schrodinger.application.desmond.stage.app.watermap module

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

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'watermap_post_analysis'
CMD = '/scr/buildbot/savedbuilds/2020-2/NB/build-063/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.app.matsci.Aacg_SiteMap_Multijob'>, 'align_core': <class 'schrodinger.application.desmond.stage.deprecate.AlignCore'>, 'analysis': <class 'schrodinger.application.desmond.stage.analysis.Analysis'>, 'assign_custom_charge': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge'>, 'assign_forcefield': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield'>, 'assign_lambda_schedule': <class 'schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule'>, 'average_cell': <class 'schrodinger.application.desmond.stage.app.matsci.AverageCell'>, 'binding_pose_fep_primer': <class 'schrodinger.application.desmond.stage.deprecate.BindingPoseFepPrimer'>, 'build_geometry': <class 'schrodinger.application.desmond.stage.prepare.structure.BuildGeometry'>, 'calc_ddg': <class 'schrodinger.application.desmond.stage.fep_mapper.CalcDdg'>, 'concatenate': <class 'schrodinger.application.desmond.stage.simulate.Concatenate'>, 'concluder': <class 'schrodinger.application.desmond.stage.workflow.Concluder'>, 'covalent_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper'>, 'desmond_extend': <class 'schrodinger.application.desmond.stage.simulate.DesmondExtend'>, 'disordered_system_builder': <class 'schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder'>, 'extern': <class 'schrodinger.application.desmond.stage.workflow.Extern'>, 'extract_solute_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure'>, 'extract_structures': <class 'schrodinger.application.desmond.stage.prepare.structure.ExtractStructures'>, 'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_fep_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher'>, 'fep_absolute_binding_fep_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer'>, 'fep_absolute_binding_md_launcher': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher'>, 'fep_absolute_binding_structure_primer': <class 'schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer'>, 'fep_analysis': <class 'schrodinger.application.desmond.stage.analysis.FepAnalysis'>, 'fep_binding_pose_primer': <class 'schrodinger.application.desmond.stage.app.binding_pose.FepBindingPosePrimer'>, 'fep_launcher': <class 'schrodinger.application.desmond.stage.launcher.FepLauncher'>, 'fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapper'>, 'fep_mapper_cleanup': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup'>, 'fep_mapper_report': <class 'schrodinger.application.desmond.stage.fep_mapper.FepMapperReport'>, 'fep_vrun': <class 'schrodinger.application.desmond.stage.simulate.FepVrun'>, 'ffbuilder': <class 'schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder'>, 'fragment_linking_primer': <class 'schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer'>, 'generate_solubility_fep_structures': <class 'schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures'>, 'generic': <class 'schrodinger.application.desmond.stage.simulate.GCMCCapable'>, 'hash_structure_title': <class 'schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle'>, 'lambda_hopping': <class 'schrodinger.application.desmond.stage.simulate.LambdaHopping'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure'>, 'matsci_analysis': <class 'schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis'>, 'minimize': <class 'schrodinger.application.desmond.stage.deprecate.Minimize'>, 'mixed_solvent_analysis': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis'>, 'mixed_solvent_cleanup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup'>, 'mixed_solvent_setup': <class 'schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup'>, 'multisim': <class 'schrodinger.application.desmond.stage.launcher.Multisim'>, 'pl_analysis': <class 'schrodinger.application.desmond.stage.analysis.PLAnalysis'>, 'primer': <class 'schrodinger.application.desmond.stage.workflow.Primer'>, 'protein_fep_mapper': <class 'schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper'>, 'protein_mutation_generator': <class 'schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator'>, 'replica_exchange': <class 'schrodinger.application.desmond.stage.simulate.ReplicaExchange'>, 'replicate_structure': <class 'schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure'>, 'simulate': <class 'schrodinger.application.desmond.stage.simulate.Simulate'>, 'solubility_fep_analysis': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis'>, 'solubility_fep_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher'>, 'solubility_md_launcher': <class 'schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher'>, 'solvate_pocket': <class 'schrodinger.application.desmond.stage.deprecate.SolvatePocket'>, 'stop': <class 'schrodinger.application.desmond.stage.workflow.Stop'>, 'system_builder': <class 'schrodinger.application.desmond.stage.utils.SystemBuilder'>, 'task': <class 'schrodinger.application.desmond.stage.workflow.Task'>, 'trim': <class 'schrodinger.application.desmond.stage.workflow.Trim'>, 'vacuum_report': <class 'schrodinger.application.desmond.stage.fep_mapper.VacuumReport'>, 'vrun': <class 'schrodinger.application.desmond.stage.simulate.Vrun'>, 'watermap_cluster': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapCluster'>, 'watermap_post_analysis': <class 'schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis'>}
stage_obj = {}
time_stage()