schrodinger.application.desmond.stage module¶
Various multisim concrete stage classes.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.desmond.stage.
get_ngpus
(arg: List[str]) → int¶ Returns the number of GPUs from command line arguments.
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schrodinger.application.desmond.stage.
fep_gpgpu_lic
(arg: List[str]) → List[str]¶ Returns the command line arguments that should be added to properly handle the FEP GPU license. This will also add the JAGUAR_MAIN license if needed.
Parameters: arg – List of command line arguments.
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schrodinger.application.desmond.stage.
md_gpgpu_lic
(arg: List[str]) → List[str]¶ Returns the command line arguments that should be added to properly handle the MD GPU license.
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schrodinger.application.desmond.stage.
jaguar_lic
() → List[str]¶ Returns the command line arguments that should be added to properly handle the Jaguar main license.
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class
schrodinger.application.desmond.stage.
Primer
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
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NAME
= 'primer'¶
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__init__
(*arg, **kwarg)¶
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describe
()¶
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start
(fname_in)¶
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PARAM
= <schrodinger.utils.sea.Map object>¶
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capture
(job)¶
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check_param
()¶
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count
= 0¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
determine
()¶
-
hook_captured_successful_job
(job)¶
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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’.
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restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
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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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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'>}¶
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stage_obj
= {}¶
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time_stage
()¶
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class
schrodinger.application.desmond.stage.
Concluder
(fname_out=None, *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This stage does not create any jobs for the ‘cmj.QUEUE’.
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NAME
= 'concluder'¶
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__init__
(fname_out=None, *arg, **kwarg)¶
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describe
()¶
-
release
()¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
poststage
()¶
-
prestage
()¶
-
push
(job)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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'>}¶
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stage_obj
= {}¶
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time_stage
()¶
-
-
class
schrodinger.application.desmond.stage.
Multisim
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
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NAME
= 'multisim'¶
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PARAM
= <schrodinger.utils.sea.Map object>¶
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RELAY_KEYS
= ['RETRIES', 'DEBUG', 'debug', 'verbose']¶
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__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
capture
(job)¶
-
restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
-
collect_inputfile
(jobs: Optional[schrodinger.utils.sea.List] = None) → List[str]¶ Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.
Parameters: jobs – List of jobs to include. Returns: The filenames needed to run this stage.
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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’.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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'>}¶
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stage_obj
= {}¶
-
time_stage
()¶
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-
class
schrodinger.application.desmond.stage.
FepLauncher
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.Multisim
-
NAME
= 'fep_launcher'¶
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PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
-
collect_inputfile
(jobs: Optional[schrodinger.utils.sea.List] = None) → List[str]¶ Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.
Parameters: jobs – List of jobs to include. Returns: The filenames needed to run this stage.
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restart_edges
(edges: List[str], sim_protocols: Optional[Dict[str, str]] = None)¶ Restart the jobs for a given list of edges. Each edge is specified as ‘{from_short_id}_{to_short_id}’. This will create the jobs if missing from the list of existing jobs.
Parameters: sim_protocols – This will be used for reconstructing missing jobs (if any).
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RELAY_KEYS
= ['RETRIES', 'DEBUG', 'debug', 'verbose']¶
-
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’.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
DesmondJob
(task='', gid=None, permanent_restrain=None, permanent_group=None, *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.Job
-
static
err_handler
(job)¶
-
__init__
(task='', gid=None, permanent_restrain=None, permanent_group=None, *arg, **kwarg)¶
-
describe
()¶
-
class
Time
(launch, start, end, num_cpu, cpu_time, duration)¶ Bases:
object
-
__init__
(launch, start, end, num_cpu, cpu_time, duration)¶
-
-
finish
()¶
-
get_proc_time
()¶
-
static
get_time
(jctrl, num_cpu)¶
-
launch
(host=None)¶ Launches the job via jobcontrol.
-
process_completed_job
()¶ Check for valid output and set status of job, assuming job is already complete.
-
update
()¶
-
static
-
class
schrodinger.application.desmond.stage.
FepJob
(fepid=None, n_win=None, i_win=None, fepout=None, egout=None, fragname=None, *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.DesmondJob
,schrodinger.application.desmond.picklejar.Picklable
-
id
= 0¶
-
__init__
(fepid=None, n_win=None, i_win=None, fepout=None, egout=None, fragname=None, *arg, **kwarg)¶
-
describe
()¶
-
class
Time
(launch, start, end, num_cpu, cpu_time, duration)¶ Bases:
object
-
__init__
(launch, start, end, num_cpu, cpu_time, duration)¶
-
-
static
err_handler
(job)¶
-
finish
()¶
-
get_proc_time
()¶
-
static
get_time
(jctrl, num_cpu)¶
-
launch
(host=None)¶ Launches the job via jobcontrol.
-
process_completed_job
()¶ Check for valid output and set status of job, assuming job is already complete.
-
update
()¶
-
-
class
schrodinger.application.desmond.stage.
Task
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'task'¶
-
gid
= 0¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
set_family
()¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
ForcefieldBuilder
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'ffbuilder'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(should_pack=True)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
AssignCustomCharge
(*args, **kwargs)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This sets up and runs the custom charge script for the ligand cts in the input file. Ligands must be in separate cts, otherwise custom charges will not be assigned. Other cts will be passed unchanged. This must be called prior to the AssignForcefield stage.
-
NAME
= 'assign_custom_charge'¶
-
TAG
= 'ASSIGN_CUSTOM_CHARGE'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*args, **kwargs)¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
BuildGeometry
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'build_geometry'¶
-
BG_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/utilities/system_builder'¶
-
SOLVENT
= {'DMSO': 'dmso.box.mae', 'METHANOL': 'methanol.box.mae', 'OCTANOL': 'octanol.box.mae', 'SPC': 'spc.box.mae', 'SPCFW': 'spcfw.box.mae', 'TIP3P': 'tip3p.box.mae', 'TIP4P': 'tip4p.box.mae', 'TIP4PD': 'tip4pd.box.mae', 'TIP4PEW': 'tip4pew.box.mae', 'TIP5P': 'tip5p.box.mae', 'WATER': 'spc.box.mae'}¶
-
OPLS
= ['OPLS_2005', 'OPLS2.1', 'OPLS3', 'OPLS3e']¶
-
DEFAULT_ALCHEMICAL_EXCLUDE_DIST
= 5¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
AssignForcefield
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'assign_forcefield'¶
-
OPLS
= ['OPLS_2005', 'OPLS2.1', 'OPLS3', 'OPLS3e']¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
static
get_water_ct_indices
(model)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
SystemBuilder
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'system_builder'¶
-
SOLVENT
= {'SPC': 'spc.box.mae', 'SPCFW': 'spcfw.box.mae', 'TIP3P': 'tip3p.box.mae', 'TIP4P': 'tip4p.box.mae', 'TIP4PD': 'tip4pd.box.mae', 'TIP4PEW': 'tip4pew.box.mae', 'TIP5P': 'tip5p.box.mae'}¶
-
SB_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/utilities/system_builder'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
CROSS_LINK
= {}¶
-
static
gen_restraint
(model, setting, job)¶ Generates restraints.
-
static
merge_atom_group
(model, group_key)¶
-
static
set_atom_group
(model, group, permanent_group=None)¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
prestage
()¶
-
poststage
()¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
pack_stage
(force=False)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
FepBindingPosePrimer
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'fep_binding_pose_primer'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
BindingPoseFepPrimer
(should_pack=True)¶ Bases:
schrodinger.application.desmond.stage.FepBindingPosePrimer
-
NAME
= 'binding_pose_fep_primer'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(should_pack=True)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
FepMapping
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'fep_mapping'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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
()¶
-
-
schrodinger.application.desmond.stage.
concatenate_and_backup
(text_fname)¶
-
schrodinger.application.desmond.stage.
backup_trajectories
(fname)¶
-
schrodinger.application.desmond.stage.
concatenate_trajectories
(trajectories)¶ Concatenate a list of previously backed-up trajectory files (or dirs) with the respective current ones.
Parameters: trajectories ( list
of `str`s) – A list of file names. Each name should have the suffix of either “_trj.previous” or “.xtc.previous”. Elements without such a suffix will be ignored without error. These are the names of the backed-up trajectories. The current trajectories should have the same basenames, but not required to be of the same format as the previous ones’. This means we can concatenate a DTR trajectory with a XTC trajectory. The final (complete) trajecotries will be in the same formats as the current ones’.
-
class
schrodinger.application.desmond.stage.
SimulateBase
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
A stage that can launch desmond simulations.
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
static
check_cms_file
(fname)¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
-
hook_captured_successful_job
(job)¶
-
capture
(job)¶
-
pack_stage
(force=False)¶
-
NAME
= 'generic'¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
poststage
()¶
-
prestage
()¶
-
push
(job)¶
-
release
(is_restarting=False)¶ Calls the ‘crunch’ method to generate new jobs objects and submits them to the ‘QUEUE’.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
RemovesInitialGCMCSolvent
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.SimulateBase
Any stage that actually does simulation should inherit from this class. Only vrun-type stages, which rely on the consistency of the previous stage’s trajectory and the cms model for the current stage, should derive from SimulateBase instead.
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
NAME
= 'generic'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
check_param
()¶
-
count
= 0¶
-
crunch
()¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
GCMC
¶ Bases:
object
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
class
schrodinger.application.desmond.stage.
SolvatePocketBase
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
- This abstract class provides the ability to equalize the number of waters
- across lambda windows to class that inherit from it.
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
poststage
()¶ After all jobs are completed, equalize the number of waters across lambda windows if requested in config.
-
NAME
= 'generic'¶
-
__init__
(should_pack=True)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
GCMCCapable
(*args, **kwargs)¶ Bases:
schrodinger.application.desmond.stage.RemovesInitialGCMCSolvent
,schrodinger.application.desmond.stage.SolvatePocketBase
An extension to SimulateBase that allows adding a GCMC plugin to the desmond simulation. Subclasses of this class become ‘GCMC-capable’. If no ‘gcmc’ block is passed to the class’s config block, this class behaves exactly as SimulateBase.
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*args, **kwargs)¶
-
check_param
()¶ See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
NAME
= 'generic'¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
count
= 0¶
-
crunch
()¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
poststage
()¶ After all jobs are completed, equalize the number of waters across lambda windows if requested in config.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
Simulate
(*args, **kwargs)¶ Bases:
schrodinger.application.desmond.stage.GCMCCapable
This class defines the GCMC-capable simulate stage, which can be thought of as the basic simulate stage, and is what the user will get when they use the name
simulate
. This is just a thin wrapper to associate the name ‘simulate’ with a corresponding class, even though it is otherwise identical to GCMCCapable. Edits to basic simulate functionality should be made to SimulateBase, not here. This class should be subclassed if GCMC support is needed, otherwise subclass SimulateBase-
NAME
= 'simulate'¶
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*args, **kwargs)¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
check_param
()¶ See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.
-
count
= 0¶
-
crunch
()¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
poststage
()¶ After all jobs are completed, equalize the number of waters across lambda windows if requested in config.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
Minimize
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.RemovesInitialGCMCSolvent
-
NAME
= 'minimize'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
check_param
()¶
-
count
= 0¶
-
crunch
()¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
ReplicaExchange
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.Simulate
-
NAME
= 'replica_exchange'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
hook_captured_successful_job
(job)¶
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
check_param
()¶ See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.
-
count
= 0¶
-
crunch
()¶
-
describe
()¶
-
determine
()¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
poststage
()¶ After all jobs are completed, equalize the number of waters across lambda windows if requested in config.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
LambdaHopping
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.ReplicaExchange
-
NAME
= 'lambda_hopping'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
-
hook_captured_successful_job
(job)¶
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
check_param
()¶ See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
poststage
()¶ After all jobs are completed, equalize the number of waters across lambda windows if requested in config.
-
prestage
()¶
-
push
(job)¶
-
release
(is_restarting=False)¶ Calls the ‘crunch’ method to generate new jobs objects and submits them to the ‘QUEUE’.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
DesmondExtend
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'desmond_extend'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
hook_captured_successful_job
(job)¶ Run after successfully completing this stage.
Parameters: job ( FepJob
) – Job object representing the captured job
-
restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
-
__init__
(should_pack=True)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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’.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
Vrun
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.SimulateBase
-
NAME
= 'vrun'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
FepVrun
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.SimulateBase
-
NAME
= 'fep_vrun'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
ConcatParam
(ark={}, parent=None)¶ Bases:
schrodinger.utils.sea.Map
-
update
(ark=None, file=None, tag={})¶ Updates this ‘Map’ object with the given ‘ark’ or with the given ‘file’.
Parameters: - file – If ‘file’ is not None, it must be the name of a file in the ark file format. If ‘file’ is given, the ‘ark’ parameter will be ignored.
- ark – ark can be a string or a dict or a ‘Map’ object. Or ark can be list of the previous objects.
-
INDEX_PATTERN
= re.compile('([^\\[]*)\\[ *([+-]*[1234567890]*) *\\]')¶
-
INDEX_PATTERN2
= re.compile('\\[ *[+-]*([1234567890]*) *\\]')¶
-
__contains__
(key)¶ Returns True if this ‘Map’ object has the ‘key’. Returns False if otherwise.
-
__init__
(ark={}, parent=None)¶ Constructs a ‘Map’ object with a given ‘ark’. The ‘ark’ can be of the following types of objects:
- dict The ‘Map’ object will be constructed consistent with the dict object.
- Map The ‘ark’ will be deep-copied.
- str The string will be parsed and the ‘Map’ object will be constructed for the parsed string.
- list The elements of the list object must be of the above types. A new ‘Map’ object will be constructed using the first elements, and then the ‘Map’ object will be updated with the remaining objects in the list.
If ‘ark’ is not provided, an empty ‘Map’ will be constructed.
User can optionally specify the ‘parent’ parameter, which will set the parent of this ‘Map’ object to the given value of the ‘parent’ parameter.
-
add_tag
(tag, propagate=True)¶ Tags this object with another string(s).
Parameters: - tag – The given ‘tag’ can be a string, or a list of strings, or a ‘set’ of strings.
- propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
-
apply
(op)¶ Recursively applies the operation as given by ‘op’ to all ‘Sea’ subobjects of this ‘Sea’ object.
-
bval
¶ Readonly. Returns a new
Map
object, which has all macros expanded and references dereferenced.
-
clear_all_tag
(propagate=True)¶ Removes all tags.
Parameters: propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
-
clone
(orig)¶ Lets this ‘Map’ object become a deep copy of the ‘orig’ ‘Map’ object.
-
dump
(tag={})¶ Converts this ‘Sea’ object into a string that looks ugly (yet syntactically correct). This method is 50%-900% faster than the __str__ method.
-
dval
¶ Readonly. Returns a new
Map
object with dereferenced values.
-
get_value
(key)¶ Returns the value of the given ‘key’.
Parameters: key – The ‘key’ can be a composite key (i.e., the pathway notation), such as, e.g., “key[1][2].key2.key3[2]”.
-
has_key
(key)¶
-
has_tag
(tag)¶ Returns True if we already tagged this object with the given ‘tag’.
Parameters: tag – The given ‘tag’ can be a string, or a list of strings, or a ‘set’ of strings.
-
key_value
(tag={}, should_sort=False)¶ Returns the key and associated value in a list. Note each element in the returned list will be a 2-tuple object. The first element of the tuple is a reference of the key, and the second element is a reference of the value. User can optionally set the ‘should_sort’ parameter to True, which will let the function return a sorted list. The sorting will be based on the alphanumeric order of ‘key’.
-
keys
(tag={})¶ Returns references of all keys in a list. Note each element in the returned list will be of the ‘Key’ type.
-
parent
()¶ Rerturns the parent of this ‘Sea’ object or None if it does not have a parent.
-
pmode
()¶ Returns the printing mode.
-
raw_val
¶ Readwrite. When read, this returns the current raw value (references and macros kept as is).
-
remove_tag
(tag, propagate=True)¶ Removes a tag.
Parameters: - tag – The given ‘tag’ can be a string, or a list of strings, or a ‘set’ of strings.
- propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
-
reset_tag
(tag, propagate=True)¶ Resets the tag of this object to the given ‘tag’.
Parameters: - tag – The given ‘tag’ can be a string, or a list of strings, or a ‘set’ of strings.
- propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
-
set_parent
(parent)¶ Sets the parent of this ‘Sea’ object to the given ‘parent’.
-
set_pmode
(pmode, propagate=True)¶ Resets the printing mode of this object to the given ‘pmode’.
Parameters: propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
-
set_value
(key, value, tag={})¶ Associates the given value with the given key. The difference between this function and the __setitem__ operator is that the former allows us to reset the tag of the value.
Parameters: - key – The ‘key’ can be a composite key (i.e., the pathway notation), e.g., “key[1].key2[0].key3”.
- tag – If the “tag” parameter is specified, the value of ‘tag’ will be used to tag the ‘value’.
-
set_value_fast
(key, value, tag={})¶ Similar to
set_value
method. The difference is that ifvalue
is aSea
object thevalue
object itself (as opposed to a copy) will be included into thisMap
object after this function call, as a result, the originalSea
objectvalue
might be mutated as necessary. This function is much faster thanset_value
.
-
sval
¶ Readonly. Returns the current
Sea
object.
-
tag
()¶ Returns tags, which are ‘set’ objects.
-
val
¶ Readwrite. When read, this returns the current value (macros will be expanded, and references will be dereferenced.
-
values
(tag={})¶ Returns references of all values in a list. Note each element in the returned list will be of the ‘Sea’ type.
-
-
class
schrodinger.application.desmond.stage.
Concatenate
(*args, **kwargs)¶ Bases:
schrodinger.application.desmond.stage.Simulate
-
NAME
= 'concatenate'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*args, **kwargs)¶
-
param
¶
-
check_param
()¶ See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.
-
DESMOND_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'¶
-
capture
(job)¶
-
static
check_cms_file
(fname)¶
-
count
= 0¶
-
crunch
()¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
parameter_string
= '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '¶
-
poststage
()¶ After all jobs are completed, equalize the number of waters across lambda windows if requested in config.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
Reporter
(fname, plotter='gchart')¶ Bases:
object
-
__init__
(fname, plotter='gchart')¶
-
plot
(*arg, **kwarg)¶ Generates the plot and returns an url to the plot.
-
plot_2d
(*arg, **kwarg)¶ Generates the plot and returns an url to the plot.
-
write
(msg)¶
-
close
()¶
-
-
class
schrodinger.application.desmond.stage.
AnalysisJob
(model_fname, traj_fname, reporter, title, *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.Job
-
__init__
(model_fname, traj_fname, reporter, title, *arg, **kwarg)¶
-
run
()¶
-
class
Time
(launch, start, end, num_cpu, cpu_time, duration)¶ Bases:
object
-
__init__
(launch, start, end, num_cpu, cpu_time, duration)¶
-
-
describe
()¶
-
finish
()¶
-
get_proc_time
()¶
-
static
get_time
(jctrl, num_cpu)¶
-
launch
(host=None)¶ Launches the job via jobcontrol.
-
process_completed_job
()¶ Check for valid output and set status of job, assuming job is already complete.
-
update
()¶
-
-
class
schrodinger.application.desmond.stage.
TimeSeriesAnalysisJob
(time_series, prob_profile, *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.AnalysisJob
-
Y_MARKER
= {'angle': ('angle (deg)', 'x', 'purple', 'red'), 'dihedral': ('dihe (deg)', 'circle', 'skyblue', 'blue'), 'distance': ('dist (A)', 'diamond', 'grey', 'black')}¶
-
TS_NAME
= {'angle': 'angle(t)', 'dihedral': 'dihe(t)', 'distance': 'dist(t)'}¶
-
PR_NAME
= {'angle': 'P(angle)', 'dihedral': 'P(dihe)', 'distance': 'P(dist)'}¶
-
__init__
(time_series, prob_profile, *arg, **kwarg)¶
-
run
()¶
-
class
Time
(launch, start, end, num_cpu, cpu_time, duration)¶ Bases:
object
-
__init__
(launch, start, end, num_cpu, cpu_time, duration)¶
-
-
describe
()¶
-
finish
()¶
-
get_proc_time
()¶
-
static
get_time
(jctrl, num_cpu)¶
-
launch
(host=None)¶ Launches the job via jobcontrol.
-
process_completed_job
()¶ Check for valid output and set status of job, assuming job is already complete.
-
update
()¶
-
-
class
schrodinger.application.desmond.stage.
MetadynamicsAnalysisJob
(meta_setting, reporter, title='', *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.Job
-
__init__
(meta_setting, reporter, title='', *arg, **kwarg)¶
-
run
()¶
-
class
Time
(launch, start, end, num_cpu, cpu_time, duration)¶ Bases:
object
-
__init__
(launch, start, end, num_cpu, cpu_time, duration)¶
-
-
describe
()¶
-
finish
()¶
-
get_proc_time
()¶
-
static
get_time
(jctrl, num_cpu)¶
-
launch
(host=None)¶ Launches the job via jobcontrol.
-
process_completed_job
()¶ Check for valid output and set status of job, assuming job is already complete.
-
update
()¶
-
-
class
schrodinger.application.desmond.stage.
SeaJob
(SEA, *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.AnalysisJob
-
__init__
(SEA, *arg, **kwarg)¶
-
run
()¶
-
class
Time
(launch, start, end, num_cpu, cpu_time, duration)¶ Bases:
object
-
__init__
(launch, start, end, num_cpu, cpu_time, duration)¶
-
-
describe
()¶
-
finish
()¶
-
get_proc_time
()¶
-
static
get_time
(jctrl, num_cpu)¶
-
launch
(host=None)¶ Launches the job via jobcontrol.
-
process_completed_job
()¶ Check for valid output and set status of job, assuming job is already complete.
-
update
()¶
-
-
class
schrodinger.application.desmond.stage.
MatSciAnalysis
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This class sets up and runs automatic analysis for material-science related jobs.
-
NAME
= 'matsci_analysis'¶
-
DEFAULT_BULK_TYPE
= 'cohes_e density heat_vap pressure_tensor sol_param volume'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶ initialization of Material Science Analysis stage
-
getMSJobKeywords
()¶ This returns the keywords used for this job type.
Returns: Standard job keywords Return type: list of ark objects
-
crunch
()¶ do all the setup and submit the calculations
-
hook_captured_successful_job
(job)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
PLAnalysis
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This class sets up and runs automatic analysis for protein-ligand complex
-
NAME
= 'pl_analysis'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶ initialization of pl-analysis stage
-
crunch
()¶ do all the setup and submit the calculations
-
hook_captured_successful_job
(job)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
Analysis
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'analysis'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
DEFAULT_PROB_PROFILE_SETTING
= {'angel': [2, 0, 180, True], 'dihedral': [2, 0, 360, True]}¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
FepanaJob
(fepid=None, n_win=None, sim_job=None, mutation=None, temperature=300.0, correct_restr=False, correct_coul=False, correct_vdw=False, bennett=None, reporter=None, fep_type=None, include_sid=True, *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.DesmondJob
,schrodinger.application.desmond.picklejar.Picklable
-
id
= 0¶
-
__init__
(fepid=None, n_win=None, sim_job=None, mutation=None, temperature=300.0, correct_restr=False, correct_coul=False, correct_vdw=False, bennett=None, reporter=None, fep_type=None, include_sid=True, *arg, **kwarg)¶
-
describe
()¶
-
get_endpoint_cmsfiles
()¶
-
run
()¶
-
class
Time
(launch, start, end, num_cpu, cpu_time, duration)¶ Bases:
object
-
__init__
(launch, start, end, num_cpu, cpu_time, duration)¶
-
-
static
err_handler
(job)¶
-
finish
()¶
-
get_proc_time
()¶
-
static
get_time
(jctrl, num_cpu)¶
-
launch
(host=None)¶ Launches the job via jobcontrol.
-
process_completed_job
()¶ Check for valid output and set status of job, assuming job is already complete.
-
update
()¶
-
-
class
schrodinger.application.desmond.stage.
FepAnalysis
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'fep_analysis'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
poststage
()¶
-
__init__
(should_pack=True)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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
()¶
-
-
schrodinger.application.desmond.stage.
FepAnalysis2
¶
-
class
schrodinger.application.desmond.stage.
CalcDdg
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'calc_ddg'¶
-
CMD
= ['run', '-FROM', 'desmond', 'calculate_ddg.py']¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
FepMapperReport
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'fep_mapper_report'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
prestage
()¶
-
compatible_graph
(g)¶
-
crunch
()¶
-
poststage
()¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
VacuumReport
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.FepMapperReport
-
NAME
= 'vacuum_report'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶
-
__init__
(*arg, **kwarg)¶
-
capture
(job)¶
-
check_param
()¶
-
compatible_graph
(g)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
WaterMap
¶ Bases:
object
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
class
schrodinger.application.desmond.stage.
Trajectory
¶ Bases:
object
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
class
schrodinger.application.desmond.stage.
WaterMapCluster
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'watermap_cluster'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
poststage
()¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
WaterMapAnaJob
(output_file, cluster_file, ligand_file, protein_file, water_file, input_cms, input_trj, do_not_return_trajectory, cavity, cavity_cns, hbond_stat, ene, ligand_distance=10.0, sampling_freq=50, hs_radius=1.0, *arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.Job
-
__init__
(output_file, cluster_file, ligand_file, protein_file, water_file, input_cms, input_trj, do_not_return_trajectory, cavity, cavity_cns, hbond_stat, ene, ligand_distance=10.0, sampling_freq=50, hs_radius=1.0, *arg, **kwarg)¶
-
run
()¶
-
read_cluster_file
()¶
-
get_translation_vector
()¶
-
average_cavity
()¶
-
average_cavity_cns
()¶
-
average_hbond
()¶
-
average_energy
()¶
-
transform_watermap
()¶
-
write_watermap
()¶
-
decorate_watermap
()¶
-
calculateAverageDipole
()¶
-
calculateWaterMapDensity
()¶
-
transformWaterMapTrajectory
()¶
-
writeHSWater
()¶
-
writeFrameWater
()¶
-
writeGridData
()¶
-
class
Time
(launch, start, end, num_cpu, cpu_time, duration)¶ Bases:
object
-
__init__
(launch, start, end, num_cpu, cpu_time, duration)¶
-
-
describe
()¶
-
finish
()¶
-
get_proc_time
()¶
-
static
get_time
(jctrl, num_cpu)¶
-
launch
(host=None)¶ Launches the job via jobcontrol.
-
process_completed_job
()¶ Check for valid output and set status of job, assuming job is already complete.
-
update
()¶
-
-
class
schrodinger.application.desmond.stage.
WaterMapPostAnalysis
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'watermap_post_analysis'¶
-
CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/run'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
SolvatePocket
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.SolvatePocketBase
-
NAME
= 'solvate_pocket'¶
-
SOLVATE_POCKET_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/utilities/solvate_pocket'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
DEFAULT_SPD
= '\n name = "standard solvate_pocket command file"\n chemical_potential = -7.17\n init_chemical_potential = -6.2\n temperature = 300.0\n cut_off = 9.0\n init_num_passes = 7500\n num_passes = 100000\n update_frequency = 100\n pass_term_window = 5000\n term_std_slope = 0.00001\n num_trans_rot = 100\n num_delete = 35\n num_output = 1\n num_insert = 35\n max_disp = 0.105\n max_dpsi = 0.318\n max_dctheta = 0.0654\n short_dist = 0.5\n distribution_window = 10000\n trajectory_freq = 200\n output_structure = most_frequent # most_frequent | match_distribution\n cnt_cms_from = 1\n '¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
pack_stage
(force=False)¶
-
poststage
()¶ After all jobs are completed, equalize the number of waters across lambda windows if requested in config.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
McproStageBase
¶ Bases:
object
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
class
schrodinger.application.desmond.stage.
McproSystemBuilder
¶ Bases:
object
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
class
schrodinger.application.desmond.stage.
McproSimulate
¶ Bases:
object
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
class
schrodinger.application.desmond.stage.
Extern
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'extern'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
serialize
(attribute)¶
-
crunch
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
Trim
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'trim'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
Stop
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'stop'¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
prestage
()¶
-
poststage
()¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
ProteinMutationGenerator
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'protein_mutation_generator'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ We will either read the mutations from a file or directly from the msj where mutations are defined as a list of space seperated strings
mutations = [“C:23->ALA” “C:23->SER”]
-
create_mutation_file
(mutation_file)¶
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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
()¶
-
-
schrodinger.application.desmond.stage.
move_to_base_dir
(fname, _print, jobname, master_jobname, base_dir)¶
-
class
schrodinger.application.desmond.stage.
CovalentFepMapper
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'covalent_fep_mapper'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
ProteinFepMapper
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'protein_fep_mapper'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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
()¶
-
-
schrodinger.application.desmond.stage.
FepProteinMapper
¶ alias of
schrodinger.application.desmond.stage.ProteinFepMapper
-
class
schrodinger.application.desmond.stage.
FepMapper
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'fep_mapper'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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
()¶
-
-
schrodinger.application.desmond.stage.
LeadOptMap
¶
-
class
schrodinger.application.desmond.stage.
AlignCore
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'align_core'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
findCore
(target_st)¶
-
findCoreAtomList
(target_st)¶
-
splitStructure
(fname)¶
-
crunch
()¶
-
hook_captured_successful_job
(job)¶
-
capture
(job)¶
-
check_param
()¶
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
FepMapperCleanup
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'fep_mapper_cleanup'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
poststage
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
Aacg_SiteMap_Multijob
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This class runs multiple SiteMap jobs for mixed resolution cosolvent simulations
-
NAME
= 'aacg_sitemap'¶
-
SITEMAP_CMD
= '/scr/buildbot/savedbuilds/2019-4/NB/build-139/sitemap'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶ Initialize the aacg-sitemap-multijob stage
-
crunch
()¶ Submit the multiple SiteMap jobs
-
capture
(job)¶ Keeps tarck of the failed jobs and decides whether to proceed to NEXT STAGE or not
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
DisorderedSystemBuilder
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This sets up and runs the disordered system builder, which takes in a ct and creates a disordered solid system for it.
-
NAME
= 'disordered_system_builder'¶
-
TAG
= 'DISORDERED_SYSTEM_BUILDER'¶
-
OPLS
= ['OPLS_2005', 'OPLS2.1', 'OPLS3', 'OPLS3e']¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
GenerateSolubilityFepStructures
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This analyzes the results of an MD simulation containing a solvated disordered system and sets up the structures that will be used for sublimation and hydration fep.
If more than 10% of the molecules are over 90% solvent exposed, this marks the molecules as soluble and sublimation fep should not be run. The first structure is the baseline structure used for hydration fep. The
num_sublimation_strucs
strucutres after it are for sublimation fep.-
NAME
= 'generate_solubility_fep_structures'¶
-
TAG
= 'GENERATE_SOLUBILITY_FEP_STRUCTURES'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
ExtractSoluteStructure
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This extracts a solute structure from the output cms of an MD run, and clears the simulation box if present.
-
NAME
= 'extract_solute_structure'¶
-
TAG
= 'EXTRACT_SOLUTE_STRUCTURE'¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
ExtractStructures
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This extracts one or more structures from an input mae file and passes it to the next stage.
-
NAME
= 'extract_structures'¶
-
TAG
= 'EXTRACT_STRUCTURES'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
HashStructureTitle
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This stores the structure title and corresponding hash id for one or more structures from an input mae file and passes it to the next stage.
-
NAME
= 'hash_structure_title'¶
-
TAG
= 'HASH_STRUCTURE_TITLE'¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
SolubilityMdLauncher
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.Multisim
Launches the solubility md workflow.
-
NAME
= 'solubility_md_launcher'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ Set up the simulation by extracting the structures for each job.
-
restart_subjobs
(jobs: List[schrodinger.application.desmond.cmj.Job]) → None¶ Prepare the subjobs for restart.
-
collect_inputfile
(jobs: Optional[schrodinger.utils.sea.List] = None) → List[str]¶ Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.
Parameters: jobs – List of jobs to include. Returns: The filenames needed to run this stage.
-
RELAY_KEYS
= ['RETRIES', 'DEBUG', 'debug', 'verbose']¶
-
__init__
(*arg, **kwarg)¶
-
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’.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
SolubilityFepLauncher
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.Multisim
Launches the solubility fep workflow.
-
NAME
= 'solubility_fep_launcher'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ Set up the simulation by extracting the structures for each job.
-
restart_subjobs
(jobs: List[schrodinger.application.desmond.cmj.Job]) → None¶ Prepare the subjobs for restart.
-
restart_ligands
(ligands: List[str], restart_hydration=True, restart_sublimation=True) → List[str]¶ Restart the jobs for a given list of ligands. Each ligand is specified as the ligand name. Returns the list of restart job names.
Parameters: - ligands – List of ligand names to restart.
- restart_hydration – Set to False to disable restart of the hydration stage. Default is True.
- restart_sublimation – Set to False to disable restart of the sublimation stage. Default is True.
-
collect_inputfile
(jobs: Optional[schrodinger.utils.sea.List] = None) → List[str]¶ Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.
Parameters: jobs – List of jobs to include. Returns: The filenames needed to run this stage.
-
RELAY_KEYS
= ['RETRIES', 'DEBUG', 'debug', 'verbose']¶
-
__init__
(*arg, **kwarg)¶
-
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’.
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
SolubilityFepAnalysis
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
This runs the solubility fep analysis.
-
NAME
= 'solubility_fep_analysis'¶
-
TAG
= 'SOLUBILITY_FEP_ANALYSIS'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
__init__
(should_pack=True)¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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.stage.
AverageCell
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'average_cell'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
__init__
(*arg, **kwarg)¶
-
crunch
()¶
-
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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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'>}¶
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stage_obj
= {}¶
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time_stage
()¶
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schrodinger.application.desmond.stage.
all_stage_family
()¶
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schrodinger.application.desmond.stage.
systrait_is
(stage, map_msj, arg)¶
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schrodinger.application.desmond.stage.
systype_is
(stage, map_msj, arg)¶
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schrodinger.application.desmond.stage.
has_file
(stage, map_msj, arg)¶
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schrodinger.application.desmond.stage.
has_dir
(stage, map_msj, arg)¶
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schrodinger.application.desmond.stage.
is_debugging
(stage, map_msj, arg)¶
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exception
schrodinger.application.desmond.stage.
AssignLambdaScheduleError
¶ Bases:
Exception
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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class
schrodinger.application.desmond.stage.
AssignLambdaSchedule
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
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NAME
= 'assign_lambda_schedule'¶
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PARAM
= <schrodinger.utils.sea.Map object>¶
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crunch
() → None¶
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__init__
(should_pack=True)¶
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capture
(job)¶
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check_param
()¶
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count
= 0¶
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describe
()¶
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determine
()¶
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static
get_n_vdw_and_charge_div
(norm_dipole_per_atom: float, n_win: int) → Tuple[int, float]¶ Compute number of van der Waals windows and fraction of charges.
Uses a “broken stick” function to determine the partition of the lambda windows into van der Waals and electrostatic interactions.
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hook_captured_successful_job
(job)¶
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pack_stage
(force=False)¶
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poststage
()¶
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prestage
()¶
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push
(job)¶
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release
(is_restarting=False)¶ Calls the ‘crunch’ method to generate new jobs objects and submits them to the ‘QUEUE’.
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restart_subjobs
(jobs)¶ Subclass should override this if it supports subjob restarting.
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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'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, '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_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, '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'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, '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'>}¶
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stage_obj
= {}¶
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time_stage
()¶
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