#include <Constraints.hh>

Inheritance diagram for core::scoring::constraints::Constraints:

Public Types
typedef id::AtomID	AtomID

typedef conformation::Residue	Residue

typedef conformation::Conformation	Conformation

typedef ConstraintCOPs::const_iterator	const_iterator

Public Member Functions
	~Constraints () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	Constraints ()
	Default constructor creates an empy Constraints object. More...

	Constraints (Constraints const &)
	Copy constructor copies all of the Constraint pointers so that two Poses may share the same constraints – this only works if constraints are immutable. More...

ConstraintsOP	clone () const
	Create a copy of this Constraints object using the shallow-copy-constructor. More...

ConstraintsOP	deep_clone () const
	Create a deep copy of this Constraints object, cloning all of the individual constraints. More...

Constraints &	operator= (Constraints const &rhs)
	Copy the contents of the rhs Constraints object into this Constraints object. More...

void	setup_for_scoring (core::scoring::func::XYZ_Func const &xyz_func, ScoreFunction const &scfxn) const

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

void	residue_pair_energy (Residue const &rsd1, Residue const &rsd2, EnergyMap const &weights, EnergyMap &emap) const
	will fail if Residues dont contain all the necessary atoms More...

void	intra_residue_energy (Residue const &rsd, EnergyMap const &weights, EnergyMap &emap) const
	will fail if Residue doesnt contain all the necessary atoms More...

void	conformation_energy (Conformation const &conformation, EnergyMap const &weights, EnergyMap &emap) const

void	eval_intrares_atom_derivative (id::AtomID const &atom_id, conformation::Residue const &residue, EnergyMap const &weights, Vector &F1, Vector &F2) const
	Evaluate derivatives giving the Constraint objects held within this object a single residue. Warning: if this Constraints object contains Constraint objects that operate on other residues besides the one being given them, then this function will cause the program to exit. More...

void	eval_respair_atom_derivative (id::AtomID const &atom_id, conformation::Residue const &residue1, conformation::Residue const &residue2, EnergyMap const &weights, Vector &F1, Vector &F2) const
	Evaluate derivatives giving the Constraint objects held within this object two residues. Warning: if this Constraints object contains Constraint objects that operate on other residues besides the two being given them, then this function will cause the program to exit. More...

void	eval_ws_atom_derivative (AtomID const &atom_id, Conformation const &conformation, EnergyMap const &weights, Vector &F1, Vector &F2) const
	Evaluate derivatives giving the Constraint objects held within this object the entire Conformation (a whole structure, ws) with which to work. More...

void	add_constraint (ConstraintCOP cst)

bool	remove_constraint (ConstraintCOP cst, bool object_comparison)
	Returns true iff the constraint was successfully found and removed. More...

const_iterator	begin () const

const_iterator	end () const

void	show (std::ostream &out)

void	show_definition (std::ostream &out, pose::Pose const &pose) const

virtual Size	show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, core::Real threshold=1)

Size	size () const

void	clear ()

ConstraintCOPs const &	constraints () const

Private Member Functions
void	energy (core::scoring::func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const

void	copy_from (Constraints const &)

void	deep_copy_from (Constraints const &)

Private Attributes
ConstraintCOPs	constraints_

Member Typedef Documentation

typedef id::AtomID core::scoring::constraints::Constraints::AtomID

typedef conformation::Conformation core::scoring::constraints::Constraints::Conformation

typedef ConstraintCOPs::const_iterator core::scoring::constraints::Constraints::const_iterator

typedef conformation::Residue core::scoring::constraints::Constraints::Residue

Constructor & Destructor Documentation

core::scoring::constraints::Constraints::~Constraints ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

core::scoring::constraints::Constraints::Constraints ( )

Default constructor creates an empy Constraints object.

Referenced by clone(), and deep_clone().

core::scoring::constraints::Constraints::Constraints ( Constraints const & other )

Copy constructor copies all of the Constraint pointers so that two Poses may share the same constraints – this only works if constraints are immutable.

References copy_from().

Member Function Documentation

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

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::add_constraint().

Constraints::const_iterator core::scoring::constraints::Constraints::begin ( ) const

References constraints_.

void core::scoring::constraints::Constraints::clear ( )

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::clear().

ConstraintsOP core::scoring::constraints::Constraints::clone ( ) const

Create a copy of this Constraints object using the shallow-copy-constructor.

References Constraints().

void core::scoring::constraints::Constraints::conformation_energy	(	Conformation const &	conformation,
		EnergyMap const &	weights,
		EnergyMap &	emap
	)		const

References energy().

Referenced by core::scoring::constraints::ConstraintSet::eval_non_residue_pair_energy().

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

inline

References constraints_.

void core::scoring::constraints::Constraints::copy_from ( Constraints const & other )

private

References constraints_.

Referenced by Constraints(), and operator=().

ConstraintsOP core::scoring::constraints::Constraints::deep_clone ( ) const

Create a deep copy of this Constraints object, cloning all of the individual constraints.

References Constraints().

void core::scoring::constraints::Constraints::deep_copy_from ( Constraints const & other )

private

References constraints_.

Constraints::const_iterator core::scoring::constraints::Constraints::end ( ) const

References constraints_.

void core::scoring::constraints::Constraints::energy	(	core::scoring::func::XYZ_Func const &	xyz_func,
		EnergyMap const &	weights,
		EnergyMap &	emap
	)		const

private

private does not zero the emap entries before accumulating

References constraints_.

Referenced by conformation_energy(), intra_residue_energy(), and residue_pair_energy().

void core::scoring::constraints::Constraints::eval_intrares_atom_derivative	(	id::AtomID const &	atom_id,
		conformation::Residue const &	residue,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

Evaluate derivatives giving the Constraint objects held within this object a single residue. Warning: if this Constraints object contains Constraint objects that operate on other residues besides the one being given them, then this function will cause the program to exit.

References constraints_.

Referenced by core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives().

void core::scoring::constraints::Constraints::eval_respair_atom_derivative	(	id::AtomID const &	atom_id,
		conformation::Residue const &	residue1,
		conformation::Residue const &	residue2,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

Evaluate derivatives giving the Constraint objects held within this object two residues. Warning: if this Constraints object contains Constraint objects that operate on other residues besides the two being given them, then this function will cause the program to exit.

References constraints_.

Referenced by core::scoring::constraints::ConstraintsEnergy::eval_residue_pair_derivatives().

void core::scoring::constraints::Constraints::eval_ws_atom_derivative	(	id::AtomID const &	atom_id,
		conformation::Conformation const &	conformation,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

Evaluate derivatives giving the Constraint objects held within this object the entire Conformation (a whole structure, ws) with which to work.

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative(), and core::scoring::constraints::ConstraintSet::eval_multibody_atom_derivative().

void core::scoring::constraints::Constraints::intra_residue_energy	(	Residue const &	rsd,
		EnergyMap const &	weights,
		EnergyMap &	emap
	)		const

will fail if Residue doesnt contain all the necessary atoms

will fail if Residues dont contain all the necessary atoms

References energy().

Referenced by core::scoring::constraints::ConstraintsEnergy::eval_intrares_energy_ext().

Constraints & core::scoring::constraints::Constraints::operator= ( Constraints const & rhs )

Copy the contents of the rhs Constraints object into this Constraints object.

References copy_from().

bool core::scoring::constraints::Constraints::remove_constraint	(	ConstraintCOP	cst,
		bool	object_comparison
	)

Returns true iff the constraint was successfully found and removed.

If this list contains the same constraint multiple times, only one copy of it is removed. I can't imagine why that scenario would ever come up, but still... flo jan '11 added object_comparison bool that triggers removal of constraint if the actual constraints are identical, even though they're different objects

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::remove_constraint().

void core::scoring::constraints::Constraints::residue_pair_energy	(	Residue const &	rsd1,
		Residue const &	rsd2,
		EnergyMap const &	weights,
		EnergyMap &	emap
	)		const

will fail if Residues dont contain all the necessary atoms

References energy().

Referenced by core::scoring::constraints::ConstraintSet::residue_pair_energy(), and core::scoring::constraints::ConstraintsEnergy::residue_pair_energy_ext().

void core::scoring::constraints::Constraints::setup_for_derivatives	(	core::scoring::func::XYZ_Func const &	xyz_func,
		ScoreFunction const &	scfxn
	)		const

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::setup_for_derivatives(), core::scoring::constraints::ConstraintsEnergy::setup_for_derivatives_for_residue(), and core::scoring::constraints::ConstraintsEnergy::setup_for_derivatives_for_residue_pair().

void core::scoring::constraints::Constraints::setup_for_scoring	(	core::scoring::func::XYZ_Func const &	xyz_func,
		ScoreFunction const &	scfxn
	)		const

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::setup_for_scoring(), core::scoring::constraints::ConstraintsEnergy::setup_for_scoring_for_residue(), and core::scoring::constraints::ConstraintsEnergy::setup_for_scoring_for_residue_pair().

void core::scoring::constraints::Constraints::show ( std::ostream & out )

References constraints_, and core::scoring::constraints::Constraint::show().

void core::scoring::constraints::Constraints::show_definition	(	std::ostream &	out,
		pose::Pose const &	pose
	)		const

References constraints_, and core::scoring::constraints::Constraint::show_def().

Size core::scoring::constraints::Constraints::show_violations	(	std::ostream &	out,
		pose::Pose const &	pose,
		Size	verbose_level,
		core::Real	threshold = `1`
	)