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()