#include <Constraints.hh>

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

Collaboration 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
virtual	~Constraints ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	Constraints ()

	Constraints (Constraints const &)

ConstraintsOP	clone () const

Constraints const &	operator= (Constraints const &)

void	setup_for_scoring (XYZ_Func const &xyz_func, ScoreFunction const &scfxn) const

void	setup_for_derivatives (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 (XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const

void	copy_from (Constraints const &)

Private Attributes
ConstraintCOPs	constraints_

Detailed Description

Definition at line 49 of file Constraints.hh.

Member Typedef Documentation

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

Definition at line 53 of file Constraints.hh.

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

Definition at line 55 of file Constraints.hh.

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

Definition at line 56 of file Constraints.hh.

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

Definition at line 54 of file Constraints.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 37 of file Constraints.cc.

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

Definition at line 39 of file Constraints.cc.

Referenced by clone().

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

Definition at line 42 of file Constraints.cc.

References copy_from().

Member Function Documentation

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

Definition at line 216 of file Constraints.cc.

References constraints_.

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

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

Definition at line 221 of file Constraints.cc.

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::get_all_constraints(), core::scoring::constraints::ConstraintSet::show_definition(), and core::scoring::constraints::ConstraintSet::show_violations().

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

Definition at line 305 of file Constraints.cc.

References constraints_.

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

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

Definition at line 51 of file Constraints.cc.

References Constraints().

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

Definition at line 204 of file Constraints.cc.

References energy().

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

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

inline

Definition at line 164 of file Constraints.hh.

References constraints_.

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

private

Definition at line 68 of file Constraints.cc.

References constraints_.

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

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

Definition at line 222 of file Constraints.cc.

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::get_all_constraints(), core::scoring::constraints::ConstraintSet::show_definition(), and core::scoring::constraints::ConstraintSet::show_violations().

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

private

private does not zero the emap entries before accumulating

Definition at line 164 of file Constraints.cc.

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

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.

Definition at line 98 of file Constraints.cc.

References constraints_, and core::scoring::constraints::Constraint::fill_f1_f2().

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.

Definition at line 118 of file Constraints.cc.

References constraints_, and core::scoring::constraints::Constraint::fill_f1_f2().

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.

Definition at line 139 of file Constraints.cc.

References constraints_, and core::scoring::constraints::Constraint::fill_f1_f2().

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

Definition at line 192 of file Constraints.cc.

References energy().

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

Definition at line 60 of file Constraints.cc.

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

Definition at line 232 of file Constraints.cc.

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

Definition at line 179 of file Constraints.cc.

References energy().

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

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

Definition at line 89 of file Constraints.cc.

References constraints_.

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

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

Definition at line 80 of file Constraints.cc.

References constraints_.

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

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

Definition at line 256 of file Constraints.cc.

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

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

Definition at line 266 of file Constraints.cc.

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`
	)