Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points. More...

#include <IdealizeMover.hh>

Public Types
typedef core::Real	Real

typedef core::pose::Pose	Pose

Public Types inherited from protocols::moves::Mover
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
	IdealizeMover ()

virtual moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

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

IdealizeMover &	atom_pair_constraint_weight (core::Real const setting)

IdealizeMover &	coordinate_constraint_weight (core::Real const setting)

IdealizeMover &	fast (bool const setting)

IdealizeMover &	chainbreaks (bool const setting)

IdealizeMover &	report_CA_rmsd (bool const setting)

void	apply (Pose &pose)

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

void	set_pos_list (utility::vector1< Size > pos_list)
	Sets the list of residue positions to idealize. More...

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

utility::vector1< core::Size >	ignore_residues_in_csts () const

void	ignore_residues_in_csts (utility::vector1< core::Size > const i)

void	impose_constraints (bool const i)

bool	impose_constraints () const

bool	constraints_only () const

void	constraints_only (bool const c)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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	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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Member Functions
void	setup_idealize_constraints (Pose &pose)
	Add the idealize constraints to the pose's constraint set. More...

Additional Inherited Members
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

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

Protected Member Functions inherited from protocols::moves::Mover
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...

Detailed Description

Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points.

Member Typedef Documentation

typedef core::pose::Pose protocols::idealize::IdealizeMover::Pose

typedef core::Real protocols::idealize::IdealizeMover::Real

Constructor & Destructor Documentation

protocols::idealize::IdealizeMover::IdealizeMover ( )

inline

References ignore_residues_in_csts_.

Referenced by clone(), and fresh_instance().

Member Function Documentation

void protocols::idealize::IdealizeMover::apply ( pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::all_atom_rmsd(), core::pose::Pose::append_residue_by_jump(), atom_pair_constraint, protocols::idealize::basic_idealize(), core::scoring::CA_rmsd(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), coordinate_constraint, core::conformation::ResidueFactory::create_residue(), basic::options::OptionKeys::run::dry_run, dslf_cs_ang, dslf_ss_dst, core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), midpoint(), core::chemical::ResidueTypeSet::name_map(), nres, option, pro_close, core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), scoring, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and protocols::idealize::TR.

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::abinitio::AbrelaxApplication::fold(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), and protocols::jobdist::universal_main().

IdealizeMover& protocols::idealize::IdealizeMover::atom_pair_constraint_weight ( core::Real const setting )

inline

References atom_pair_constraint_weight_.

IdealizeMover& protocols::idealize::IdealizeMover::chainbreaks ( bool const setting )

inline

References chainbreaks_.

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply().

virtual moves::MoverOP protocols::idealize::IdealizeMover::clone ( ) const

inlinevirtual

clone has to be overridden only if clone invocation is expected.

Reimplemented from protocols::moves::Mover.

References IdealizeMover().

bool protocols::idealize::IdealizeMover::constraints_only ( ) const

inline

References constraints_only_.

void protocols::idealize::IdealizeMover::constraints_only ( bool const c )

inline

References constraints_only_.

IdealizeMover& protocols::idealize::IdealizeMover::coordinate_constraint_weight ( core::Real const setting )

inline

References coordinate_constraint_weight_.

IdealizeMover& protocols::idealize::IdealizeMover::fast ( bool const setting )

inline

References fast_.

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::farna::create_rna_vall_torsions(), protocols::abinitio::AbrelaxApplication::fold(), protocols::antibody::GraftOneCDRLoop::init(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), and protocols::jobdist::universal_main().

virtual moves::MoverOP protocols::idealize::IdealizeMover::fresh_instance ( ) const

inlinevirtual

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.

Reimplemented from protocols::moves::Mover.

References IdealizeMover().

std::string protocols::idealize::IdealizeMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

utility::vector1< core::Size > protocols::idealize::IdealizeMover::ignore_residues_in_csts ( ) const

void protocols::idealize::IdealizeMover::ignore_residues_in_csts ( utility::vector1< core::Size > const i )

void protocols::idealize::IdealizeMover::impose_constraints ( bool const i )

inline

References impose_constraints_.

bool protocols::idealize::IdealizeMover::impose_constraints ( ) const

inline

References impose_constraints_.

void protocols::idealize::IdealizeMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::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.

Reimplemented from protocols::moves::Mover.

References chainbreaks, fast, core::pose::get_resnum_list(), and protocols::idealize::TR.

IdealizeMover& protocols::idealize::IdealizeMover::report_CA_rmsd ( bool const setting )

inline

References report_CA_rmsd_.

Referenced by protocols::match::downstream::LigandConformerBuilder::initialize_conformers().

void protocols::idealize::IdealizeMover::set_pos_list ( utility::vector1< Size > pos_list )

inline

Sets the list of residue positions to idealize.

References pos_list_.

void protocols::idealize::IdealizeMover::setup_idealize_constraints ( Pose & pose )

private

Add the idealize constraints to the pose's constraint set.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), begin, core::pose::Pose::conformation(), end, core::pose::symmetry::is_symmetric(), j, nres, core::pose::Pose::residue(), runtime_assert, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and protocols::idealize::TR.

Member Data Documentation

Real protocols::idealize::IdealizeMover::atom_pair_constraint_weight_

private

Referenced by atom_pair_constraint_weight().

bool protocols::idealize::IdealizeMover::chainbreaks_

private

Referenced by chainbreaks().

bool protocols::idealize::IdealizeMover::constraints_only_

private

Referenced by constraints_only().

Real protocols::idealize::IdealizeMover::coordinate_constraint_weight_

private

Referenced by coordinate_constraint_weight().

bool protocols::idealize::IdealizeMover::fast_

private

Referenced by fast().

utility::vector1< core::Size > protocols::idealize::IdealizeMover::ignore_residues_in_csts_

private

Referenced by IdealizeMover().

bool protocols::idealize::IdealizeMover::impose_constraints_

private

Referenced by impose_constraints().

utility::vector1< Size > protocols::idealize::IdealizeMover::pos_list_

private

Referenced by set_pos_list().

bool protocols::idealize::IdealizeMover::report_CA_rmsd_

private

Referenced by report_CA_rmsd().

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

symlinks/rosetta/src/protocols/idealize/IdealizeMover.hh
symlinks/rosetta/src/protocols/idealize/IdealizeMover.cc

Private Attributes
utility::vector1< Size >	pos_list_

Real	atom_pair_constraint_weight_

Real	coordinate_constraint_weight_

utility::vector1< core::Size >	ignore_residues_in_csts_

bool	fast_

bool	chainbreaks_

bool	report_CA_rmsd_

bool	impose_constraints_

bool	constraints_only_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation