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)

Check for valid output and set status of job, assuming job is already complete.

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)

Check for valid output and set status of job, assuming job is already complete.

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)

Check for valid output and set status of job, assuming job is already complete.

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)

Check for valid output and set status of job, assuming job is already complete.

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'>, '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.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'>, '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.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)

Check for valid output and set status of job, assuming job is already complete.

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'>, '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()