#include <AtomCoordinateCstMover.hh>

Inheritance diagram for protocols::relax::AtomCoordinateCstMover:

[legend]

Public Types
typedef moves::Mover	parent

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

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

Public Member Functions
	AtomCoordinateCstMover ()

	AtomCoordinateCstMover (AtomCoordinateCstMover const &)

	~AtomCoordinateCstMover () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

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

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

virtual void	set_refstruct (core::pose::PoseCOP ref)

void	cst_sd (core::Real sd)

core::Real	cst_sd () const

void	bounded (bool bound)

bool	bounded () const

void	cst_width (core::Real width)

core::Real	cst_width () const

void	cst_sidechain (bool sidechains)

bool	cst_sidechain () const

void	ambiguous_hnq (bool flip_hnq)

bool	ambiguous_hnq () const

void	func_groups (bool b)

bool	func_groups () const

void	set_loop_segments (protocols::loops::LoopsCOP loops)

void	set_task_segments (core::pack::task::TaskFactoryCOP taskfactory)

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

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

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

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

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Member Functions
core::select::residue_selector::ResidueSubset	compute_residue_subset (core::pose::Pose const &pose) const

core::pose::PoseOP	get_constraint_target_pose (core::pose::Pose const &pose) const

core::id::SequenceMapping	generate_seqmap (core::pose::Pose const &pose, core::pose::Pose const &constraint_target_pose) const

core::scoring::constraints::ConstraintCOPs	generate_constraints (core::pose::Pose const &pose)

core::scoring::constraints::ConstraintCOPs	set_constraints_on_func_groups (core::pose::Pose const &pose)

Private Attributes
core::pose::PoseCOP	refpose_
	If set, the pose to make the constraints to. More...

core::Real	cst_sd_
	The strenght (standard deviation) of the constraints. More...

bool	bounded_
	Use bounded constraints instead of harmonic. More...

core::Real	cst_width_
	The width for bounded constraints. More...

bool	cst_sidechain_
	Also constrain sidechains? More...

bool	amb_hnq_
	When making sidechain constraints, should we allow for flipping HNQ residue sidechains? More...

protocols::loops::LoopsCOP	loop_segments_
	A loop definition of constrained segments. More...

core::pack::task::TaskFactoryCOP	task_segments_
	A task definition of constrained segments. More...

bool	func_groups_
	If set to true then coordinate constraints are applied only to the functional groups of the side_chain. More...

Additional Inherited Members
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...

Member Typedef Documentation

◆ parent

typedef moves::Mover protocols::relax::AtomCoordinateCstMover::parent

Constructor & Destructor Documentation

◆ AtomCoordinateCstMover() [1/2]

protocols::relax::AtomCoordinateCstMover::AtomCoordinateCstMover ( )

◆ AtomCoordinateCstMover() [2/2]

protocols::relax::AtomCoordinateCstMover::AtomCoordinateCstMover ( AtomCoordinateCstMover const & )

default

◆ ~AtomCoordinateCstMover()

protocols::relax::AtomCoordinateCstMover::~AtomCoordinateCstMover ( )

overridedefault

Member Function Documentation

◆ ambiguous_hnq() [1/2]

bool protocols::relax::AtomCoordinateCstMover::ambiguous_hnq ( ) const

inline

References amb_hnq_.

Referenced by parse_my_tag().

◆ ambiguous_hnq() [2/2]

void protocols::relax::AtomCoordinateCstMover::ambiguous_hnq ( bool flip_hnq )

inline

References amb_hnq_.

Referenced by protocols::relax::RelaxProtocolBase::set_up_constraints().

◆ apply()

void protocols::relax::AtomCoordinateCstMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::add_constraints(), and generate_constraints().

Referenced by protocols::indel::IndelOptimizationMover::apply(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::relax::RelaxProtocolBase::set_up_constraints(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

◆ bounded() [1/2]

bool protocols::relax::AtomCoordinateCstMover::bounded ( ) const

inline

References bounded_.

Referenced by parse_my_tag().

◆ bounded() [2/2]

void protocols::relax::AtomCoordinateCstMover::bounded ( bool bound )

inline

References bounded_.

Referenced by protocols::relax::RelaxProtocolBase::set_up_constraints().

◆ clone()

protocols::moves::MoverOP protocols::relax::AtomCoordinateCstMover::clone ( ) const

overridevirtual

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.

Reimplemented from protocols::moves::Mover.

Referenced by protocols::mpi_refinement::StructAvrgMover::weighted_average().

◆ compute_residue_subset()

core::select::residue_selector::ResidueSubset protocols::relax::AtomCoordinateCstMover::compute_residue_subset ( core::pose::Pose const & pose ) const

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, loop_segments_, core::pose::Pose::residue(), core::pose::Pose::size(), and task_segments_.

Referenced by generate_constraints(), and set_constraints_on_func_groups().

◆ cst_sd() [1/2]

core::Real protocols::relax::AtomCoordinateCstMover::cst_sd ( ) const

inline

References cst_sd_.

Referenced by parse_my_tag().

◆ cst_sd() [2/2]

void protocols::relax::AtomCoordinateCstMover::cst_sd ( core::Real sd )

inline

References cst_sd_.

Referenced by protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::relax::RelaxProtocolBase::set_up_constraints(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

◆ cst_sidechain() [1/2]

bool protocols::relax::AtomCoordinateCstMover::cst_sidechain ( ) const

inline

References cst_sidechain_.

Referenced by parse_my_tag().

◆ cst_sidechain() [2/2]

void protocols::relax::AtomCoordinateCstMover::cst_sidechain ( bool sidechains )

inline

References cst_sidechain_.

Referenced by protocols::relax::RelaxProtocolBase::set_up_constraints().

◆ cst_width() [1/2]

core::Real protocols::relax::AtomCoordinateCstMover::cst_width ( ) const

inline

References cst_width_.

Referenced by parse_my_tag().

◆ cst_width() [2/2]

void protocols::relax::AtomCoordinateCstMover::cst_width ( core::Real width )

inline

References cst_width_.

Referenced by protocols::relax::RelaxProtocolBase::set_up_constraints().

◆ fresh_instance()

protocols::moves::MoverOP protocols::relax::AtomCoordinateCstMover::fresh_instance ( ) const

overridevirtual

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.

◆ func_groups() [1/2]

bool protocols::relax::AtomCoordinateCstMover::func_groups ( ) const

inline

References func_groups_.

Referenced by parse_my_tag().

◆ func_groups() [2/2]

void protocols::relax::AtomCoordinateCstMover::func_groups ( bool b )

inline

References protocols::match::upstream::b, and func_groups_.

◆ generate_constraints()

core::scoring::constraints::ConstraintCOPs protocols::relax::AtomCoordinateCstMover::generate_constraints ( core::pose::Pose const & pose )

private

Referenced by apply().

◆ generate_seqmap()

core::id::SequenceMapping protocols::relax::AtomCoordinateCstMover::generate_seqmap	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	constraint_target_pose
	)		const

private

◆ get_constraint_target_pose()

core::pose::PoseOP protocols::relax::AtomCoordinateCstMover::get_constraint_target_pose ( core::pose::Pose const & pose ) const

private

References core::pose::Pose::clone(), and refpose_.

Referenced by generate_constraints(), and set_constraints_on_func_groups().

◆ get_name()

std::string protocols::relax::AtomCoordinateCstMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References protocols::relax::AtomCoordinateCstMoverCreator::mover_name().

◆ mover_name()

std::string protocols::relax::AtomCoordinateCstMover::mover_name ( )

static

Referenced by protocols::relax::AtomCoordinateCstMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::relax::AtomCoordinateCstMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References ambiguous_hnq(), bounded(), core::io::pdb::build_pose_from_pdb_as_is(), cst_sd(), cst_sidechain(), cst_width(), func_groups(), core::pack::task::parse_task_operations(), refpose_, and set_task_segments().

◆ provide_xml_schema()

void protocols::relax::AtomCoordinateCstMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::relax::AtomCoordinateCstMoverCreator::provide_xml_schema().

◆ set_constraints_on_func_groups()

core::scoring::constraints::ConstraintCOPs protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups ( core::pose::Pose const & pose )

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::relax::add_coordinate_constraint_func_atoms(), core::conformation::Residue::atom_index(), bounded_, compute_residue_subset(), cst_sd_, core::sequence::end, protocols::rosetta_scripts::find_nearest_res(), get_constraint_target_pose(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::relax::TR().

Referenced by generate_constraints().

◆ set_loop_segments()

void protocols::relax::AtomCoordinateCstMover::set_loop_segments ( protocols::loops::LoopsCOP loops )

References loop_segments_.

Referenced by protocols::relax::RelaxProtocolBase::set_up_constraints().

◆ set_refstruct()

void protocols::relax::AtomCoordinateCstMover::set_refstruct ( core::pose::PoseCOP ref )

virtual

References core::scoring::ref, and refpose_.

Referenced by protocols::indel::IndelOptimizationMover::apply(), and protocols::relax::RelaxProtocolBase::set_up_constraints().

◆ set_task_segments()

void protocols::relax::AtomCoordinateCstMover::set_task_segments ( core::pack::task::TaskFactoryCOP taskfactory )

References task_segments_.

Referenced by parse_my_tag().

Member Data Documentation

◆ amb_hnq_

bool protocols::relax::AtomCoordinateCstMover::amb_hnq_

private

When making sidechain constraints, should we allow for flipping HNQ residue sidechains?

Referenced by ambiguous_hnq(), and generate_constraints().

◆ bounded_

bool protocols::relax::AtomCoordinateCstMover::bounded_

private

Use bounded constraints instead of harmonic.

Referenced by bounded(), generate_constraints(), and set_constraints_on_func_groups().

◆ cst_sd_

core::Real protocols::relax::AtomCoordinateCstMover::cst_sd_

private

The strenght (standard deviation) of the constraints.

Referenced by cst_sd(), generate_constraints(), and set_constraints_on_func_groups().

◆ cst_sidechain_

bool protocols::relax::AtomCoordinateCstMover::cst_sidechain_

private

Also constrain sidechains?

Referenced by cst_sidechain(), and generate_constraints().

◆ cst_width_

core::Real protocols::relax::AtomCoordinateCstMover::cst_width_

private

The width for bounded constraints.

Referenced by cst_width(), and generate_constraints().

◆ func_groups_

bool protocols::relax::AtomCoordinateCstMover::func_groups_

private

If set to true then coordinate constraints are applied only to the functional groups of the side_chain.

Referenced by func_groups(), and generate_constraints().

◆ loop_segments_

protocols::loops::LoopsCOP protocols::relax::AtomCoordinateCstMover::loop_segments_

private

A loop definition of constrained segments.

Referenced by compute_residue_subset(), and set_loop_segments().

◆ refpose_

core::pose::PoseCOP protocols::relax::AtomCoordinateCstMover::refpose_

private

If set, the pose to make the constraints to.

Referenced by generate_constraints(), get_constraint_target_pose(), parse_my_tag(), and set_refstruct().

◆ task_segments_

core::pack::task::TaskFactoryCOP protocols::relax::AtomCoordinateCstMover::task_segments_

private

A task definition of constrained segments.

Referenced by compute_residue_subset(), and set_task_segments().

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

src/protocols/relax/AtomCoordinateCstMover.hh
src/protocols/relax/AtomCoordinateCstMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ AtomCoordinateCstMover() [1/2]

◆ AtomCoordinateCstMover() [2/2]

◆ ~AtomCoordinateCstMover()

Member Function Documentation

◆ ambiguous_hnq() [1/2]

◆ ambiguous_hnq() [2/2]

◆ apply()

◆ bounded() [1/2]

◆ bounded() [2/2]

◆ clone()

◆ compute_residue_subset()

◆ cst_sd() [1/2]

◆ cst_sd() [2/2]

◆ cst_sidechain() [1/2]

◆ cst_sidechain() [2/2]

◆ cst_width() [1/2]

◆ cst_width() [2/2]

◆ fresh_instance()

◆ func_groups() [1/2]

◆ func_groups() [2/2]

◆ generate_constraints()

◆ generate_seqmap()

◆ get_constraint_target_pose()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_constraints_on_func_groups()

◆ set_loop_segments()

◆ set_refstruct()

◆ set_task_segments()

Member Data Documentation

◆ amb_hnq_

◆ bounded_

◆ cst_sd_

◆ cst_sidechain_

◆ cst_width_

◆ func_groups_

◆ loop_segments_

◆ refpose_

◆ task_segments_