schrodinger.application.desmond.stage.app.absolute_binding.stage module¶
-
class
schrodinger.application.desmond.stage.app.absolute_binding.stage.
FepAbsoluteBindingStructurePrimer
(*args, **kwargs)¶ Bases:
schrodinger.application.desmond.cmj.StructureStageBase
For the ligand with the matching ligand_hash_id, prepare the Absolute Binding structures for MD if the
leg
is not specified, otherwise prepare the structures for FEP. All other ligands will be ignored.-
NAME
= 'fep_absolute_binding_structure_primer'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
run
(jobname: str, mae_fname: str) → Optional[str]¶ Parameters: - jobname – Jobname for this stage.
- input_fname – Filename for the input structure.
Returns: Filename for the output structure or
None
if there was an error generating the output.
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
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.app.matsci.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.simulate.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.deprecate.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>}¶
-
stage_obj
= {}¶
-
time_stage
()¶
-
-
class
schrodinger.application.desmond.stage.app.absolute_binding.stage.
FepAbsoluteBindingFepPrimer
(*args, **kwargs)¶ Bases:
schrodinger.application.desmond.cmj.StructureStageBase
-
NAME
= 'fep_absolute_binding_fep_primer'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
run
(jobname: str, cms_fname: str) → Optional[str]¶ Parameters: - jobname – Jobname for this stage.
- input_fname – Filename for the input structure.
Returns: Filename for the output structure or
None
if there was an error generating the output.
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
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.app.matsci.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.simulate.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.deprecate.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>}¶
-
stage_obj
= {}¶
-
time_stage
()¶
-
-
class
schrodinger.application.desmond.stage.app.absolute_binding.stage.
FepAbsoluteBindingMdLauncher
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.launcher.Multisim
Launches the absolute binding FEP workflow.
-
NAME
= 'fep_absolute_binding_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])¶ Prepare the subjobs for restart.
-
collect_inputfile
() → List[str]¶ Returns a list of input fnames.
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
()¶
-
prepare_extend
() → List[str]¶ Prepare the subjobs to be extended and return the list of job names.
-
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.app.matsci.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.simulate.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.deprecate.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>}¶
-
stage_obj
= {}¶
-
time_stage
()¶
-
-
class
schrodinger.application.desmond.stage.app.absolute_binding.stage.
FepAbsoluteBindingFepLauncher
(*arg, **kwarg)¶ Bases:
schrodinger.application.desmond.stage.launcher.Multisim
Launches the absolute binding FEP workflow.
-
NAME
= 'fep_absolute_binding_fep_launcher'¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
crunch
()¶ Set up the simulation by extracting the structures for each job.
-
restart_ligands
(ligand_hashes: List[str]) → 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: ligand_hashes – List of ligand hash ids to restart.
-
RELAY_KEYS
= ['RETRIES', 'DEBUG', 'debug', 'verbose']¶
-
__init__
(*arg, **kwarg)¶
-
capture
(job)¶
-
check_param
()¶
-
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.
-
count
= 0¶
-
describe
()¶
-
determine
()¶
-
hook_captured_successful_job
(job)¶
-
pack_stage
(force=False)¶
-
poststage
()¶
-
prepare_extend
() → List[str]¶ Prepare the subjobs to be extended and return the list of job names.
-
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.app.matsci.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.simulate.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.deprecate.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>}¶
-
stage_obj
= {}¶
-
time_stage
()¶
-
-
schrodinger.application.desmond.stage.app.absolute_binding.stage.
get_csv_header
() → str¶
-
schrodinger.application.desmond.stage.app.absolute_binding.stage.
get_results_by_ligand
(sts_list: List[List[schrodinger.structure._structure.Structure]]) → dict¶ Given a list of list of structures (each list corresponds to output structure from each FEP leg), return the result for each ligand.
Returns: dict with keys of [“complex_st”, “complex_dg”, “solvent_dg”, “complex_dg_correction”, “final_dg”]. final_dg is None if any values are missing.
-
schrodinger.application.desmond.stage.app.absolute_binding.stage.
get_csv
(results_by_ligand: dict) → str¶ Return the csv content report energies for each ligand. :param: results_by_ligand is got from
get_results_by_ligand
-
schrodinger.application.desmond.stage.app.absolute_binding.stage.
get_csv_row
(ligand: str, complex_dg: schrodinger.application.desmond.measurement.Measurement, solvent_dg: schrodinger.application.desmond.measurement.Measurement, complex_dg_correction: float, final_dg: schrodinger.application.desmond.measurement.Measurement, smiles: str) → str¶ Given the results for a ligand, return a formatted row.
-
class
schrodinger.application.desmond.stage.app.absolute_binding.stage.
FepAbsoluteBindingAnalysis
(should_pack=True)¶ Bases:
schrodinger.application.desmond.cmj.StageBase
-
NAME
= 'fep_absolute_binding_analysis'¶
-
TAG
= 'FEP_ABSOLUTE_BINDING_ANALYSIS'¶
-
previous_compound_ids
= {}¶
-
PARAM
= <schrodinger.utils.sea.Map object>¶
-
collect_inputfile
()¶
-
crunch
()¶ This is where jobs of this stage are created. This function should be overriden by the subclass.
-
__init__
(should_pack=True)¶ Initialize self. See help(type(self)) for accurate signature.
-
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.app.matsci.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.simulate.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.deprecate.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>}¶
-
stage_obj
= {}¶
-
time_stage
()¶
-
-
class
schrodinger.application.desmond.stage.app.absolute_binding.stage.
FepAbsoluteBindingMdPrimer
¶ Bases:
object
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-