UBQ_GTPase_disulfide_Mover Class Reference

Inheritance diagram for UBQ_GTPase_disulfide_Mover:

Public Member Functions
	UBQ_GTPase_disulfide_Mover ()
virtual void	init_on_new_input ()
	init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply(). More...
	~UBQ_GTPase_disulfide_Mover () override=default
void	apply (core::pose::Pose &pose) override
void	analyze_and_filter (core::pose::Pose &pose)
protocols::moves::MoverOP	fresh_instance () const override
bool	reinitialize_for_each_job () const override
bool	reinitialize_for_new_input () const override
std::string	get_name () const override

Private Attributes
bool	init_for_input_yet_ {false}
core::scoring::ScoreFunctionOP	fullatom_scorefunction_
core::pack::task::TaskFactoryOP	task_factory_
core::kinematics::MoveMapOP	disulfide_mm_
protocols::loops::Loop	loop_
utility::vector1< core::id::AtomID >	atomIDs
	vector contains atomIDs for disulfide bond and atoms before/after bond to determine various torsions More...
core::pose::Pose	starting_pose_
std::string const	InterfaceSasaDefinition_
protocols::analysis::InterfaceAnalyzerMoverOP	IAM_
core::Size	GTPase_cyd_
utility::vector1< core::Size >	extra_bodies_chains_
	used to track which chains are "extra" nonmoving bodies in extra bodies mode More...

Constructor & Destructor Documentation

UBQ_GTPase_disulfide_Mover()

UBQ_GTPase_disulfide_Mover::UBQ_GTPase_disulfide_Mover ( )

inline

References fullatom_scorefunction_, pyrosetta.distributed.io::get_score_function(), IAM_, InterfaceSasaDefinition_, basic::options::OptionKeys::frags::scoring::scoring, and TR.

~UBQ_GTPase_disulfide_Mover()

UBQ_GTPase_disulfide_Mover::~UBQ_GTPase_disulfide_Mover ( )

overridedefault

Member Function Documentation

analyze_and_filter()

void UBQ_GTPase_disulfide_Mover::analyze_and_filter ( core::pose::Pose &  pose )

inline

References atomIDs, erraser_util::copy(), apps::public1::scenarios::chemically_conjugated_docking::create_extra_output(), numeric::conversions::degrees(), basic::options::OptionKeys::chemically_conjugated_docking::extra_bodies, fullatom_scorefunction_, GTPase_cyd_, IAM_, InterfaceSasaDefinition_, basic::options::option, basic::options::OptionKeys::chemically_conjugated_docking::pdz, beta_nonlocal::pose, basic::options::OptionKeys::chemically_conjugated_docking::publication, basic::options::OptionKeys::chemically_conjugated_docking::SASAfilter, create_a3b_hbs::score, basic::options::OptionKeys::chemically_conjugated_docking::scorefilter, TR, basic::options::OptionKeys::inout::dbms::user, basic::MetricValue< T >::value(), and value.

Referenced by apply().

apply()

void UBQ_GTPase_disulfide_Mover::apply ( core::pose::Pose &  pose )

inlineoverride

References analyze_and_filter(), atomIDs, basic::options::OptionKeys::coupled_moves::backbone_mover, disulfide_mm_, fullatom_scorefunction_, GTPase_cyd_, create_a3b_hbs::i, init_for_input_yet_, init_on_new_input(), loop_, mc, vancomycin::min_mover, basic::options::OptionKeys::run::min_type, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::option, option, test.Workshop6test::pack_mover, beta_nonlocal::pose, basic::options::OptionKeys::AnchoredDesign::refine_cycles, basic::options::OptionKeys::AnchoredDesign::refine_repack_cycles, basic::options::OptionKeys::AnchoredDesign::refine_temp, basic::options::OptionKeys::repack_cycles, test.Workshop5test::shear_mover, test.Workshop5test::small_mover, starting_pose_, task_factory_, TR, and value.

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), and pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

fresh_instance()

protocols::moves::MoverOP UBQ_GTPase_disulfide_Mover::fresh_instance ( ) const

inlineoverride

get_name()

std::string UBQ_GTPase_disulfide_Mover::get_name ( ) const

inlineoverride

init_on_new_input()

virtual void UBQ_GTPase_disulfide_Mover::init_on_new_input ( )

inlinevirtual

init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply().

References apps::public1::scenarios::chemically_conjugated_docking::add_extra_bodies(), atomIDs, disulfide_mm_, basic::options::OptionKeys::score::empty, end, basic::Tracer::Error, basic::options::OptionKeys::chemically_conjugated_docking::extra_bodies, extra_bodies_chains_, create_a3b_hbs::first, GTPase_cyd_, basic::options::OptionKeys::chemically_conjugated_docking::GTPase_residue, basic::options::OptionKeys::chemically_conjugated_docking::GTPasepdb, create_a3b_hbs::i, init_for_input_yet_, create_a3b_hbs::j, loop_, basic::options::OptionKeys::loops::loop_file, basic::options::OptionKeys::chemically_conjugated_docking::n_tail_res, basic::options::option, apps::public1::scenarios::chemically_conjugated_docking::pack_extra_bodies(), pyrosetta.distributed.io::pose_from_file(), numeric::conversions::radians(), test.G101_Functions_Output::regions, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::in::file::residue_type_set, runtime_assert, starting_pose_, vancomycin::task, task_factory_, TR, basic::options::OptionKeys::chemically_conjugated_docking::UBQpdb, basic::options::OptionKeys::inout::dbms::user, and value.

Referenced by apply().

reinitialize_for_each_job()

bool UBQ_GTPase_disulfide_Mover::reinitialize_for_each_job ( ) const

inlineoverride

reinitialize_for_new_input()

bool UBQ_GTPase_disulfide_Mover::reinitialize_for_new_input ( ) const

inlineoverride

Member Data Documentation

atomIDs

utility::vector1< core::id::AtomID > UBQ_GTPase_disulfide_Mover::atomIDs

private

vector contains atomIDs for disulfide bond and atoms before/after bond to determine various torsions

Referenced by analyze_and_filter(), apply(), and init_on_new_input().

disulfide_mm_

core::kinematics::MoveMapOP UBQ_GTPase_disulfide_Mover::disulfide_mm_

private

Referenced by apply(), and init_on_new_input().

extra_bodies_chains_

utility::vector1< core::Size > UBQ_GTPase_disulfide_Mover::extra_bodies_chains_

private

used to track which chains are "extra" nonmoving bodies in extra bodies mode

Referenced by init_on_new_input().

fullatom_scorefunction_

core::scoring::ScoreFunctionOP UBQ_GTPase_disulfide_Mover::fullatom_scorefunction_

private

Referenced by analyze_and_filter(), apply(), and UBQ_GTPase_disulfide_Mover().

GTPase_cyd_

core::Size UBQ_GTPase_disulfide_Mover::GTPase_cyd_

private

Referenced by analyze_and_filter(), apply(), and init_on_new_input().

IAM_

protocols::analysis::InterfaceAnalyzerMoverOP UBQ_GTPase_disulfide_Mover::IAM_

private

Referenced by analyze_and_filter(), and UBQ_GTPase_disulfide_Mover().

init_for_input_yet_

bool UBQ_GTPase_disulfide_Mover::init_for_input_yet_ {false}

private

Referenced by apply(), and init_on_new_input().

InterfaceSasaDefinition_

std::string const UBQ_GTPase_disulfide_Mover::InterfaceSasaDefinition_

private

Referenced by analyze_and_filter(), and UBQ_GTPase_disulfide_Mover().

loop_

protocols::loops::Loop UBQ_GTPase_disulfide_Mover::loop_

private

Referenced by apply(), and init_on_new_input().

starting_pose_

core::pose::Pose UBQ_GTPase_disulfide_Mover::starting_pose_

private

Referenced by apply(), and init_on_new_input().

task_factory_

core::pack::task::TaskFactoryOP UBQ_GTPase_disulfide_Mover::task_factory_

private

Referenced by apply(), and init_on_new_input().

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The documentation for this class was generated from the following file:

• src/apps/public/scenarios/chemically_conjugated_docking/UBQ_Gp_CYD-CYD.cc