schrodinger.application.desmond.absolute_binding.stage module

class schrodinger.application.desmond.absolute_binding.stage.FepAbsoluteBindingPrimer(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_absolute_binding_primer'

TAG = 'FEP_ABSOLUTE_BINDING_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 = {'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_primer': <class 'schrodinger.application.desmond.absolute_binding.stage.FepAbsoluteBindingPrimer'>, 'generic': <class 'schrodinger.application.desmond.cmj.StageBase'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>}

stage_obj = {}

time_stage()

class schrodinger.application.desmond.absolute_binding.stage.FepAbsoluteBindingAnalysis(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_absolute_binding_analysis'

TAG = 'FEP_ABSOLUTE_BINDING_ANALYSIS'

previous_compound_ids = {}

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 = {'fep_absolute_binding_analysis': <class 'schrodinger.application.desmond.absolute_binding.stage.FepAbsoluteBindingAnalysis'>, 'fep_absolute_binding_primer': <class 'schrodinger.application.desmond.absolute_binding.stage.FepAbsoluteBindingPrimer'>, 'generic': <class 'schrodinger.application.desmond.cmj.StageBase'>, 'load_restraints_from_structure': <class 'schrodinger.application.desmond.restraint.restraint_stage.LoadRestraintsFromStructure'>}

stage_obj = {}

time_stage()