schrodinger.application.desmond.stage.app.watermap module¶
- class schrodinger.application.desmond.stage.app.watermap.WaterMapCluster(*arg, **kwarg)¶
Bases:
schrodinger.application.desmond.cmj.StageBase
- NAME = 'watermap_cluster'¶
- PARAM = <schrodinger.utils.sea.sea.Map object>¶
- __init__(*arg, **kwarg)¶
- crunch()¶
- RESTARTABLE = False¶
- add_job(job: schrodinger.application.desmond.cmj.Job)¶
Shortcut for
add_jobs
- add_jobs(jobs: Iterable[schrodinger.application.desmond.cmj.Job])¶
Add jobs to the stage’s job manager
- check_param()¶
- count = 0¶
- describe()¶
- determine()¶
- filter_jobs(**kwargs) List[schrodinger.application.desmond.cmj.Job] ¶
Return a list of jobs based on a matching a set of criteria given as arguments. Read
JobManager.filter_jobs
for available arguments.
- finalize_job(job: schrodinger.application.desmond.cmj.Job)¶
Call
hook_captured_successful_job
on any successful jobs and write a checkpoint
- finalize_stage()¶
If the stage is done running, pack the stage, and if the stage is successful, continue to the next stage
- get_output_jobs() List[schrodinger.application.desmond.cmj.Job] ¶
Get the stage’s output jobs
- get_prejobs() List[schrodinger.application.desmond.cmj.Job] ¶
Get the stage’s input jobs
- hook_captured_successful_job(job)¶
- property jobs: List[schrodinger.application.desmond.cmj.Job]¶
- migrate_param(param: schrodinger.utils.sea.sea.Map)¶
Subclasses can implement this to migrate params to provide backward compatibility with older msj files, ideally with a deprecation warning.
- 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 = {'generic': <class 'schrodinger.application.desmond.stage.simulate.VrunBase'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_membrane_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepMembraneLauncher'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'reinit': <class 'schrodinger.application.desmond.stage.simulate.ReInit'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'forcefield_builder_launcher': <class 'schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'group_waters': <class 'schrodinger.application.desmond.stage.prepare.structure.GroupWaters'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_launcher_base': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'ramd': <class 'schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD'>, 'ramd_reactive_path': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdGenerateUnbindingPath'>, 'ramd_setup': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdSetup'>, 'ramd_cleanup': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdCleanup'>, 'path_unbinding': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbinding'>, 'path_unbinding_analysis': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingAnalysis'>, 'path_unbind_cleanup': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup'>, 'lambda_dynamics_mapper': <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper'>, 'lambda_dynamics_md_launcher': <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher'>, 'aacg_sitemap': <class 'schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'deform_cell': <class 'schrodinger.application.desmond.stage.app.matsci.DeformCell'>, 'solvate_slab_builder': <class 'schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'ses_stage': <class 'schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent'>, 'extract_subsystem': <class 'schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>, 'constant_ph_analysis': <class 'schrodinger.application.desmond.stage.app.constant_ph.ConstantpHAnalysis'>, None: <class 'schrodinger.application.desmond.stage.deprecate.MustSkip'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.deprecate.VacuumReport'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.deprecate.FepMapperReport'>}¶
- stage_obj = {}¶
- time_stage()¶
- class schrodinger.application.desmond.stage.app.watermap.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)¶
- USE_GPU = False¶
- describe()¶
- property failed: bool¶
- finish()¶
- get_proc_time()¶
- static get_time(jctrl, num_cpu)¶
- property is_for_jc: bool¶
Whether or not this job should be submitted to job control
- property is_incomplete: bool¶
- property is_launchable: bool¶
- property is_restartable¶
- property is_retriable: bool¶
- process_completed_job(jctrl: schrodinger.job.jobcontrol.Job, checkpoint_requested=False, restart_requested=False)¶
Check for valid output and set status of job, assuming job is already complete.
- Parameters
checkpoint_requested – Set to True if the job should checkpoint. Default if False.
restart_requested – Set to True if the job should checkpoint and restart. Default if False.
- requeue(jctrl: schrodinger.job.jobcontrol.Job)¶
- class schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis(*arg, **kwarg)¶
Bases:
schrodinger.application.desmond.cmj.StageBase
- NAME = 'watermap_post_analysis'¶
- CMD = '/scr/buildbot/savedbuilds/2024-1/NB/build-133/run'¶
- PARAM = <schrodinger.utils.sea.sea.Map object>¶
- __init__(*arg, **kwarg)¶
- crunch()¶
- hook_captured_successful_job(job)¶
- RESTARTABLE = False¶
- add_job(job: schrodinger.application.desmond.cmj.Job)¶
Shortcut for
add_jobs
- add_jobs(jobs: Iterable[schrodinger.application.desmond.cmj.Job])¶
Add jobs to the stage’s job manager
- check_param()¶
- count = 0¶
- describe()¶
- determine()¶
- filter_jobs(**kwargs) List[schrodinger.application.desmond.cmj.Job] ¶
Return a list of jobs based on a matching a set of criteria given as arguments. Read
JobManager.filter_jobs
for available arguments.
- finalize_job(job: schrodinger.application.desmond.cmj.Job)¶
Call
hook_captured_successful_job
on any successful jobs and write a checkpoint
- finalize_stage()¶
If the stage is done running, pack the stage, and if the stage is successful, continue to the next stage
- get_output_jobs() List[schrodinger.application.desmond.cmj.Job] ¶
Get the stage’s output jobs
- get_prejobs() List[schrodinger.application.desmond.cmj.Job] ¶
Get the stage’s input jobs
- property jobs: List[schrodinger.application.desmond.cmj.Job]¶
- migrate_param(param: schrodinger.utils.sea.sea.Map)¶
Subclasses can implement this to migrate params to provide backward compatibility with older msj files, ideally with a deprecation warning.
- 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 = {'generic': <class 'schrodinger.application.desmond.stage.simulate.VrunBase'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_membrane_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepMembraneLauncher'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'reinit': <class 'schrodinger.application.desmond.stage.simulate.ReInit'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, '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'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'forcefield_builder_launcher': <class 'schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'group_waters': <class 'schrodinger.application.desmond.stage.prepare.structure.GroupWaters'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_launcher_base': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'ramd': <class 'schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD'>, 'ramd_reactive_path': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdGenerateUnbindingPath'>, 'ramd_setup': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdSetup'>, 'ramd_cleanup': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdCleanup'>, 'path_unbinding': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbinding'>, 'path_unbinding_analysis': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingAnalysis'>, 'path_unbind_cleanup': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup'>, 'lambda_dynamics_mapper': <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper'>, 'lambda_dynamics_md_launcher': <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher'>, 'aacg_sitemap': <class 'schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'deform_cell': <class 'schrodinger.application.desmond.stage.app.matsci.DeformCell'>, 'solvate_slab_builder': <class 'schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'ses_stage': <class 'schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent'>, 'extract_subsystem': <class 'schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>, 'constant_ph_analysis': <class 'schrodinger.application.desmond.stage.app.constant_ph.ConstantpHAnalysis'>, None: <class 'schrodinger.application.desmond.stage.deprecate.MustSkip'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.deprecate.VacuumReport'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.deprecate.FepMapperReport'>}¶
- stage_obj = {}¶
- time_stage()¶