#include <SheetConstraintsRCG.hh>

Inheritance diagram for protocols::fldsgn::SheetConstraintsRCG:

Collaboration diagram for protocols::fldsgn::SheetConstraintsRCG:

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef protocols::jd2::parser::BluePrintOP	BluePrintOP

Public Types inherited from protocols::forge::remodel::RemodelConstraintGenerator
typedef protocols::forge::components::VarLengthBuildAP	VarLengthBuildAP

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

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
	SheetConstraintsRCG ()

	SheetConstraintsRCG (SheetConstraintsRCG const &rval)
	@ copy constructor More...

	SheetConstraintsRCG (BluePrintOP const &blue)

	SheetConstraintsRCG (BluePrintOP const &blue, Real const coef)
	value constructor More...

	SheetConstraintsRCG (BluePrintOP const &blue, Real const coef, Real const dist)
	value constructor More...

virtual	~SheetConstraintsRCG ()

virtual void	parse_my_tag (TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::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
	Each derived class must specify its name. The class name. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

virtual void	generate_remodel_constraints (Pose const &pose)

void	set_blueprint (std::string const &blueprint_file)
	sets teh blueprint file used for determining proper sheet pairing This function will create the blueprint object for you from the file and use it More...

void	set_blueprint (BluePrintOP const &blue)
	sets the blueprint object used for determining proper sheet pairing More...

void	set_weight (Real const coef)
	set the weight of the sheet constraints More...

void	set_distance (Real const dist)
	set the maximum Ca-Ca distance between paired residues More...

void	set_angle_tolerance (Real const angle_tolerance)
	set the flat-bottom tolerance for the backbone angle between strands for each pair This is N1-C1-C2 and N2-C2-C1 for parallel sheets, and N1-C1-N2/N2-C2-N1 for antiparallel. More...

void	set_cacb_dihedral_tolerance (Real const dihedral_tolerance)
	set the flat-bottom tolerance for the Cb1-Ca1-Ca2-Cb2 dihedral angle (0 = optimal) More...

void	set_bb_dihedral_tolerance (Real const dihedral_tolerance)
	set the flat-bottom tolerance for the backbone dihedrals (0=optimal) Dihedral 1 = O1-N1-C1-C2, Dihedral 2 = O2-N2-C2-C1 More...

void	set_constrain_dist_only (bool const constrain_dist_only)
	sets whether we should constrain distance only, and not generate dihedral and angle constraints More...

Public Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
virtual	~RemodelConstraintGenerator ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

virtual void	apply (core::pose::Pose &pose)
	generates constraints and adds them to the pose More...

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	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	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

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
	this function informs 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
	this function informs 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

Private Attributes
Real	weight_

Real	dist_

Real	angle_tolerance_

Real	cacb_dihedral_tolerance_

Real	bb_dihedral_tolerance_

bool	constrain_dist_only_

BluePrintOP	blueprint_

Additional Inherited Members
Static Public Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
static core::scoring::constraints::ConstraintCOPs const	lookup_stored_constraints (std::string const &id)

Protected Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
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 ()

Member Typedef Documentation

typedef protocols::jd2::parser::BluePrintOP protocols::fldsgn::SheetConstraintsRCG::BluePrintOP

typedef core::pose::Pose protocols::fldsgn::SheetConstraintsRCG::Pose

typedef core::Real protocols::fldsgn::SheetConstraintsRCG::Real

typedef core::Size protocols::fldsgn::SheetConstraintsRCG::Size

Constructor & Destructor Documentation

protocols::fldsgn::SheetConstraintsRCG::SheetConstraintsRCG ( )

Referenced by clone(), and fresh_instance().

protocols::fldsgn::SheetConstraintsRCG::SheetConstraintsRCG ( SheetConstraintsRCG const & rval)

@ copy constructor

protocols::fldsgn::SheetConstraintsRCG::SheetConstraintsRCG ( BluePrintOP const & blue)

protocols::fldsgn::SheetConstraintsRCG::SheetConstraintsRCG	(	BluePrintOP const &	blue,
		Real const	coef
	)

value constructor

protocols::fldsgn::SheetConstraintsRCG::SheetConstraintsRCG	(	BluePrintOP const &	blue,
		Real const	coef,
		Real const	dist
	)

value constructor

protocols::fldsgn::SheetConstraintsRCG::~SheetConstraintsRCG ( )

virtual

Member Function Documentation

protocols::moves::MoverOP protocols::fldsgn::SheetConstraintsRCG::clone ( ) const

virtual

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

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.

References SheetConstraintsRCG().

protocols::moves::MoverOP protocols::fldsgn::SheetConstraintsRCG::fresh_instance ( ) const

virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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 SheetConstraintsRCG().

void protocols::fldsgn::SheetConstraintsRCG::generate_remodel_constraints ( Pose const & pose)

virtual

Implements protocols::forge::remodel::RemodelConstraintGenerator.

References protocols::forge::remodel::RemodelConstraintGenerator::add_constraints(), angle_tolerance_, core::chemical::ResidueType::atom_index(), bb_dihedral_tolerance_, blueprint_, cacb_dihedral_tolerance_, constrain_dist_only_, dist_, core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::name3(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), protocols::fldsgn::TR(), and weight_.

std::string protocols::fldsgn::SheetConstraintsRCG::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

References protocols::fldsgn::SheetCstGeneratorCreator::mover_name().

void protocols::fldsgn::SheetConstraintsRCG::parse_my_tag	(	TagPtr const	tag,
		protocols::moves::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 angle_tolerance_, bb_dihedral_tolerance_, cacb_dihedral_tolerance_, constrain_dist_only_, dist_, set_angle_tolerance(), set_bb_dihedral_tolerance(), set_blueprint(), set_cacb_dihedral_tolerance(), set_constrain_dist_only(), set_distance(), set_weight(), and weight_.

void protocols::fldsgn::SheetConstraintsRCG::set_angle_tolerance ( Real const angle_tolerance)

set the flat-bottom tolerance for the backbone angle between strands for each pair This is N1-C1-C2 and N2-C2-C1 for parallel sheets, and N1-C1-N2/N2-C2-N1 for antiparallel.

References angle_tolerance_.

Referenced by parse_my_tag().

void protocols::fldsgn::SheetConstraintsRCG::set_bb_dihedral_tolerance ( Real const dihedral_tolerance)

set the flat-bottom tolerance for the backbone dihedrals (0=optimal) Dihedral 1 = O1-N1-C1-C2, Dihedral 2 = O2-N2-C2-C1

References bb_dihedral_tolerance_.

Referenced by parse_my_tag().

void protocols::fldsgn::SheetConstraintsRCG::set_blueprint ( std::string const & blueprint_file)

sets teh blueprint file used for determining proper sheet pairing This function will create the blueprint object for you from the file and use it

References blueprint_.

Referenced by parse_my_tag().

void protocols::fldsgn::SheetConstraintsRCG::set_blueprint ( BluePrintOP const & blue)

sets the blueprint object used for determining proper sheet pairing