schrodinger.application.desmond.stage.app.solubility module

class schrodinger.application.desmond.stage.app.solubility.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.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)

Initialize self. See help(type(self)) for accurate signature.

capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(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'>, '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'>, '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'>, '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'>, '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'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, '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'>, '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'>, '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'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 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'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.launcher.Multisim

Launches the solubility md workflow.

NAME = 'solubility_md_launcher'
PARAM = <schrodinger.utils.sea.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.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)
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’.

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'>, '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'>, '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'>, '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'>, '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'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, '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'>, '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'>, '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'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 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'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.launcher.Multisim

Launches the solubility fep workflow.

NAME = 'solubility_fep_launcher'
PARAM = <schrodinger.utils.sea.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(ligand_hashes: 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
  • ligand_hashes – List of ligand hashed 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.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)
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’.

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'>, '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'>, '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'>, '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'>, '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'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, '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'>, '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'>, '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'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 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'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.app.solubility.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.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)

Initialize self. See help(type(self)) for accurate signature.

capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(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'>, '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'>, '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'>, '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'>, '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'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, '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'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, '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'>, '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'>, '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'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 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'>}
stage_obj = {}
time_stage()