schrodinger.application.desmond.stage.prepare.forcefield module

schrodinger.application.desmond.stage.prepare.forcefield.is_valid_opls_name(name: str) → bool
class schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

This sets up and runs the custom charge script for the ligand cts in the input file. Ligands must be in separate cts, otherwise custom charges will not be assigned. Other cts will be passed unchanged. This must be called prior to the AssignForcefield stage.

NAME = 'assign_custom_charge'
PARAM = <schrodinger.utils.sea.sea.Map object>
run(jobname: str, mae_fname: str) → Optional[str]
Parameters

  • jobname – Jobname for this stage.

  • input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

RESTARTABLE = False
__init__(*args, **kwargs)
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
crunch()

This is where jobs of this stage are created. This function should be overriden by the subclass.

describe()
determine()
filter_jobs(**kwargs) → List[schrodinger.application.desmond.cmj.Job]

Return a list of jobs based on a matching a set of criteria given as arguments. Read JobManager.filter_jobs for available arguments.

finalize_job(job: schrodinger.application.desmond.cmj.Job)

Call hook_captured_successful_job on any successful jobs and write a checkpoint

finalize_stage()

If the stage is done running, pack the stage, and if the stage is successful, continue to the next stage

get_output_jobs() → List[schrodinger.application.desmond.cmj.Job]

Get the stage’s output jobs

get_prejobs() → List[schrodinger.application.desmond.cmj.Job]

Get the stage’s input jobs

hook_captured_successful_job(job)
property jobs: List[schrodinger.application.desmond.cmj.Job]
migrate_param(param: schrodinger.utils.sea.sea.Map)

Subclasses can implement this to migrate params to provide backward compatibility with older msj files, ideally with a deprecation warning.

pack_stage(force=False)
poststage()
prestage()
push(job)
release(is_restarting=False)

Calls the ‘crunch’ method to generate new jobs objects and submits them to the ‘QUEUE’.

restart_subjobs(jobs)

Subclass should override this if it supports subjob restarting.

stage_cls = {'generic': <class 'schrodinger.application.desmond.stage.simulate.VrunBase'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_membrane_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepMembraneLauncher'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'reinit': <class 'schrodinger.application.desmond.stage.simulate.ReInit'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'forcefield_builder_launcher': <class 'schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'group_waters': <class 'schrodinger.application.desmond.stage.prepare.structure.GroupWaters'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_launcher_base': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'ramd': <class 'schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD'>, 'ramd_reactive_path': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdGenerateUnbindingPath'>, 'ramd_setup': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdSetup'>, 'ramd_cleanup': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdCleanup'>, 'path_unbinding': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbinding'>, 'path_unbinding_analysis': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingAnalysis'>, 'path_unbind_cleanup': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup'>, 'lambda_dynamics_mapper': <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper'>, 'lambda_dynamics_md_launcher': <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher'>, 'aacg_sitemap': <class 'schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'deform_cell': <class 'schrodinger.application.desmond.stage.app.matsci.DeformCell'>, 'solvate_slab_builder': <class 'schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'ses_stage': <class 'schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent'>, 'extract_subsystem': <class 'schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>, 'constant_ph_analysis': <class 'schrodinger.application.desmond.stage.app.constant_ph.ConstantpHAnalysis'>, None: <class 'schrodinger.application.desmond.stage.deprecate.MustSkip'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.deprecate.VacuumReport'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.deprecate.FepMapperReport'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StageBase

Variables

ff_builder_args – a list storing arguments passed to desmond_ff_builder so that the same arguments can be passed to generate_titration_states.

NAME = 'assign_forcefield'
FFLD_WATER = {'SPC': 'SPC', 'SPCE': 'SPCE', 'TIP3P': 'T3P', 'TIP4P': 'T4P', 'TIP4P2005': 'T4P5', 'TIP4PD': 'T4PD', 'TIP4PEW': 'T4PE', 'TIP5P': 'T5P'}
parameter_string = '\n    DATA = {\n    forcefield = OPLS_2005\n    water      = SPC\n    humble     = no\n    fepio_mode = 2\n    restrain   = none\n    restraints = {\n        new = []\n        existing = ignore\n    }\n    print_restraint = false\n    atom_group = retain\n    fep_retain_angle = yes\n    core_hopping_fepio = on\n    hydrogen_mass_repartition = off\n    make_alchemical_water = on\n    fep_enhance_sampling_dihedral = off\n    assign_is_infinite = off\n    fail_on_lewis_failure = on\n    use_zob_property = on\n    pose_conf_restraint = {\n        enable = false\n        name = harm\n        schedule = pose_dihedral_restraint\n        fc = 50.0\n        sigma = 10.0\n        alpha = 1.0\n        dihedral_schedule = ""\n        max_ring_size = 999\n    }\n    macromolecule_conf_restraint = {\n        enable = false\n        dihedral_schedule = ""\n        backbone = {\n            name = harm\n            schedule = ""\n            fc = 50.0\n            sigma = 10.0\n            alpha = 1.0\n        }\n        sidechain = {\n            name = harm\n            schedule = ""\n            fc = 50.0\n            sigma = 10.0\n            alpha = 1.0\n        }\n        calpha_rung = {\n            name = harm\n            schedule = ""\n            fc = 5.0\n            alpha = 1.0\n        }\n    }\n    }\n\n    VALIDATE = {\n    forcefield = {type = str _check = check_forcefield}\n    water      = {type = enum range = [SPC SPCE TIP3P TIP4P TIP4P2005 TIP4PEW TIP4PD TIP5P none]}\n    humble     = {type = bool}\n    fepio_mode = {type = int  range = [1 3]}\n    atom_group = [\n       {type = enum range = [retain none]}\n       {atom  = {type = str}\n        name  = {type = str}\n        index = {type = int range = [0 7]}\n       }\n       {type = list size = 0\n        elem = {atom  = {type = str}\n                name  = {type = str}\n                index = {type = int range = [0 7]}\n               }\n       }\n    ]\n    restrain   = [\n       {type = enum range = [retain none]}\n       {_mapcheck = check_restrain _skip = all}\n       {type = list size = -1\n        elem = {_mapcheck = check_restrain _skip = all}\n       }\n    ]\n    restraints = {\n        existing = {type = enum range = [retain ignore ignore_posre]}\n        new = [{type = list} {_skip = all}]\n    }\n    print_restraint = {type = bool }\n    fep_retain_angle = {type = bool}\n    core_hopping_fepio = {type = bool}\n    hydrogen_mass_repartition = {type = bool}\n    make_alchemical_water = {type = bool}\n    fep_enhance_sampling_dihedral = {type = bool}\n    assign_is_infinite = {type = bool}\n    fail_on_lewis_failure = {type = bool}\n    use_zob_property = {type = bool}\n    pose_conf_restraint = {\n        enable = {type = bool}\n        name = {type = enum range = [harm fbhw soft]}\n        fc = {type = float+}\n        sigma = {type = float+}\n        alpha = {type = float+}\n        schedule = {type = str}\n        dihedral_schedule = {type = str}\n        max_ring_size = {type = int}\n        _mapcheck = check_pose_conf_restraint\n        }\n    macromolecule_conf_restraint = {\n        enable = {type = bool}\n        dihedral_schedule = {type = str}\n        backbone = {\n            name = {type = enum range = [harm fbhw soft]}\n            schedule = {type = str}\n            fc = {type = float+}\n            sigma = {type = float+}\n            alpha = {type = float+}\n        }\n        sidechain = {\n            name = {type = enum range = [harm fbhw soft]}\n            schedule = {type = str}\n            fc = {type = float+}\n            sigma = {type = float+}\n            alpha = {type = float+}\n        }\n        calpha_rung = {\n            name = {type = enum range = [harm]}\n            schedule = {type = str}\n            fc = {type = float+}\n            alpha = {type = float+}\n        }\n    }\n    }\n    '
PARAM = <schrodinger.utils.sea.sea.Map object>
__init__(*args, **kwargs)
crunch()
hook_captured_successful_job(job)
static get_water_atom_indices(st: schrodinger.structure._structure.Structure) → List[int]

Method that returns a generator for all the water atoms in a structure.

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()
exception schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaScheduleError

Bases: Exception

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'assign_lambda_schedule'
PARAM = <schrodinger.utils.sea.sea.Map object>
crunch() → None
static get_n_vdw_and_charge_div(norm_dipole_per_atom: float, n_win: int) → Tuple[int, float]

Compute number of van der Waals windows and fraction of charges.

Uses a “broken stick” function to determine the partition of the lambda windows into van der Waals and electrostatic interactions.

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)
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()
schrodinger.application.desmond.stage.prepare.forcefield.encode_restraints(ct: schrodinger.structure._structure.Structure, restraints: List[schrodinger.utils.sea.sea.Map])

Encode the restraints in the FEP_ENCODED_RESTRAINTS ct property.

Parameters

  • ct – Structure to modify in place.

  • restraints – List of restraints as sea.Map objects.

schrodinger.application.desmond.stage.prepare.forcefield.decode_restraints(ct: schrodinger.structure._structure.Structure) → List[schrodinger.utils.sea.sea.Map]

Decode the restraints in the FEP_ENCODED_RESTRAINTS ct property.

Parameters

ct – Structure to read the restraints from.

Returns

If found, restraints that can be passed to schrodinger.application.desmond.packages.restraint.RestraintsBuilder. Otherwise, return None.

schrodinger.application.desmond.stage.prepare.forcefield.clear_restraints(ct: schrodinger.structure._structure.Structure)

Clear the FEP_ENCODED_RESTRAINTS ct property and FEP_RESTRAIN atom property from a given structure.

Parameters

ct – Structure to modify in place.

schrodinger.application.desmond.stage.prepare.forcefield.add_restraint_reference(st: schrodinger.structure._structure.Structure, restraints: List[schrodinger.utils.sea.sea.Map])

Add the reference values for Boresch type distance/angle/dihedral restraints.

Parameters

  • st – Reference structure.

  • restraints – List of restraints, updated in place.

schrodinger.application.desmond.stage.prepare.forcefield.calculate_restraint_correction_term(restraints: List[schrodinger.utils.sea.sea.Map], temperature: float) → float

Calculate the correction to the free energy due to the restraints.

Parameters

  • restraints – List of restraints.

  • temperature – The temperature for the simulation.

Returns

The correction term in kcal/mol.

schrodinger.application.desmond.stage.prepare.forcefield.add_restraint_atom_marker(st: schrodinger.structure._structure.Structure, ligand_asl: str) → Dict[int, int]

Update st to mark the ligand atoms that could be part of a restraint. Returns a dictionary mapping the FEP_RESTRAIN values to the structure atom indicies.

Parameters

  • st – This will be updated in place to add atom properties to mark the ligand atoms.

  • ligand_asl – ASL to identify the ligand.

class schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

Load the restraints encoded in the structure using encode_restraints and store to the cms. By default this stage will append to any existing restraints, set ‘load_restraints_from_structure.existing = ignore’ to ignore existing restraints in the structure.

The restraints can be used by setting ‘restrain.existing = retain’ in the subsequent simulate stage.

NAME = 'load_restraints_from_structure'
PARAM = <schrodinger.utils.sea.sea.Map object>
run(jobname: str, cms_fname: str) → Optional[str]
Parameters

  • jobname – Jobname for this stage.

  • input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

RESTARTABLE = False
__init__(*args, **kwargs)
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
crunch()

This is where jobs of this stage are created. This function should be overriden by the subclass.

describe()
determine()
filter_jobs(**kwargs) → List[schrodinger.application.desmond.cmj.Job]

Return a list of jobs based on a matching a set of criteria given as arguments. Read JobManager.filter_jobs for available arguments.

finalize_job(job: schrodinger.application.desmond.cmj.Job)

Call hook_captured_successful_job on any successful jobs and write a checkpoint

finalize_stage()

If the stage is done running, pack the stage, and if the stage is successful, continue to the next stage

get_output_jobs() → List[schrodinger.application.desmond.cmj.Job]

Get the stage’s output jobs

get_prejobs() → List[schrodinger.application.desmond.cmj.Job]

Get the stage’s input jobs

hook_captured_successful_job(job)
property jobs: List[schrodinger.application.desmond.cmj.Job]
migrate_param(param: schrodinger.utils.sea.sea.Map)

Subclasses can implement this to migrate params to provide backward compatibility with older msj files, ideally with a deprecation warning.

pack_stage(force=False)
poststage()
prestage()
push(job)
release(is_restarting=False)

Calls the ‘crunch’ method to generate new jobs objects and submits them to the ‘QUEUE’.

restart_subjobs(jobs)

Subclass should override this if it supports subjob restarting.

stage_cls = {'generic': <class 'schrodinger.application.desmond.stage.simulate.VrunBase'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_membrane_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepMembraneLauncher'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'reinit': <class 'schrodinger.application.desmond.stage.simulate.ReInit'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'forcefield_builder_launcher': <class 'schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'group_waters': <class 'schrodinger.application.desmond.stage.prepare.structure.GroupWaters'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_launcher_base': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'ramd': <class 'schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD'>, 'ramd_reactive_path': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdGenerateUnbindingPath'>, 'ramd_setup': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdSetup'>, 'ramd_cleanup': <class 'schrodinger.application.desmond.stage.app.kinetics.RamdCleanup'>, 'path_unbinding': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbinding'>, 'path_unbinding_analysis': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingAnalysis'>, 'path_unbind_cleanup': <class 'schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup'>, 'lambda_dynamics_mapper': <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper'>, 'lambda_dynamics_md_launcher': <class 'schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher'>, 'aacg_sitemap': <class 'schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'deform_cell': <class 'schrodinger.application.desmond.stage.app.matsci.DeformCell'>, 'solvate_slab_builder': <class 'schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'ses_stage': <class 'schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent'>, 'extract_subsystem': <class 'schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'generate_mxmd_box': <class 'schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox'>, 'analyze_mxmd_probe_mixture': <class 'schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>, 'constant_ph_analysis': <class 'schrodinger.application.desmond.stage.app.constant_ph.ConstantpHAnalysis'>, None: <class 'schrodinger.application.desmond.stage.deprecate.MustSkip'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.deprecate.VacuumReport'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.deprecate.FepMapperReport'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'forcefield_builder_launcher'
PARAM = <schrodinger.utils.sea.sea.Map object>
crunch()

This is where jobs of this stage are created. This function should be overriden by the subclass.

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)
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()