schrodinger.application.desmond.restraint.restraint_stage module¶
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schrodinger.application.desmond.restraint.restraint_stage.
encode_restraints
(ct: schrodinger.structure.structure.Structure, restraints: List[schrodinger.utils.sea.Map])¶ Encode the restraints in the
FEP_ENCODED_RESTRAINTS
ct property.Parameters: - ct – Structure to modify in place.
- restraints – List of restraints as sea.Map objects.
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schrodinger.application.desmond.restraint.restraint_stage.
decode_restraints
(ct: schrodinger.structure.structure.Structure) → List[schrodinger.utils.sea.Map]¶ Decode the restraints in the
FEP_ENCODED_RESTRAINTS
ct property.Parameters: ct – Structure to read the restraints from. Returns: If found, restraints that can be passed to schrodinger.application.desmond.packages.restraint.RestraintsBuilder
. Otherwise, returnNone
.
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schrodinger.application.desmond.restraint.restraint_stage.
clear_restraints
(ct: schrodinger.structure.structure.Structure)¶ Clear the
FEP_ENCODED_RESTRAINTS
ct property andFEP_RESTRAIN
atom property from a given structure.Parameters: ct – Structure to modify in place.
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schrodinger.application.desmond.restraint.restraint_stage.
calculate_restraint_correction_term
(restraints: List[schrodinger.utils.sea.Map], temperature: float) → float¶ Calculate the correction to the free energy due to the restraints.
Parameters: - restraints – List of restraints.
- temperature – The temperature for the simulation.
Returns: The correction term in kcal/mol.
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class
schrodinger.application.desmond.restraint.restraint_stage.
LoadRestraintsFromStructure
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
Load the restraints encoded in the structure using
encode_restraints
and store to the cms. By default this stage will append to any existing restraints, set ‘load_restraints_from_structure.existing = ignore’ to ignore existing restraints in the structure.The restraints can be used by setting ‘restrain.existing = retain’ in the subsequent simulate stage.
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NAME
= 'load_restraints_from_structure'¶
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TAG
= 'LOAD_RESTRAINTS_FROM_STRUCTURE'¶
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PARAM
= <schrodinger.utils.sea.Map object>¶
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crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
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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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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_absolute_binding_analysis': <class 'schrodinger.application.desmond.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_primer': <class 'schrodinger.application.desmond.absolute_binding.stage.FepAbsoluteBindingPrimer'>, '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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