schrodinger.application.desmond.stage.analysis module¶

class schrodinger.application.desmond.stage.analysis.Reporter(fname, plotter='gchart')¶

Bases: object

__init__(fname, plotter='gchart')¶

plot(*arg, **kwarg)¶: Generates the plot and returns an url to the plot.

plot_2d(*arg, **kwarg)¶: Generates the plot and returns an url to the plot.

write(msg)¶

close()¶

class schrodinger.application.desmond.stage.analysis.AnalysisJob(model_fname, traj_fname, reporter, title, *arg, **kwarg)¶

Bases: schrodinger.application.desmond.cmj.Job

__init__(model_fname, traj_fname, reporter, title, *arg, **kwarg)¶

run()¶

class Time(launch, start, end, num_cpu, cpu_time, duration)¶

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)¶

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.analysis.TimeSeriesAnalysisJob(time_series, prob_profile, *arg, **kwarg)¶

Bases: schrodinger.application.desmond.stage.analysis.AnalysisJob

Y_MARKER = {'angle': ('angle (deg)', 'x', 'purple', 'red'), 'dihedral': ('dihe (deg)', 'circle', 'skyblue', 'blue'), 'distance': ('dist (A)', 'diamond', 'grey', 'black')}¶

TS_NAME = {'angle': 'angle(t)', 'dihedral': 'dihe(t)', 'distance': 'dist(t)'}¶

PR_NAME = {'angle': 'P(angle)', 'dihedral': 'P(dihe)', 'distance': 'P(dist)'}¶

__init__(time_series, prob_profile, *arg, **kwarg)¶

run()¶

class Time(launch, start, end, num_cpu, cpu_time, duration)¶

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)¶

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.analysis.MetadynamicsAnalysisJob(meta_setting, reporter, title='', *arg, **kwarg)¶

Bases: schrodinger.application.desmond.cmj.Job

__init__(meta_setting, reporter, title='', *arg, **kwarg)¶

run()¶

class Time(launch, start, end, num_cpu, cpu_time, duration)¶

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)¶

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.analysis.SeaJob(SEA, *arg, **kwarg)¶

Bases: schrodinger.application.desmond.stage.analysis.AnalysisJob

__init__(SEA, *arg, **kwarg)¶

run()¶

class Time(launch, start, end, num_cpu, cpu_time, duration)¶

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)¶

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.analysis.PLAnalysis(*arg, **kwarg)¶

Bases: schrodinger.application.desmond.cmj.StageBase

This class sets up and runs analysis for protein-ligand complex. The input parameters are ligand and protein ASLs, if not specified the class will automatically try to detect appropriate values, if “none” is specified the class will ignore analysis for the parameter and in other cases use the parameter value to run the analysis job.

NAME = 'pl_analysis'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

__init__(*arg, **kwarg)¶: initialization of pl-analysis stage

crunch()¶: do all the setup and submit the calculations

hook_captured_successful_job(job)¶

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()¶

class schrodinger.application.desmond.stage.analysis.Analysis(*arg, **kwarg)¶

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'analysis'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

DEFAULT_PROB_PROFILE_SETTING = {'angle': [2, 0, 180, True], 'dihedral': [2, 0, 360, True]}¶

__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()¶

class schrodinger.application.desmond.stage.analysis.FepanaJob(fepid=None, n_win=None, sim_job=None, mutation=None, temperature=300.0, correct_restr=False, correct_coul=False, correct_vdw=False, bennett=None, reporter=None, fep_type=None, include_sid=True, *arg, **kwarg)¶

Bases: schrodinger.application.desmond.stage.jobs.DesmondJob, schrodinger.application.desmond.picklejar.Picklable

id = 0¶

__init__(fepid=None, n_win=None, sim_job=None, mutation=None, temperature=300.0, correct_restr=False, correct_coul=False, correct_vdw=False, bennett=None, reporter=None, fep_type=None, include_sid=True, *arg, **kwarg)¶

describe()¶

get_endpoint_cmsfiles()¶

run()¶

class Time(launch, start, end, num_cpu, cpu_time, duration)¶

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)¶

USE_GPU = False¶

static err_handler(job)¶

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.analysis.FepAnalysis(should_pack=True)¶

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_analysis'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

crunch()¶

poststage()¶

RESTARTABLE = False¶

__init__(should_pack=True)¶

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)¶

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()¶