pure virtual base class More...

#include <RemodelConstraintGenerator.hh>

Inheritance diagram for protocols::forge::remodel::RemodelConstraintGenerator:

Public Types
typedef protocols::forge::components::VarLengthBuildAP	VarLengthBuildAP

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
	~RemodelConstraintGenerator () override
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

void	apply (core::pose::Pose &pose) override
	generates constraints and adds them to the pose 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 &) override
	This is called if this mover is instantiated from XML. More...

	RemodelConstraintGenerator ()

	RemodelConstraintGenerator (RemodelConstraintGenerator const &rval)

void	add_remodel_constraints_to_pose (core::pose::Pose &pose)

void	remove_remodel_constraints_from_pose (core::pose::Pose &pose) const

virtual void	generate_remodel_constraints (core::pose::Pose const &pose)=0

virtual void	init (core::pose::Pose const &)
	Pose-specific setup routines go here. More...

VarLengthBuildAP	vlb () const

void	set_vlb (VarLengthBuildAP vlb)

std::string	id () const

void	set_id (std::string const &id)

void	set_seqmap (core::id::SequenceMappingCOP seqmap)

core::id::SequenceMappingCOP	seqmap () const

core::scoring::constraints::ConstraintCOPs const &	constraints () const

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 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 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 core::scoring::constraints::ConstraintCOPs const	lookup_stored_constraints (std::string const &id)

static void	attributes_for_remodel_constraint_generator (utility::tag::AttributeList &)

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
void	add_constraint (core::scoring::constraints::ConstraintCOP cst)

void	add_constraints (core::scoring::constraints::ConstraintCOPs csts)

void	clear_constraints ()

void	clear_stored_constraints ()

void	store_constraints ()

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...

Private Attributes
std::string	id_

core::scoring::constraints::ConstraintCOPs	csts_

core::id::SequenceMappingCOP	seqmap_

VarLengthBuildAP	vlb_

Static Private Attributes
static std::map< std::string, core::scoring::constraints::ConstraintCOPs >	cst_map_

Detailed Description

pure virtual base class

Member Typedef Documentation

typedef protocols::forge::components::VarLengthBuildAP protocols::forge::remodel::RemodelConstraintGenerator::VarLengthBuildAP

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelConstraintGenerator::~RemodelConstraintGenerator ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::forge::remodel::RemodelConstraintGenerator::RemodelConstraintGenerator ( )

protocols::forge::remodel::RemodelConstraintGenerator::RemodelConstraintGenerator ( RemodelConstraintGenerator const & rval )

Member Function Documentation

void protocols::forge::remodel::RemodelConstraintGenerator::add_constraint ( core::scoring::constraints::ConstraintCOP cst )

protected

References csts_.

Referenced by add_constraints(), and protocols::forge::constraints::InvrotTreeRCG::generate_remodel_constraints().

void protocols::forge::remodel::RemodelConstraintGenerator::add_constraints ( core::scoring::constraints::ConstraintCOPs csts )

protected

References add_constraint().

Referenced by protocols::fldsgn::SheetRemodelConstraintGenerator::generate_remodel_constraints(), protocols::forge::constraints::NtoCConstraintGenerator::generate_remodel_constraints(), protocols::forge::constraints::InverseRotamersRCG::generate_remodel_constraints(), protocols::forge::remodel::GenericRemodelConstraintGenerator::generate_remodel_constraints(), and protocols::forge::remodel::ResidueVicinityRCG::generate_remodel_constraints().

void protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose ( core::pose::Pose & pose )

References core::pose::Pose::add_constraints(), clear_constraints(), csts_, generate_remodel_constraints(), and store_constraints().

Referenced by apply(), and protocols::forge::constraints::InvrotTreeRCG::apply().

void protocols::forge::remodel::RemodelConstraintGenerator::apply ( core::pose::Pose & pose )

overridevirtual

generates constraints and adds them to the pose

When called, generates constraints for the pose, and adds them to the pose

Implements protocols::moves::Mover.

References add_remodel_constraints_to_pose(), and init().

void protocols::forge::remodel::RemodelConstraintGenerator::attributes_for_remodel_constraint_generator ( utility::tag::AttributeList & attlist )

static

Referenced by protocols::forge::remodel::ResidueVicinityRCG::provide_xml_schema().

void protocols::forge::remodel::RemodelConstraintGenerator::clear_constraints ( )

protected

References clear_stored_constraints(), and csts_.

Referenced by add_remodel_constraints_to_pose().

void protocols::forge::remodel::RemodelConstraintGenerator::clear_stored_constraints ( )

protected

References cst_map_, protocols::moves::Mover::get_name(), id_, and protocols::forge::remodel::TR().

Referenced by clear_constraints(), and store_constraints().

core::scoring::constraints::ConstraintCOPs const & protocols::forge::remodel::RemodelConstraintGenerator::constraints ( ) const

References csts_.

virtual void protocols::forge::remodel::RemodelConstraintGenerator::generate_remodel_constraints ( core::pose::Pose const & pose )

pure virtual

Implemented in protocols::forge::remodel::ResidueVicinityRCG, protocols::forge::remodel::GenericRemodelConstraintGenerator, protocols::forge::constraints::InverseRotamersRCG, protocols::forge::constraints::InvrotTreeRCG, protocols::forge::constraints::NtoCConstraintGenerator, and protocols::fldsgn::SheetRemodelConstraintGenerator.

Referenced by add_remodel_constraints_to_pose().

std::string protocols::forge::remodel::RemodelConstraintGenerator::id ( ) const

References id_.

Referenced by set_id().

virtual void protocols::forge::remodel::RemodelConstraintGenerator::init ( core::pose::Pose const & )

inlinevirtual

Pose-specific setup routines go here.

Reimplemented in protocols::forge::constraints::InvrotTreeRCG.

Referenced by apply().

core::scoring::constraints::ConstraintCOPs const protocols::forge::remodel::RemodelConstraintGenerator::lookup_stored_constraints ( std::string const & id )

static

References cst_map_.

Referenced by protocols::forge::constraints::RemoveRemodelCsts::apply().

void protocols::forge::remodel::RemodelConstraintGenerator::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)

overridevirtual

This is called if this mover is instantiated from XML.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::forge::remodel::ResidueVicinityRCG.

References protocols::moves::Mover::get_name(), id_, and protocols::forge::remodel::TR().

Referenced by protocols::forge::remodel::ResidueVicinityRCG::parse_my_tag().

void protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose ( core::pose::Pose & pose ) const

References csts_, protocols::moves::Mover::get_name(), core::pose::Pose::remove_constraints(), and protocols::forge::remodel::TR().

core::id::SequenceMappingCOP protocols::forge::remodel::RemodelConstraintGenerator::seqmap ( ) const

References seqmap_.

Referenced by protocols::forge::constraints::InverseRotamersRCG::generate_remodel_constraints(), protocols::forge::remodel::ResidueVicinityRCG::generate_remodel_constraints(), protocols::forge::remodel::ResidueVicinityRCG::generate_remodel_constraints_for_respair(), and set_seqmap().

void protocols::forge::remodel::RemodelConstraintGenerator::set_id ( std::string const & id )

References id(), and id_.

Referenced by protocols::forge::remodel::GenericRemodelConstraintGenerator::GenericRemodelConstraintGenerator().

void protocols::forge::remodel::RemodelConstraintGenerator::set_seqmap ( core::id::SequenceMappingCOP seqmap )

References seqmap(), and seqmap_.

void protocols::forge::remodel::RemodelConstraintGenerator::set_vlb ( VarLengthBuildAP vlb )

References vlb(), and vlb_.

void protocols::forge::remodel::RemodelConstraintGenerator::store_constraints ( )

protected

References clear_stored_constraints(), cst_map_, csts_, and id_.

Referenced by add_remodel_constraints_to_pose().

RemodelConstraintGenerator::VarLengthBuildAP protocols::forge::remodel::RemodelConstraintGenerator::vlb ( ) const

References vlb_.

Referenced by protocols::forge::constraints::InvrotTreeRCG::init(), and set_vlb().

Member Data Documentation

std::map< std::string, core::scoring::constraints::ConstraintCOPs > protocols::forge::remodel::RemodelConstraintGenerator::cst_map_

staticprivate

Referenced by clear_stored_constraints(), lookup_stored_constraints(), and store_constraints().

core::scoring::constraints::ConstraintCOPs protocols::forge::remodel::RemodelConstraintGenerator::csts_

private

Referenced by add_constraint(), add_remodel_constraints_to_pose(), clear_constraints(), constraints(), remove_remodel_constraints_from_pose(), and store_constraints().

std::string protocols::forge::remodel::RemodelConstraintGenerator::id_

private

Referenced by clear_stored_constraints(), id(), parse_my_tag(), set_id(), and store_constraints().

core::id::SequenceMappingCOP protocols::forge::remodel::RemodelConstraintGenerator::seqmap_

private

Referenced by seqmap(), and set_seqmap().

VarLengthBuildAP protocols::forge::remodel::RemodelConstraintGenerator::vlb_

private

Referenced by set_vlb(), and vlb().

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

src/protocols/forge/remodel/RemodelConstraintGenerator.hh
src/protocols/forge/remodel/RemodelConstraintGenerator.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation