMeta
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mxmd.mxmd_stage', '__doc__': '\n Multisim stage that builds a cosolvent system.\n Setting acetonitrile, isopropanol and pyrimidine as default probes as\n they are water-miscible.\n ', 'NAME': 'mixed_solvent_setup', 'PARAM': <schrodinger.utils.sea.Map object>, 'crunch': <function MixedSolventSetup.crunch>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getstate__
(state=None)¶
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init__
(should_pack=True)¶
-
__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.mxmd.mxmd_stage'¶
-
__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).
-
__setstate__
(state)¶
-
__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)
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
poststage
()¶
-
prestage
()¶
-
push
(job)¶
-
release
(is_restarting=False)¶ Calls the ‘crunch’ method to generate new jobs objects and submits them to the ‘QUEUE’.
-
restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
-
stage_cls
= {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}¶
-
stage_obj
= {}¶
-
time_stage
()¶
-
-
class
schrodinger.application.desmond.mxmd.mxmd_stage.
MixedSolventAnalysis
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
Analyze cosolovent probes around a the protein.
-
NAME
= 'mixed_solvent_analysis'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ Calculate occupancy grids, write .cns and .raw files
-
__class__
¶ alias of
schrodinger.application.desmond.cmj._StageBaseMeta
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mxmd.mxmd_stage', '__doc__': '\n Analyze cosolovent probes around a the protein.\n ', 'NAME': 'mixed_solvent_analysis', 'PARAM': <schrodinger.utils.sea.Map object>, 'crunch': <function MixedSolventAnalysis.crunch>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getstate__
(state=None)¶
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init__
(should_pack=True)¶
-
__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.mxmd.mxmd_stage'¶
-
__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).
-
__setstate__
(state)¶
-
__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)
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
poststage
()¶
-
prestage
()¶
-
push
(job)¶
-
release
(is_restarting=False)¶ Calls the ‘crunch’ method to generate new jobs objects and submits them to the ‘QUEUE’.
-
restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
-
stage_cls
= {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}¶
-
stage_obj
= {}¶
-
time_stage
()¶
-
-
class
schrodinger.application.desmond.mxmd.mxmd_stage.
MixedSolventCleanup
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'mixed_solvent_cleanup'¶
-
TAG
= 'MIXED_SOLVENT_CLEANUP'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
poststage
()¶
-
__class__
¶ alias of
schrodinger.application.desmond.cmj._StageBaseMeta
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.mxmd.mxmd_stage', 'NAME': 'mixed_solvent_cleanup', 'TAG': 'MIXED_SOLVENT_CLEANUP', 'PARAM': <schrodinger.utils.sea.Map object>, 'crunch': <function MixedSolventCleanup.crunch>, 'poststage': <function MixedSolventCleanup.poststage>, '__doc__': None})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getstate__
(state=None)¶
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init__
(should_pack=True)¶
-
__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.mxmd.mxmd_stage'¶
-
__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).
-
__setstate__
(state)¶
-
__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)
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
prestage
()¶
-
push
(job)¶
-
release
(is_restarting=False)¶ Calls the ‘crunch’ method to generate new jobs objects and submits them to the ‘QUEUE’.
-
restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
-
stage_cls
= {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}¶
-
stage_obj
= {}¶
-
time_stage
()¶
-