#include <FabConstraint.hh>

Public Member Functions
	FabConstraint ()
	Constructor. More...

	FabConstraint (ConstraintCOPs &cst_in)
	Constructor. More...

virtual ConstraintOP	clone () const
	Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint. More...

std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...

void	show (std::ostream &out) const
	This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms. More...

void	read_def (std::istream &data, pose::Pose const &pose, func::FuncFactory const &func_factory)
	read in constraint definition More...

Size	pose_res_no (core::pose::Pose const &pose, std::string tempres)

utility::vector1< Real >	calc_penalty_vec (Size start_res, Size stop_res, utility::vector1< Size > res1, utility::vector1< Size > res2)

void	setup_csts (core::pose::Pose const &pose, utility::vector1< Size > res1, utility::vector1< Size > res2, std::string antchains)

Public Member Functions inherited from core::scoring::constraints::MultiConstraint
	MultiConstraint (ScoreType const &t=dof_constraint)
	default Constructor More...

	MultiConstraint (const ConstraintCOPs &cst_in, ScoreType const &t=dof_constraint)
	Constructor. More...

virtual MultiConstraintOP	empty_clone () const

Size	natoms () const
	number of atoms involved in this MultiConstraint container More...

Size	size () const
	number of constraints data More...

virtual bool	operator== (Constraint const &other) const
	possibility to compare constraint according to data and not just pointers More...

virtual void	score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const
	compute score More...

virtual AtomID const &	atom (Size const n) const
	Returns the AtomID referred to by index. More...

virtual utility::vector1 < core::Size >	residues () const
	Returns the pose numbers of the residues involved in this constraint, in no particular order. More...

virtual void	setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const

virtual void	add_individual_constraint (ConstraintCOP cst_in)
	add individual constraint into MultiConstraint More...

virtual ConstraintOP	remap_resid (core::id::SequenceMapping const &seqmap) const
	apply a resid remapping to this constraint, returns the remapped constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice. More...

virtual void	fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
	compute atom deriv More...

virtual void	show_def (std::ostream &out, pose::Pose const &pose) const
	Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they'd like to use the ConstraintIO machinery. It's also not clear why this method takes a Pose, other than to be symmetric with read_def. More...

virtual Size	show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) const
	Prints the violations of this constraint to the given std::ostream. What are violations? It's not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don't know which definition is the right one. Documentation would be nice ... More...

ConstraintCOPs const &	member_constraints () const

virtual ConstraintOP	remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map=NULL) const
	Copies the data from this Constraint into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes. More...

void	set_effective_sequence_separation (core::Size setting)

virtual core::Size	choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &)

virtual core::Size	effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const

Public Member Functions inherited from core::scoring::constraints::Constraint
	Constraint (ScoreType const &t)
	Constructor for Constraint class. More...

virtual	~Constraint ()
	Virtual destructor. More...

virtual ConstraintOP	clone (core::scoring::func::FuncOP) const

virtual void	read_constraint (std::istream &, core::pose::Pose const &)
	This method is totally redundant with read_def YAY. More...

ScoreType const &	score_type () const
	Returns the ScoreType that this Constraint object will use. More...

virtual void	read_data (std::istream &)
	initialize this Constraint from the given std::istream. It's amazing that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint, More...

virtual core::Real	dist (core::pose::Pose const &) const
	return the "raw" distance before handed to the FUNC object More...

virtual core::Real	dist (core::scoring::func::XYZ_Func const &) const

virtual void	setup_for_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const

virtual Real	score (conformation::Conformation const &) const
	Returns the score of this constraint computed over the given conformation. Not necessarily implemented in all derived classes, as it's redundant with the score( XYZ_Func, EnergyMap, EnergyMap ) method defined above. Returns 0.0 if not implemented. More...

virtual void	steal_def (pose::Pose const &)

std::string	to_string () const
	Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More...

virtual core::scoring::func::Func const &	get_func () const
	Returns the func::Func object associated with this Constraint object. More...

bool	operator!= (Constraint const &other) const
	possibility to do object comparison instead of pointer comparison More...

Additional Inherited Members
Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID	AtomID

Protected Attributes inherited from core::scoring::constraints::MultiConstraint
ConstraintCOPs	member_constraints_

Constructor & Destructor Documentation

core::scoring::constraints::FabConstraint::FabConstraint ( )

Constructor.

Referenced by clone().

core::scoring::constraints::FabConstraint::FabConstraint ( ConstraintCOPs & cst_in )

Constructor.

Member Function Documentation

utility::vector1< Real > core::scoring::constraints::FabConstraint::calc_penalty_vec	(	Size	start_res,
		Size	stop_res,
		utility::vector1< Size >	res1,
		utility::vector1< Size >	res2
	)

Referenced by setup_csts().

virtual ConstraintOP core::scoring::constraints::FabConstraint::clone ( ) const

inlinevirtual

Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint.

Reimplemented from core::scoring::constraints::MultiConstraint.

References FabConstraint().

Size core::scoring::constraints::FabConstraint::pose_res_no	(	core::pose::Pose const &	pose,
		std::string	tempres
	)

References chain, core::pose::Pose::pdb_info(), and residue.

Referenced by read_def().

void core::scoring::constraints::FabConstraint::read_def	(	std::istream &	data,
		pose::Pose const &	pose,
		func::FuncFactory const &	func_factory
	)

virtual

read in constraint definition

Reimplemented from core::scoring::constraints::MultiConstraint.

References getline(), pose_res_no(), setup_csts(), and core::scoring::constraints::TR.

void core::scoring::constraints::FabConstraint::setup_csts	(	core::pose::Pose const &	pose,
		utility::vector1< Size >	res1,
		utility::vector1< Size >	res2,
		std::string	antchains
	)

References core::scoring::constraints::MultiConstraint::add_individual_constraint(), core::chemical::ResidueType::atom_index(), calc_penalty_vec(), core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), numeric::xyzVector< class >::distance(), core::pose::get_chain_id_from_chain(), j, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), runtime_assert, core::scoring::constraints::TR, and core::conformation::Residue::xyz().

Referenced by read_def().

void core::scoring::constraints::FabConstraint::show ( std::ostream & ) const

virtual

This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.

Reimplemented from core::scoring::constraints::MultiConstraint.

References begin, and core::scoring::constraints::MultiConstraint::member_constraints().

std::string core::scoring::constraints::FabConstraint::type ( ) const

inlinevirtual

Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.

Reimplemented from core::scoring::constraints::MultiConstraint.

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

symlinks/rosetta/src/core/scoring/constraints/FabConstraint.hh
symlinks/rosetta/src/core/scoring/constraints/FabConstraint.cc

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation