schrodinger.application.desmond.stage module

Various multisim concrete stage classes.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.stage.get_ngpus(arg: List[str]) → int

Returns the number of GPUs from command line arguments.

schrodinger.application.desmond.stage.fep_gpgpu_lic(arg: List[str]) → List[str]

Returns the command line arguments that should be added to properly handle the FEP GPU license. This will also add the JAGUAR_MAIN license if needed.

Parameters:arg – List of command line arguments.
schrodinger.application.desmond.stage.md_gpgpu_lic(arg: List[str]) → List[str]

Returns the command line arguments that should be added to properly handle the MD GPU license.

schrodinger.application.desmond.stage.jaguar_lic() → List[str]

Returns the command line arguments that should be added to properly handle the Jaguar main license.

class schrodinger.application.desmond.stage.Primer(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'primer'
__init__(*arg, **kwarg)
describe()
start(fname_in)
PARAM = <schrodinger.utils.sea.Map object>
capture(job)
check_param()
count = 0
crunch()

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

determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Concluder(fname_out=None, *arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

This stage does not create any jobs for the ‘cmj.QUEUE’.

NAME = 'concluder'
__init__(fname_out=None, *arg, **kwarg)
describe()
release()
PARAM = <schrodinger.utils.sea.Map object>
capture(job)
check_param()
count = 0
crunch()

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

determine()
hook_captured_successful_job(job)
pack_stage(force=False)
poststage()
prestage()
push(job)
restart_subjobs(jobs)

Subclass should override this if it supports subjob restarting.

stage_cls = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Multisim(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'multisim'
PARAM = <schrodinger.utils.sea.Map object>
RELAY_KEYS = ['RETRIES', 'DEBUG', 'debug', 'verbose']
__init__(*arg, **kwarg)
crunch()
capture(job)
restart_subjobs(jobs)

Subclass should override this if it supports subjob restarting.

collect_inputfile(jobs: Optional[schrodinger.utils.sea.List] = None) → List[str]

Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.

Parameters:jobs – List of jobs to include.
Returns:The filenames needed to run this stage.
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
poststage()
prestage()
push(job)
release(is_restarting=False)

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

stage_cls = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.FepLauncher(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.Multisim

NAME = 'fep_launcher'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
restart_subjobs(jobs)

Subclass should override this if it supports subjob restarting.

collect_inputfile(jobs: Optional[schrodinger.utils.sea.List] = None) → List[str]

Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.

Parameters:jobs – List of jobs to include.
Returns:The filenames needed to run this stage.
restart_edges(edges: List[str], sim_protocols: Optional[Dict[str, str]] = None)

Restart the jobs for a given list of edges. Each edge is specified as ‘{from_short_id}_{to_short_id}’. This will create the jobs if missing from the list of existing jobs.

Parameters:sim_protocols – This will be used for reconstructing missing jobs (if any).
RELAY_KEYS = ['RETRIES', 'DEBUG', 'debug', 'verbose']
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
poststage()
prestage()
push(job)
release(is_restarting=False)

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

stage_cls = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.DesmondJob(task='', gid=None, permanent_restrain=None, permanent_group=None, *arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.Job

static err_handler(job)
__init__(task='', gid=None, permanent_restrain=None, permanent_group=None, *arg, **kwarg)
describe()
class Time(launch, start, end, num_cpu, cpu_time, duration)

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
launch(host=None)

Launches the job via jobcontrol.

process_completed_job()

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

update()
class schrodinger.application.desmond.stage.FepJob(fepid=None, n_win=None, i_win=None, fepout=None, egout=None, fragname=None, *arg, **kwarg)

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

id = 0
__init__(fepid=None, n_win=None, i_win=None, fepout=None, egout=None, fragname=None, *arg, **kwarg)
describe()
class Time(launch, start, end, num_cpu, cpu_time, duration)

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)
static err_handler(job)
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
launch(host=None)

Launches the job via jobcontrol.

process_completed_job()

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

update()
class schrodinger.application.desmond.stage.Task(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'task'
gid = 0
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
set_family()
crunch()

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

capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.ForcefieldBuilder(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'ffbuilder'
PARAM = <schrodinger.utils.sea.Map object>
__init__(should_pack=True)
capture(job)
check_param()
count = 0
crunch()

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

describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.AssignCustomCharge(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StageBase

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'
TAG = 'ASSIGN_CUSTOM_CHARGE'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*args, **kwargs)
crunch()

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

capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.BuildGeometry(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'build_geometry'
BG_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/utilities/system_builder'
SOLVENT = {'DMSO': 'dmso.box.mae', 'METHANOL': 'methanol.box.mae', 'OCTANOL': 'octanol.box.mae', 'SPC': 'spc.box.mae', 'SPCFW': 'spcfw.box.mae', 'TIP3P': 'tip3p.box.mae', 'TIP4P': 'tip4p.box.mae', 'TIP4PD': 'tip4pd.box.mae', 'TIP4PEW': 'tip4pew.box.mae', 'TIP5P': 'tip5p.box.mae', 'WATER': 'spc.box.mae'}
OPLS = ['OPLS_2005', 'OPLS2.1', 'OPLS3', 'OPLS3e']
DEFAULT_ALCHEMICAL_EXCLUDE_DIST = 5
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
hook_captured_successful_job(job)
capture(job)
check_param()
count = 0
describe()
determine()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.AssignForcefield(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'assign_forcefield'
OPLS = ['OPLS_2005', 'OPLS2.1', 'OPLS3', 'OPLS3e']
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
hook_captured_successful_job(job)
static get_water_ct_indices(model)
capture(job)
check_param()
count = 0
describe()
determine()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.SystemBuilder(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'system_builder'
SOLVENT = {'SPC': 'spc.box.mae', 'SPCFW': 'spcfw.box.mae', 'TIP3P': 'tip3p.box.mae', 'TIP4P': 'tip4p.box.mae', 'TIP4PD': 'tip4pd.box.mae', 'TIP4PEW': 'tip4pew.box.mae', 'TIP5P': 'tip5p.box.mae'}
SB_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/utilities/system_builder'
PARAM = <schrodinger.utils.sea.Map object>
static merge_restrain(model, res, new_restr, old_restr)

`res’ is a `sea.Sea’ object.

static gen_restraint(model, setting, job)

Generates restraints.

static set_restrain(model, setting, permanent_restr=None, job=None)

`restr’ is a `sea.Sea’ object.

static merge_atom_group(model, group_key)
static set_atom_group(model, group, permanent_group=None)
__init__(*arg, **kwarg)
crunch()
hook_captured_successful_job(job)
prestage()
poststage()
capture(job)
check_param()
count = 0
describe()
determine()
pack_stage(force=False)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.FepBindingPosePrimer(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

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

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

__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.BindingPoseFepPrimer(should_pack=True)

Bases: schrodinger.application.desmond.stage.FepBindingPosePrimer

NAME = 'binding_pose_fep_primer'
PARAM = <schrodinger.utils.sea.Map object>
__init__(should_pack=True)
capture(job)
check_param()
count = 0
crunch()

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

describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.FepMapping(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_mapping'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
schrodinger.application.desmond.stage.concatenate_and_backup(text_fname)
schrodinger.application.desmond.stage.backup_trajectories(fname)
schrodinger.application.desmond.stage.concatenate_trajectories(trajectories)

Concatenate a list of previously backed-up trajectory files (or dirs) with the respective current ones.

Parameters:trajectories (list of `str`s) – A list of file names. Each name should have the suffix of either “_trj.previous” or “.xtc.previous”. Elements without such a suffix will be ignored without error. These are the names of the backed-up trajectories. The current trajectories should have the same basenames, but not required to be of the same format as the previous ones’. This means we can concatenate a DTR trajectory with a XTC trajectory. The final (complete) trajecotries will be in the same formats as the current ones’.
class schrodinger.application.desmond.stage.SimulateBase(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

A stage that can launch desmond simulations.

DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
PARAM = <schrodinger.utils.sea.Map object>
static check_cms_file(fname)
__init__(*arg, **kwarg)
crunch()
restart_subjobs(jobs)

Subclass should override this if it supports subjob restarting.

hook_captured_successful_job(job)
capture(job)
pack_stage(force=False)
NAME = 'generic'
check_param()
count = 0
describe()
determine()
poststage()
prestage()
push(job)
release(is_restarting=False)

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

stage_cls = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.RemovesInitialGCMCSolvent(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.SimulateBase

Any stage that actually does simulation should inherit from this class. Only vrun-type stages, which rely on the consistency of the previous stage’s trajectory and the cms model for the current stage, should derive from SimulateBase instead.

DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
NAME = 'generic'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
capture(job)
static check_cms_file(fname)
check_param()
count = 0
crunch()
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.GCMC

Bases: object

__init__

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

class schrodinger.application.desmond.stage.SolvatePocketBase(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

This abstract class provides the ability to equalize the number of waters
across lambda windows to class that inherit from it.
PARAM = <schrodinger.utils.sea.Map object>
poststage()

After all jobs are completed, equalize the number of waters across lambda windows if requested in config.

NAME = 'generic'
__init__(should_pack=True)
capture(job)
check_param()
count = 0
crunch()

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

describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.GCMCCapable(*args, **kwargs)

Bases: schrodinger.application.desmond.stage.RemovesInitialGCMCSolvent, schrodinger.application.desmond.stage.SolvatePocketBase

An extension to SimulateBase that allows adding a GCMC plugin to the desmond simulation. Subclasses of this class become ‘GCMC-capable’. If no ‘gcmc’ block is passed to the class’s config block, this class behaves exactly as SimulateBase.

PARAM = <schrodinger.utils.sea.Map object>
__init__(*args, **kwargs)
check_param()

See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.

DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
NAME = 'generic'
capture(job)
static check_cms_file(fname)
count = 0
crunch()
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
poststage()

After all jobs are completed, equalize the number of waters across lambda windows if requested in config.

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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Simulate(*args, **kwargs)

Bases: schrodinger.application.desmond.stage.GCMCCapable

This class defines the GCMC-capable simulate stage, which can be thought of as the basic simulate stage, and is what the user will get when they use the name simulate. This is just a thin wrapper to associate the name ‘simulate’ with a corresponding class, even though it is otherwise identical to GCMCCapable. Edits to basic simulate functionality should be made to SimulateBase, not here. This class should be subclassed if GCMC support is needed, otherwise subclass SimulateBase

NAME = 'simulate'
DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*args, **kwargs)
capture(job)
static check_cms_file(fname)
check_param()

See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.

count = 0
crunch()
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
poststage()

After all jobs are completed, equalize the number of waters across lambda windows if requested in config.

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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Minimize(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.RemovesInitialGCMCSolvent

NAME = 'minimize'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
capture(job)
static check_cms_file(fname)
check_param()
count = 0
crunch()
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.ReplicaExchange(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.Simulate

NAME = 'replica_exchange'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
hook_captured_successful_job(job)
DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
capture(job)
static check_cms_file(fname)
check_param()

See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.

count = 0
crunch()
describe()
determine()
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
poststage()

After all jobs are completed, equalize the number of waters across lambda windows if requested in config.

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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.LambdaHopping(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.ReplicaExchange

NAME = 'lambda_hopping'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
restart_subjobs(jobs)

Subclass should override this if it supports subjob restarting.

hook_captured_successful_job(job)
DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
capture(job)
static check_cms_file(fname)
check_param()

See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.

count = 0
describe()
determine()
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
poststage()

After all jobs are completed, equalize the number of waters across lambda windows if requested in config.

prestage()
push(job)
release(is_restarting=False)

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

stage_cls = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.DesmondExtend(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

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

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

hook_captured_successful_job(job)

Run after successfully completing this stage.

Parameters:job (FepJob) – Job object representing the captured job
restart_subjobs(jobs)

Subclass should override this if it supports subjob restarting.

__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
pack_stage(force=False)
poststage()
prestage()
push(job)
release(is_restarting=False)

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

stage_cls = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Vrun(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.SimulateBase

NAME = 'vrun'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
capture(job)
static check_cms_file(fname)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.FepVrun(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.SimulateBase

NAME = 'fep_vrun'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
hook_captured_successful_job(job)
DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
capture(job)
static check_cms_file(fname)
check_param()
count = 0
describe()
determine()
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.ConcatParam(ark={}, parent=None)

Bases: schrodinger.utils.sea.Map

update(ark=None, file=None, tag={})

Updates this ‘Map’ object with the given ‘ark’ or with the given ‘file’.

Parameters:
  • file – If ‘file’ is not None, it must be the name of a file in the ark file format. If ‘file’ is given, the ‘ark’ parameter will be ignored.
  • ark – ark can be a string or a dict or a ‘Map’ object. Or ark can be list of the previous objects.
INDEX_PATTERN = re.compile('([^\\[]*)\\[ *([+-]*[1234567890]*) *\\]')
INDEX_PATTERN2 = re.compile('\\[ *[+-]*([1234567890]*) *\\]')
__contains__(key)

Returns True if this ‘Map’ object has the ‘key’. Returns False if otherwise.

__init__(ark={}, parent=None)

Constructs a ‘Map’ object with a given ‘ark’. The ‘ark’ can be of the following types of objects:

  • dict The ‘Map’ object will be constructed consistent with the dict object.
  • Map The ‘ark’ will be deep-copied.
  • str The string will be parsed and the ‘Map’ object will be constructed for the parsed string.
  • list The elements of the list object must be of the above types. A new ‘Map’ object will be constructed using the first elements, and then the ‘Map’ object will be updated with the remaining objects in the list.

If ‘ark’ is not provided, an empty ‘Map’ will be constructed.

User can optionally specify the ‘parent’ parameter, which will set the parent of this ‘Map’ object to the given value of the ‘parent’ parameter.

add_tag(tag, propagate=True)

Tags this object with another string(s).

Parameters:
  • tag – The given ‘tag’ can be a string, or a list of strings, or a ‘set’ of strings.
  • propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
apply(op)

Recursively applies the operation as given by ‘op’ to all ‘Sea’ subobjects of this ‘Sea’ object.

bval

Readonly. Returns a new Map object, which has all macros expanded and references dereferenced.

clear_all_tag(propagate=True)

Removes all tags.

Parameters:propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
clone(orig)

Lets this ‘Map’ object become a deep copy of the ‘orig’ ‘Map’ object.

dump(tag={})

Converts this ‘Sea’ object into a string that looks ugly (yet syntactically correct). This method is 50%-900% faster than the __str__ method.

dval

Readonly. Returns a new Map object with dereferenced values.

get_value(key)

Returns the value of the given ‘key’.

Parameters:key – The ‘key’ can be a composite key (i.e., the pathway notation), such as, e.g., “key[1][2].key2.key3[2]”.
has_key(key)
has_tag(tag)

Returns True if we already tagged this object with the given ‘tag’.

Parameters:tag – The given ‘tag’ can be a string, or a list of strings, or a ‘set’ of strings.
key_value(tag={}, should_sort=False)

Returns the key and associated value in a list. Note each element in the returned list will be a 2-tuple object. The first element of the tuple is a reference of the key, and the second element is a reference of the value. User can optionally set the ‘should_sort’ parameter to True, which will let the function return a sorted list. The sorting will be based on the alphanumeric order of ‘key’.

keys(tag={})

Returns references of all keys in a list. Note each element in the returned list will be of the ‘Key’ type.

parent()

Rerturns the parent of this ‘Sea’ object or None if it does not have a parent.

pmode()

Returns the printing mode.

raw_val

Readwrite. When read, this returns the current raw value (references and macros kept as is).

remove_tag(tag, propagate=True)

Removes a tag.

Parameters:
  • tag – The given ‘tag’ can be a string, or a list of strings, or a ‘set’ of strings.
  • propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
reset_tag(tag, propagate=True)

Resets the tag of this object to the given ‘tag’.

Parameters:
  • tag – The given ‘tag’ can be a string, or a list of strings, or a ‘set’ of strings.
  • propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
set_parent(parent)

Sets the parent of this ‘Sea’ object to the given ‘parent’.

set_pmode(pmode, propagate=True)

Resets the printing mode of this object to the given ‘pmode’.

Parameters:propagate – If True, the function will propagate the operation to all ‘Sea’ subobjects.
set_value(key, value, tag={})

Associates the given value with the given key. The difference between this function and the __setitem__ operator is that the former allows us to reset the tag of the value.

Parameters:
  • key – The ‘key’ can be a composite key (i.e., the pathway notation), e.g., “key[1].key2[0].key3”.
  • tag – If the “tag” parameter is specified, the value of ‘tag’ will be used to tag the ‘value’.
set_value_fast(key, value, tag={})

Similar to set_value method. The difference is that if value is a Sea object the value object itself (as opposed to a copy) will be included into this Map object after this function call, as a result, the original Sea object value might be mutated as necessary. This function is much faster than set_value.

sval

Readonly. Returns the current Sea object.

tag()

Returns tags, which are ‘set’ objects.

val

Readwrite. When read, this returns the current value (macros will be expanded, and references will be dereferenced.

values(tag={})

Returns references of all values in a list. Note each element in the returned list will be of the ‘Sea’ type.

class schrodinger.application.desmond.stage.Concatenate(*args, **kwargs)

Bases: schrodinger.application.desmond.stage.Simulate

NAME = 'concatenate'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*args, **kwargs)
param
check_param()

See super for details. This subclass implementation checks if the gcmc block was passed in by the user to determine if this stage needs to do gcmc-functionality.

DESMOND_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/desmond'
capture(job)
static check_cms_file(fname)
count = 0
crunch()
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
parameter_string = '\n DATA = {\n jobname = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"\n host = "$SUBHOST"\n fep.type = small_molecule\n fep.model_file = []\n jin_file = []\n jin_must_transfer_file= []\n jout = ""\n cfg_file = ""\n window = ?\n atom_group = none\n restraints.new = []\n restraints.existing = ignore\n print_restraint = false\n jlaunch_opt= [""]\n }\n\n VALIDATE = {\n host = {type = str range = [1 10000000000]}\n fep.type = {type = enum range = [prm_stability protein_selectivity covalent_ligand small_molecule metalloprotein ligand_selectivity binding_pose]}\n fep.model_file = {type = list size = 0 elem = [[{type = none} {type = str range = [0 10000000000]}]]}\n cfg_file = {type = str range = [0 10000000000]}\n jin_file = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n jin_must_transfer_file = {type = list size = 0 elem = {type = str range = [0 10000000000]}}\n jout = [\n {type = str range = [0 10000000000]}\n {type = list size = 0\n elem = {type = str range = [0 10000000000]}}\n ]\n window = [\n {type = none}\n {type = int0 _check = check_iwindow}\n {type = list size = 0 elem = {type = int0 _check = check_iwindow}}\n ]\n atom_group = [\n {type = enum range = [retain none]}\n {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 255]}\n }\n {type = list size = 0\n elem = {atom = {type = str range = [0 10000000000]}\n name = {type = str range = [0 10000000000]}\n index = {type = int range = [0 7]}\n }\n }\n ]\n restraints.existing = {type = enum range = [retain ignore]}\n restraints.new = [ {type = list}\n {_skip = all}\n ]\n print_restraint = {type = bool}\n jlaunch_opt.black_list = ["!append!" "-exec" "-PROCS" "-in" "-c" "-overwrite"]\n }\n '
poststage()

After all jobs are completed, equalize the number of waters across lambda windows if requested in config.

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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.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.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)
describe()
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
launch(host=None)

Launches the job via jobcontrol.

process_completed_job()

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

update()
class schrodinger.application.desmond.stage.TimeSeriesAnalysisJob(time_series, prob_profile, *arg, **kwarg)

Bases: schrodinger.application.desmond.stage.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)
describe()
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
launch(host=None)

Launches the job via jobcontrol.

process_completed_job()

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

update()
class schrodinger.application.desmond.stage.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)
describe()
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
launch(host=None)

Launches the job via jobcontrol.

process_completed_job()

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

update()
class schrodinger.application.desmond.stage.SeaJob(SEA, *arg, **kwarg)

Bases: schrodinger.application.desmond.stage.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)
describe()
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
launch(host=None)

Launches the job via jobcontrol.

process_completed_job()

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

update()
class schrodinger.application.desmond.stage.MatSciAnalysis(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

This class sets up and runs automatic analysis for material-science related jobs.

NAME = 'matsci_analysis'
DEFAULT_BULK_TYPE = 'cohes_e density heat_vap pressure_tensor sol_param volume'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)

initialization of Material Science Analysis stage

getMSJobKeywords()

This returns the keywords used for this job type.

Returns:Standard job keywords
Return type:list of ark objects
crunch()

do all the setup and submit the calculations

hook_captured_successful_job(job)
capture(job)
check_param()
count = 0
describe()
determine()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.PLAnalysis(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

This class sets up and runs automatic analysis for protein-ligand complex

NAME = 'pl_analysis'
PARAM = <schrodinger.utils.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()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Analysis(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'analysis'
PARAM = <schrodinger.utils.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()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.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.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)
static err_handler(job)
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
launch(host=None)

Launches the job via jobcontrol.

process_completed_job()

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

update()
class schrodinger.application.desmond.stage.FepAnalysis(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_analysis'
PARAM = <schrodinger.utils.sea.Map object>
crunch()
hook_captured_successful_job(job)
poststage()
__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
schrodinger.application.desmond.stage.FepAnalysis2

alias of schrodinger.application.desmond.stage.FepAnalysis

class schrodinger.application.desmond.stage.CalcDdg(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'calc_ddg'
CMD = ['run', '-FROM', 'desmond', 'calculate_ddg.py']
PARAM = <schrodinger.utils.sea.Map object>
crunch()
__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.FepMapperReport(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_mapper_report'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
prestage()
compatible_graph(g)
crunch()
poststage()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.VacuumReport(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.FepMapperReport

NAME = 'vacuum_report'
PARAM = <schrodinger.utils.sea.Map object>
crunch()
__init__(*arg, **kwarg)
capture(job)
check_param()
compatible_graph(g)
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.WaterMap

Bases: object

__init__

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

class schrodinger.application.desmond.stage.Trajectory

Bases: object

__init__

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

class schrodinger.application.desmond.stage.WaterMapCluster(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'watermap_cluster'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
hook_captured_successful_job(job)
poststage()
capture(job)
check_param()
count = 0
describe()
determine()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.WaterMapAnaJob(output_file, cluster_file, ligand_file, protein_file, water_file, input_cms, input_trj, do_not_return_trajectory, cavity, cavity_cns, hbond_stat, ene, ligand_distance=10.0, sampling_freq=50, hs_radius=1.0, *arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.Job

__init__(output_file, cluster_file, ligand_file, protein_file, water_file, input_cms, input_trj, do_not_return_trajectory, cavity, cavity_cns, hbond_stat, ene, ligand_distance=10.0, sampling_freq=50, hs_radius=1.0, *arg, **kwarg)
run()
read_cluster_file()
get_translation_vector()
average_cavity()
average_cavity_cns()
average_hbond()
average_energy()
transform_watermap()
write_watermap()
decorate_watermap()
calculateAverageDipole()
calculateWaterMapDensity()
transformWaterMapTrajectory()
writeHSWater()
writeFrameWater()
writeGridData()
class Time(launch, start, end, num_cpu, cpu_time, duration)

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)
describe()
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
launch(host=None)

Launches the job via jobcontrol.

process_completed_job()

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

update()
class schrodinger.application.desmond.stage.WaterMapPostAnalysis(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'watermap_post_analysis'
CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/run'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
hook_captured_successful_job(job)
capture(job)
check_param()
count = 0
describe()
determine()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.SolvatePocket(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.SolvatePocketBase

NAME = 'solvate_pocket'
SOLVATE_POCKET_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/utilities/solvate_pocket'
PARAM = <schrodinger.utils.sea.Map object>
DEFAULT_SPD = '\n name = "standard solvate_pocket command file"\n chemical_potential = -7.17\n init_chemical_potential = -6.2\n temperature = 300.0\n cut_off = 9.0\n init_num_passes = 7500\n num_passes = 100000\n update_frequency = 100\n pass_term_window = 5000\n term_std_slope = 0.00001\n num_trans_rot = 100\n num_delete = 35\n num_output = 1\n num_insert = 35\n max_disp = 0.105\n max_dpsi = 0.318\n max_dctheta = 0.0654\n short_dist = 0.5\n distribution_window = 10000\n trajectory_freq = 200\n output_structure = most_frequent # most_frequent | match_distribution\n cnt_cms_from = 1\n '
__init__(*arg, **kwarg)
crunch()
hook_captured_successful_job(job)
capture(job)
check_param()
count = 0
describe()
determine()
pack_stage(force=False)
poststage()

After all jobs are completed, equalize the number of waters across lambda windows if requested in config.

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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.McproStageBase

Bases: object

__init__

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

class schrodinger.application.desmond.stage.McproSystemBuilder

Bases: object

__init__

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

class schrodinger.application.desmond.stage.McproSimulate

Bases: object

__init__

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

class schrodinger.application.desmond.stage.Extern(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'extern'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
serialize(attribute)
crunch()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Trim(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'trim'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Stop(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'stop'
__init__(*arg, **kwarg)
crunch()
prestage()
poststage()
PARAM = <schrodinger.utils.sea.Map object>
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.ProteinMutationGenerator(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

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

We will either read the mutations from a file or directly from the msj where mutations are defined as a list of space seperated strings

mutations = [“C:23->ALA” “C:23->SER”]

create_mutation_file(mutation_file)
__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
schrodinger.application.desmond.stage.move_to_base_dir(fname, _print, jobname, master_jobname, base_dir)
class schrodinger.application.desmond.stage.CovalentFepMapper(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'covalent_fep_mapper'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.ProteinFepMapper(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'protein_fep_mapper'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
schrodinger.application.desmond.stage.FepProteinMapper

alias of schrodinger.application.desmond.stage.ProteinFepMapper

class schrodinger.application.desmond.stage.FepMapper(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_mapper'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
schrodinger.application.desmond.stage.LeadOptMap

alias of schrodinger.application.desmond.stage.FepMapper

class schrodinger.application.desmond.stage.AlignCore(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'align_core'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
findCore(target_st)
findCoreAtomList(target_st)
splitStructure(fname)
crunch()
hook_captured_successful_job(job)
capture(job)
check_param()
count = 0
describe()
determine()
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.FepMapperCleanup(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_mapper_cleanup'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
poststage()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

This class runs multiple SiteMap jobs for mixed resolution cosolvent simulations

NAME = 'aacg_sitemap'
SITEMAP_CMD = '/scr/buildbot/savedbuilds/2019-4/NB/build-139/sitemap'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)

Initialize the aacg-sitemap-multijob stage

crunch()

Submit the multiple SiteMap jobs

capture(job)

Keeps tarck of the failed jobs and decides whether to proceed to NEXT STAGE or not

check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.DisorderedSystemBuilder(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

This sets up and runs the disordered system builder, which takes in a ct and creates a disordered solid system for it.

NAME = 'disordered_system_builder'
TAG = 'DISORDERED_SYSTEM_BUILDER'
OPLS = ['OPLS_2005', 'OPLS2.1', 'OPLS3', 'OPLS3e']
PARAM = <schrodinger.utils.sea.Map object>
crunch()

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

__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.GenerateSolubilityFepStructures(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

This analyzes the results of an MD simulation containing a solvated disordered system and sets up the structures that will be used for sublimation and hydration fep.

If more than 10% of the molecules are over 90% solvent exposed, this marks the molecules as soluble and sublimation fep should not be run. The first structure is the baseline structure used for hydration fep. The num_sublimation_strucs strucutres after it are for sublimation fep.

NAME = 'generate_solubility_fep_structures'
TAG = 'GENERATE_SOLUBILITY_FEP_STRUCTURES'
PARAM = <schrodinger.utils.sea.Map object>
crunch()

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

__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.ExtractSoluteStructure(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

This extracts a solute structure from the output cms of an MD run, and clears the simulation box if present.

NAME = 'extract_solute_structure'
TAG = 'EXTRACT_SOLUTE_STRUCTURE'
crunch()

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

PARAM = <schrodinger.utils.sea.Map object>
__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.ExtractStructures(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

This extracts one or more structures from an input mae file and passes it to the next stage.

NAME = 'extract_structures'
TAG = 'EXTRACT_STRUCTURES'
PARAM = <schrodinger.utils.sea.Map object>
crunch()

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

__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.HashStructureTitle(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

This stores the structure title and corresponding hash id for one or more structures from an input mae file and passes it to the next stage.

NAME = 'hash_structure_title'
TAG = 'HASH_STRUCTURE_TITLE'
crunch()

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

PARAM = <schrodinger.utils.sea.Map object>
__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.SolubilityMdLauncher(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.Multisim

Launches the solubility md workflow.

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

Set up the simulation by extracting the structures for each job.

restart_subjobs(jobs: List[schrodinger.application.desmond.cmj.Job]) → None

Prepare the subjobs for restart.

collect_inputfile(jobs: Optional[schrodinger.utils.sea.List] = None) → List[str]

Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.

Parameters:jobs – List of jobs to include.
Returns:The filenames needed to run this stage.
RELAY_KEYS = ['RETRIES', 'DEBUG', 'debug', 'verbose']
__init__(*arg, **kwarg)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
poststage()
prestage()
push(job)
release(is_restarting=False)

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

stage_cls = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.SolubilityFepLauncher(*arg, **kwarg)

Bases: schrodinger.application.desmond.stage.Multisim

Launches the solubility fep workflow.

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

Set up the simulation by extracting the structures for each job.

restart_subjobs(jobs: List[schrodinger.application.desmond.cmj.Job]) → None

Prepare the subjobs for restart.

restart_ligands(ligands: List[str], restart_hydration=True, restart_sublimation=True) → List[str]

Restart the jobs for a given list of ligands. Each ligand is specified as the ligand name. Returns the list of restart job names.

Parameters:
  • ligands – List of ligand names to restart.
  • restart_hydration – Set to False to disable restart of the hydration stage. Default is True.
  • restart_sublimation – Set to False to disable restart of the sublimation stage. Default is True.
collect_inputfile(jobs: Optional[schrodinger.utils.sea.List] = None) → List[str]

Returns a list of input fnames for the given jobs. If jobs is passed in, use it instead of the job associated with this object. This is used for subclasses to override the jobs list used.

Parameters:jobs – List of jobs to include.
Returns:The filenames needed to run this stage.
RELAY_KEYS = ['RETRIES', 'DEBUG', 'debug', 'verbose']
__init__(*arg, **kwarg)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
pack_stage(force=False)
poststage()
prestage()
push(job)
release(is_restarting=False)

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

stage_cls = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.SolubilityFepAnalysis(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

This runs the solubility fep analysis.

NAME = 'solubility_fep_analysis'
TAG = 'SOLUBILITY_FEP_ANALYSIS'
PARAM = <schrodinger.utils.sea.Map object>
crunch()

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

__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
class schrodinger.application.desmond.stage.AverageCell(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'average_cell'
PARAM = <schrodinger.utils.sea.Map object>
__init__(*arg, **kwarg)
crunch()
capture(job)
check_param()
count = 0
describe()
determine()
hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()
schrodinger.application.desmond.stage.all_stage_family()
schrodinger.application.desmond.stage.systrait_is(stage, map_msj, arg)
schrodinger.application.desmond.stage.systype_is(stage, map_msj, arg)
schrodinger.application.desmond.stage.has_file(stage, map_msj, arg)
schrodinger.application.desmond.stage.has_dir(stage, map_msj, arg)
schrodinger.application.desmond.stage.is_debugging(stage, map_msj, arg)
exception schrodinger.application.desmond.stage.AssignLambdaScheduleError

Bases: Exception

__init__

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

args
with_traceback()

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

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

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'assign_lambda_schedule'
PARAM = <schrodinger.utils.sea.Map object>
crunch() → None
__init__(should_pack=True)
capture(job)
check_param()
count = 0
describe()
determine()
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.

hook_captured_successful_job(job)
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 = {'aacg_sitemap': <class 'schrodinger.application.desmond.stage.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.ExtractStructures'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.FepMapperReport'>, 'fep_mapping': <class 'schrodinger.application.desmond.stage.FepMapping'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.ReplicaExchange'>, 'simulate': <class 'schrodinger.application.desmond.stage.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()