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)

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

USE_GPU = False

describe()

finish()

get_proc_time()

static get_time(jctrl, num_cpu)

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)

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

USE_GPU = False

describe()

finish()

get_proc_time()

static get_time(jctrl, num_cpu)

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)

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

USE_GPU = False

describe()

finish()

get_proc_time()

static get_time(jctrl, num_cpu)

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)

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

USE_GPU = False

describe()

finish()

get_proc_time()

static get_time(jctrl, num_cpu)

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)

capture(job)

check_param()

count = 0

describe()

determine()

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'>, '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'>, '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'>, 'solvate_slab_builder': <class 'schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder'>, '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.analysis.Analysis(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'analysis'

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

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

__init__(*arg, **kwarg)

crunch()

hook_captured_successful_job(job)

capture(job)

check_param()

count = 0

describe()

determine()

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'>, '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'>, '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'>, 'solvate_slab_builder': <class 'schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder'>, '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.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)

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

USE_GPU = False

static err_handler(job)

finish()

get_proc_time()

static get_time(jctrl, num_cpu)

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()

hook_captured_successful_job(job)

poststage()

__init__(should_pack=True)

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

capture(job)

check_param()

count = 0

describe()

determine()

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'>, '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'>, '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'>, 'solvate_slab_builder': <class 'schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder'>, '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()