#include <Mover.hh>

Inherits ReferenceCount, and enable_shared_from_this< Mover >.

Public Types
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	apply (Pose &)=0
	Main Method. More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

virtual std::string	get_name () const =0
	Each derived class must specify its name. The class name. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Private Attributes
std::string	type_

std::string	current_tag_

PoseCOP	input_pose_

PoseCOP	native_pose_

MoverStatus	last_status_
	used to track if movers fail their filters - jobdist::BasicJob Distributor queries for this value More...

Strings	info_
	miscellaneous info: optional notes about mover results. Fed to Job by JobDistributor (jd2), allowing JobOutputters to optionally report this information in some way. More...

jobdist::BasicJobCOP	current_job_
	this field can be NULL or it refers to the current JOB this mover is working on. More...

Member Typedef Documentation

typedef protocols::filters::Filters_map protocols::moves::Mover::Filters_map

typedef core::pose::Pose protocols::moves::Mover::Pose

typedef core::pose::PoseCOP protocols::moves::Mover::PoseCOP

typedef std::list< std::string > protocols::moves::Mover::Strings

typedef utility::tag::TagCOP protocols::moves::Mover::TagCOP

Constructor & Destructor Documentation

protocols::moves::Mover::Mover ( )

protocols::moves::Mover::Mover ( std::string const & type_name )

sets the type for a mover; name_ has been removed (2010/05/14)

Member Function Documentation

virtual void protocols::moves::Mover::apply ( Pose & )

pure virtual

Main Method.

Referenced by protocols::comparative_modeling::RecoverSideChainsMover::apply(), protocols::jobdist::main_atom_tree_diff_mover(), protocols::jobdist::main_plain_mover(), protocols::jobdist::main_plain_pdb_mover(), protocols::jobdist::not_universal_main(), test_move(), and protocols::jobdist::universal_main().

virtual void protocols::moves::Mover::clear_info ( )

inlinevirtual

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

References info_.

MoverOP protocols::moves::Mover::clone ( ) const

virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Referenced by protocols::denovo_design::movers::BuildDeNovoBackboneMover::add_postfold_mover(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::add_prefold_mover(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::enzdes::ApplyRandomStoredRBConf::apply(), protocols::jd2::VectorPoseJobDistributor::apply_parsed_protocol_mpi(), protocols::jd2::VectorPoseJobDistributor::apply_parsed_protocol_serial(), protocols::enzdes::BackboneSampler::BackboneSampler(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), protocols::relax::RelaxProtocolBase::fresh_instance(), protocols::recces::sampler::rna::MC_RNA_OneJump::MC_RNA_OneJump(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), and protocols::symmetry::SymmetrySlider::very_far_away().

MoverOP protocols::moves::Mover::create ( )

virtual

References fresh_instance().

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

virtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Referenced by create().

core::pose::PoseOP protocols::moves::Mover::get_additional_output ( )

virtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented in protocols::hbnet::HBNet, protocols::antibody::design::AntibodyDesignMover, protocols::motif_grafting::movers::MotifGraftMover, protocols::ligand_docking::ga_ligand_dock::GALigandDock, protocols::pose_length_moves::NearNativeLoopCloser, protocols::switches::GraftSwitchMover, protocols::pose_creation::SliceToMiniProteinMover, protocols::rna::denovo::RNA_FragmentMonteCarlo, protocols::indexed_structure_store::movers::DirectSegmentLookupMover, protocols::pose_creation::MergePDBMover, protocols::pose_creation::MakeJunctionsMover, protocols::rosetta_scripts::ParsedProtocol, protocols::rosetta_scripts::MultiplePoseMover, protocols::rosetta_scripts::AdditionalOutputWrapper, protocols::rosetta_scripts::MultipleOutputWrapper, protocols::moves::IfMover, protocols::pose_length_moves::InsertResMover, and protocols::loophash::LoopHashMoverWrapper.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply().

jobdist::BasicJobCOP protocols::moves::Mover::get_current_job ( ) const

References current_job_.

Referenced by protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::Protocol::output_debug_structure(), and protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::output_debug_structure().

std::string protocols::moves::Mover::get_current_tag ( ) const

inline

A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

References current_tag_.

PoseCOP protocols::moves::Mover::get_input_pose ( ) const

References input_pose_.

Referenced by protocols::docking::stateless::SaneDockingProtocol::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::AntibodyModelerProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), and protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol().

MoverStatus protocols::moves::Mover::get_last_move_status ( ) const

end parser interface, start Job Distributor interface/////////////

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.

start Job Distributor interface//////////////////////////////////

used by job distributor to get status

References last_status_.

virtual std::string protocols::moves::Mover::get_name ( ) const

pure virtual

Each derived class must specify its name. The class name.

Referenced by protocols::forge::remodel::RemodelConstraintGenerator::clear_stored_constraints(), protocols::environment::ClientMover::initialize(), protocols::moves::operator<<(), protocols::forge::remodel::RemodelConstraintGenerator::parse_my_tag(), protocols::environment::ClientMover::passport(), protocols::environment::ClientMover::pop_passport(), protocols::environment::ClientMover::push_passport(), protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose(), protocols::environment::ClientMover::sandboxed_copy(), show(), and protocols::environment::ClientMover::state_check().

PoseCOP protocols::moves::Mover::get_native_pose ( ) const

References native_pose_.

MoverCOP protocols::moves::Mover::get_self_ptr ( ) const

inline

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::add_flexible_region(), protocols::forge::components::VarLengthBuild::add_rcg(), protocols::rosetta_scripts::ParsedProtocol::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::abinitio::abscript::FragmentJumpCM::build_claims(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::enzdes::SecondaryMatchProtocol::generate_and_dump_pose_found_residues_combinations(), protocols::canonical_sampling::BiasEnergy::initialize_simulation(), protocols::environment::ScriptCM::parse_my_tag(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perturber(), protocols::canonical_sampling::MetropolisHastingsMover::prepare_simulation(), protocols::environment::ClientMover::push_passport(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_perturber(), protocols::abinitio::abscript::StructPerturberCM::yield_claims(), protocols::abinitio::abscript::RigidChunkCM::yield_claims(), protocols::loops::loop_mover::LoopCM::yield_claims(), protocols::abinitio::abscript::AbscriptLoopCloserCM::yield_claims(), protocols::rigid::UniformRigidBodyCM::yield_claims(), and protocols::canonical_sampling::BiasEnergy::~BiasEnergy().

MoverOP protocols::moves::Mover::get_self_ptr ( )

inline

MoverCAP protocols::moves::Mover::get_self_weak_ptr ( ) const

inline

MoverAP protocols::moves::Mover::get_self_weak_ptr ( )

inline

std::string protocols::moves::Mover::get_type ( ) const

inline

References type_.

Referenced by protocols::monte_carlo::ResetBaselineMover::apply(), protocols::moves::operator<<(), protocols::monte_carlo::ResetBaselineMover::parse_my_tag(), and show().

virtual Strings& protocols::moves::Mover::info ( )

inlinevirtual

non-const accessor

References info_.

Referenced by protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::pose_creation::ExtendedPoseMover::apply(), protocols::protein_interface_design::movers::LoopOver::apply(), protocols::environment::EnvMover::apply(), protocols::dna::DnaInterfacePacker::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::rosetta_scripts::ParsedProtocol::apply_filter(), protocols::analysis::GlycanInfoMover::get_attachment_point_string(), protocols::moves::PyMOLMover::get_PyMOL_model_name(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::dna::DnaInterfacePacker::measure_bp_specificities(), protocols::minimization_packing::PackRotamersMover::note_packertask_settings(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_results(), protocols::dna::DnaInterfaceMultiStateDesign::output_results(), protocols::dna::DnaInterfacePacker::post_packing(), protocols::moves::PyMOLMover::send_any(), protocols::moves::PyMOLMover::send_energy(), protocols::moves::PyMOLMover::send_hbonds(), protocols::moves::PyMOLMover::send_RAW_Energies(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_geomcst_for_superposition_from_enz_io(), protocols::dna::DesignProteinBackboneAroundDNA::set_loop_info(), and protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs().

virtual Strings const& protocols::moves::Mover::info ( ) const

inlinevirtual

const accessor

References info_.

virtual core::Real protocols::moves::Mover::last_proposal_density_ratio ( )

inlinevirtual

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMover, protocols::moves::RandomMover, protocols::simple_moves::sidechain_moves::SidechainMoverBase, protocols::simple_moves::sidechain_moves::SidechainMCMover, protocols::simple_moves::BBGaussianMover, protocols::kinematic_closure::BalancedKicMover, and protocols::canonical_sampling::ThermodynamicMover.

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis().

bool protocols::moves::Mover::mover_is_unpublished ( ) const

virtual

Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?

Defaults to false. Derived classes may override this to provide authorship info. If set to true, the provide_authorship_info_for_unpublished() override should also be provided.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented in protocols::generalized_kinematic_closure::GeneralizedKIC, protocols::helical_bundle::BackboneGridSampler, protocols::helical_bundle::MakeBundle, protocols::cyclic_peptide::SymmetricCycpepAlign, protocols::simple_moves::SetupMetalsMover, protocols::rosetta_scripts::ParsedProtocol, protocols::helical_bundle::PerturbBundle, protocols::relax::RelaxProtocolBase, and protocols::cyclic_peptide::TryDisulfPermutations.

bool protocols::moves::Mover::mover_provides_citation_info ( ) const

virtual

Does this mover provide information about how to cite it?

Defaults to false. Derived classes may override this to provide citation info. If set to true, the provide_citation_info() override should also be provided.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented in protocols::loop_grower::LoopGrower, protocols::generalized_kinematic_closure::GeneralizedKIC, protocols::antibody::design::AntibodyDesignMover, protocols::monte_carlo::GenericMonteCarloMover, protocols::helical_bundle::BundleGridSampler, protocols::features::ReportToDB, protocols::relax::FastRelax, protocols::grafting::AnchoredGraftMover, protocols::antibody::AntibodyCDRGrafter, protocols::calc_taskop_movers::CreateSequenceMotifMover, protocols::carbohydrates::LinkageConformerMover, protocols::simple_moves::SetupMetalsMover, protocols::antibody::design::MutateFrameworkForCluster, protocols::antibody::constraints::CDRDihedralConstraintMover, protocols::rosetta_scripts::ParsedProtocol, protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover, protocols::ligand_docking::Transform, protocols::ligand_docking::ProtLigEnsemble, protocols::denovo_design::movers::FastDesign, protocols::simple_moves::SimpleThreadingMover, protocols::loop_grower::SheetSampler, protocols::antibody::constraints::ParatopeSiteConstraintMover, protocols::analysis::simple_metrics::RunSimpleMetricsMover, protocols::relax::RelaxProtocolBase, protocols::analysis::GlycanInfoMover, protocols::antibody::AntibodyNumberingConverterMover, protocols::simple_moves::BBDihedralSamplerMover, protocols::carbohydrates::GlycanTreeModeler, protocols::ligand_docking::HighResEnsemble, protocols::grafting::CCDEndsGraftMover, protocols::simple_moves::DeleteChainsMover, protocols::ligand_docking::TransformEnsemble, protocols::simple_moves::ConvertRealToVirtualMover, protocols::simple_moves::ConvertVirtualToRealMover, protocols::grafting::simple_movers::KeepRegionMover, protocols::ligand_docking::StartFrom, protocols::carbohydrates::RingPlaneFlipMover, protocols::carbohydrates::TautomerizeAnomerMover, protocols::ligand_docking::HighResDocker, protocols::loop_grower::FragmentExtension, protocols::carbohydrates::CreateGlycanSequonMover, protocols::simple_moves::RingConformationMover, protocols::grafting::simple_movers::DeleteRegionMover, protocols::carbohydrates::SimpleGlycosylateMover, protocols::grafting::simple_movers::InsertPoseIntoPoseMover, protocols::ligand_docking::InterfaceScoreCalculator, protocols::enzymatic_movers::EnzymaticMover, protocols::carbohydrates::GlycanTreeMinMover, protocols::carbohydrates::GlycanSampler, protocols::ligand_docking::FinalMinimizer, protocols::enzymatic_movers::GlycosyltransferaseMover, protocols::enzymatic_movers::KinaseMover, protocols::protein_interface_design::movers::LoopOver, protocols::grafting::simple_movers::ReplaceRegionMover, and protocols::carbohydrates::IdealizeAnomericHydrogens.

static std::string protocols::moves::Mover::name ( )

inlinestatic

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), protocols::RBSegmentRelaxImpl::apply(), protocols::loop_build::LoopBuildMover::apply(), protocols::simple_moves::DumpPdb::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::moves::StructureRestrictor::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::moves::PyMOLMover::apply(), protocols::simple_ddg::ddG::calculate(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fragments_id(), protocols::fold_from_loops::NubInitioMover::fragments_id(), protocols::ligand_docking::LigandDesign::fragments_to_string(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::stepwise::sampler::StepWiseSamplerOneValue::get_name(), protocols::moves::RandomMover::get_name_individual_mover(), protocols::relax::FastRelax::get_possible_relax_script_names(), protocols::ncbb::SecStructFinder::initialize_pose(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::label_insertion(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::pose_creation::MakeJunctionsMover::line_to_design(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::output_lookup_count(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::output_lookup_length(), protocols::ligand_docking::CompoundTranslate::parse_my_tag(), protocols::cyclic_peptide::PeptideCyclizeMover::parse_my_tag(), protocols::ligand_docking::StartFrom::parse_my_tag(), protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::cyclic_peptide::FlipChiralityMover::parse_my_tag(), protocols::rosetta_scripts::MultipleOutputWrapper::parse_my_tag(), protocols::ligand_docking::InterfaceScoreCalculator::parse_my_tag(), protocols::rosetta_scripts::AdditionalOutputWrapper::parse_my_tag(), protocols::canonical_sampling::MetricRecorder::parse_my_tag(), protocols::abinitio::abscript::AbscriptMover::parse_my_tag(), protocols::ligand_docking::StartFrom::parse_pdb_file(), protocols::enzymatic_movers::DNAMethyltransferaseMover::perform_reaction(), protocols::moves::StructureRestrictor::pose_name(), protocols::recces::RECCES_Mover::prepare_output_torsion_ids(), protocols::simple_moves::RingConformationMover::provide_xml_schema(), protocols::carbohydrates::RingPlaneFlipMover::provide_xml_schema(), protocols::carbohydrates::TautomerizeAnomerMover::provide_xml_schema(), protocols::nonlocal::SingleFragmentMover::provide_xml_schema(), protocols::normalmode::NormalModeRelaxMover::provide_xml_schema(), protocols::moves::PyMOLMover::send_any(), protocols::moves::PyMOLMover::send_energy(), protocols::moves::PyMOLMover::send_hbonds(), protocols::moves::PyMOLMover::send_membrane_planes(), protocols::moves::PyMOLMover::send_RAW_Energies(), protocols::simple_moves::bin_transitions::InitializeByBins::set_binfile_and_load(), protocols::simple_moves::bin_transitions::PerturbByBins::set_binfile_and_load(), protocols::dna::DnaInterfacePacker::set_filename_root(), protocols::simple_moves::StructProfileMover::set_profile_save_name(), protocols::moves::PyMOLMover::set_PyMOL_model_name(), protocols::residue_selectors::StoreResidueSubsetMover::set_subset(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::cutoutdomain::CutOutDomain::source_pdb_name(), and protocols::indexed_structure_store::movers::DirectSegmentLookupMover::stored_subset_name().

void protocols::moves::Mover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	filters,
		Movers_map const &	movers,
		Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

References protocols::moves::TR().

Referenced by protocols::canonical_sampling::SimulatedTempering::parse_my_tag().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::moves::Mover::provide_authorship_info_for_unpublished ( ) const

virtual

Provide a list of authors and their e-mail addresses, as strings.

Returns: A list of pairs of (author, e-mail address). Empty list if not unpublished.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Referenced by protocols::grafting::AnchoredGraftMover::provide_authorship_info_for_unpublished().

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::moves::Mover::provide_citation_info ( ) const

virtual

Provide the citation.

Returns: A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

The default implementation of this function provides an empty vector. It may be overriden by Movers wishing to provide citation information.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented in protocols::loop_grower::LoopGrower, protocols::generalized_kinematic_closure::GeneralizedKIC, protocols::antibody::design::AntibodyDesignMover, protocols::monte_carlo::GenericMonteCarloMover, protocols::helical_bundle::BackboneGridSampler, protocols::helical_bundle::BundleGridSampler, protocols::features::ReportToDB, protocols::relax::FastRelax, protocols::grafting::AnchoredGraftMover, protocols::antibody::AntibodyCDRGrafter, protocols::calc_taskop_movers::CreateSequenceMotifMover, protocols::carbohydrates::LinkageConformerMover, protocols::simple_moves::SetupMetalsMover, protocols::antibody::design::MutateFrameworkForCluster, protocols::rosetta_scripts::ParsedProtocol, protocols::antibody::constraints::CDRDihedralConstraintMover, protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover, protocols::ligand_docking::Transform, protocols::ligand_docking::ProtLigEnsemble, protocols::denovo_design::movers::FastDesign, protocols::relax::RelaxProtocolBase, protocols::antibody::constraints::ParatopeSiteConstraintMover, protocols::simple_moves::BBDihedralSamplerMover, protocols::loop_grower::SheetSampler, protocols::antibody::AntibodyNumberingConverterMover, protocols::ligand_docking::HighResEnsemble, protocols::grafting::CCDEndsGraftMover, protocols::simple_moves::ConvertRealToVirtualMover, protocols::ligand_docking::TransformEnsemble, protocols::simple_moves::ConvertVirtualToRealMover, protocols::simple_moves::DeleteChainsMover, protocols::grafting::simple_movers::KeepRegionMover, protocols::ligand_docking::StartFrom, protocols::ligand_docking::HighResDocker, protocols::loop_grower::FragmentExtension, protocols::grafting::simple_movers::DeleteRegionMover, protocols::simple_moves::RingConformationMover, protocols::grafting::simple_movers::InsertPoseIntoPoseMover, protocols::moves::MoverContainer, protocols::ligand_docking::InterfaceScoreCalculator, protocols::ligand_docking::FinalMinimizer, protocols::protein_interface_design::movers::LoopOver, protocols::grafting::simple_movers::ReplaceRegionMover, and protocols::carbohydrates::IdealizeAnomericHydrogens.

Referenced by protocols::grafting::CCDEndsGraftMover::provide_citation_info(), and protocols::grafting::AnchoredGraftMover::provide_citation_info().

static void protocols::moves::Mover::register_options ( )

inlinestatic

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

bool protocols::moves::Mover::reinitialize_for_each_job ( ) const

virtual

Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented in protocols::analysis::InterfaceAnalyzerMover, protocols::carbohydrates::GlycanSampler, protocols::carbohydrates::LinkageConformerMover, protocols::ligand_docking::LigandDockMain, protocols::canonical_sampling::MetropolisHastingsMover, protocols::canonical_sampling::TemperatureController, protocols::ligand_docking::ProtLigEnsemble, protocols::canonical_sampling::MetricRecorder, protocols::rotamer_recovery::RotamerRecoveryMover, protocols::ligand_docking::HighResEnsemble, protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover, protocols::analysis::GlycanInfoMover, protocols::floppy_tail::FloppyTailMover, protocols::splice::TailSegmentMover, and protocols::anchored_design::AnchoredDesignMover.

bool protocols::moves::Mover::reinitialize_for_new_input ( ) const

virtual

Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

Movers default to not regenerating

Reimplemented in protocols::analysis::InterfaceAnalyzerMover, protocols::carbohydrates::LinkageConformerMover, protocols::ligand_docking::LigandDockMain, protocols::docking::DockingProtocol, protocols::canonical_sampling::MetropolisHastingsMover, protocols::canonical_sampling::TemperatureController, protocols::rotamer_recovery::RotamerRecoveryMover, protocols::legacy_sewing::LegacyAssemblyMover, protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover, protocols::hotspot_hashing::movers::PlaceSurfaceProbe, protocols::antibody::snugdock::SnugDock, protocols::floppy_tail::FloppyTailMover, protocols::antibody::snugdock::SnugDockProtocol, protocols::loops::loop_mover::refine::LoopRefineInnerCycle, protocols::loops::loop_mover::refine::ShearMinCCDTrial, protocols::loops::loop_mover::refine::SmallMinCCDTrial, protocols::loops::loop_mover::refine::RepackTrial, protocols::splice::TailSegmentMover, protocols::hotspot_hashing::movers::PlaceProbeMover, protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer, protocols::analysis::LoopAnalyzerMover, and protocols::anchored_design::AnchoredDesignMover.

void protocols::moves::Mover::reset_status ( )

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

References last_status_, and protocols::moves::MS_SUCCESS.

Referenced by protocols::carbohydrates::LinkageConformerMover::apply(), protocols::abinitio::Protocol::apply(), and protocols::denovo_design::movers::FastDesign::apply().

void protocols::moves::Mover::set_current_job ( protocols::jobdist::BasicJobCOP job )

References current_job_.

Referenced by protocols::abinitio::AbrelaxApplication::fold().

virtual void protocols::moves::Mover::set_current_tag ( std::string const & new_tag )

inlinevirtual

Reimplemented in protocols::moves::MoverContainer.

References current_tag_.

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::docking::SlideIntoContact::apply(), protocols::abinitio::abscript::AbscriptLoopCloserCM::attempt_ccd(), protocols::abinitio::AbrelaxApplication::fold(), protocols::abinitio::AbrelaxApplication::relax(), protocols::moves::MoverContainer::set_current_tag(), and protocols::jobdist::universal_main().

void protocols::moves::Mover::set_input_pose ( PoseCOP pose )

virtual

setter for poses contained for rms

Reimplemented in protocols::moves::TrialMover, protocols::simple_moves::CoupledMover, protocols::simple_moves::ShortBackrubMover, and protocols::moves::MoverContainer.

References input_pose_.

Referenced by protocols::docking::stateless::SaneDockingProtocol::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::antibody::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody::AntibodyModelerProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), protocols::jobdist::main_plain_mover(), protocols::moves::MoverContainer::set_input_pose(), and protocols::moves::TrialMover::set_input_pose().

void protocols::moves::Mover::set_last_move_status ( MoverStatus status )

protected

nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says.

use this function for implementing filtering in your protocol - failed jobs should set the status to something other than "SUCCESS".

References last_status_.

void protocols::moves::Mover::set_native_pose ( PoseCOP pose )

virtual

setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe

Reimplemented in protocols::moves::TrialMover, protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer, protocols::moves::MoverContainer, and protocols::stepwise::monte_carlo::StepWiseMonteCarlo.

References native_pose_.

void protocols::moves::Mover::set_type ( std::string const & setting )

inline

Set the 'type' string.

References type_.

void protocols::moves::Mover::show ( std::ostream & output = std::cout ) const

virtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

References get_current_tag(), get_name(), and get_type().

virtual void protocols::moves::Mover::test_move ( Pose & pose )

inlinevirtual

: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMover, protocols::simple_moves::BackboneMover, protocols::simple_moves::ScoreMover, protocols::contact_map::ContactMap, and protocols::moves::NullMover.

References apply().

void protocols::moves::Mover::type ( const std::string & type_in )

inline

Set the 'type' string.

References type_.

Referenced by protocols::enzdes::BackboneSampler::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::topology_broker::DisulfJumpClaimer::new_decoy(), and protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis().

std::string const& protocols::moves::Mover::type ( ) const

inline

Get the set 'type' string.

References type_.

Member Data Documentation

jobdist::BasicJobCOP protocols::moves::Mover::current_job_

private

this field can be NULL or it refers to the current JOB this mover is working on.

Referenced by get_current_job(), and set_current_job().

std::string protocols::moves::Mover::current_tag_

private

Referenced by get_current_tag(), and set_current_tag().

Strings protocols::moves::Mover::info_

private

miscellaneous info: optional notes about mover results. Fed to Job by JobDistributor (jd2), allowing JobOutputters to optionally report this information in some way.

Referenced by clear_info(), and info().

PoseCOP protocols::moves::Mover::input_pose_

private

Referenced by get_input_pose(), and set_input_pose().

MoverStatus protocols::moves::Mover::last_status_

private

used to track if movers fail their filters - jobdist::BasicJob Distributor queries for this value

Referenced by get_last_move_status(), reset_status(), and set_last_move_status().

PoseCOP protocols::moves::Mover::native_pose_

private

Referenced by get_native_pose(), and set_native_pose().

std::string protocols::moves::Mover::type_