Classes
class	AmberPeriodicFunc
	function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) More...

class	AmbiguousConstraint

class	AmbiguousNMRConstraint

class	AmbiguousNMRDistanceConstraint

class	AngleConstraint
	An Angular Constraint. More...

class	AtomPairConstraint

class	BackboneStubConstraint
	This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location. More...

class	AtomPairConstraintCreator
	Mover creator for the AtomPairConstraint constraint. More...

class	AngleConstraintCreator
	Mover creator for the AngleConstraint constraint. More...

class	DihedralConstraintCreator
	Mover creator for the DihedralConstraint constraint. More...

class	DihedralPairConstraintCreator
	Constraint creator for DihedralPairConstraint. More...

class	BigBinConstraintCreator
	Mover creator for the BigBinConstraint constraint. More...

class	MultiConstraintCreator
	Mover creator for the MultiConstraint constraint. More...

class	AmbiguousConstraintCreator
	Mover creator for the AmbiguousConstraint constraint. More...

class	KofNConstraintCreator
	Mover creator for the KofNConstraint constraint. More...

class	CoordinateConstraintCreator
	Mover creator for the CoordinateConstraint constraint. More...

class	LocalCoordinateConstraintCreator
	Mover creator for the LocalCoordinateConstraint constraint. More...

class	AmbiguousNMRDistanceConstraintCreator
	Mover creator for the AmbiguousNMRDistanceConstraint constraint. More...

class	AmbiguousNMRConstraintCreator
	Mover creator for the AmbiguousNMRConstraint constraint. More...

class	SiteConstraintCreator
	Mover creator for the SiteConstraint constraint. More...

class	SiteConstraintResiduesCreator
	Mover creator for the SiteConstraintResidues constraint. More...

class	FabConstraintCreator
	Mover creator for the FabConstraint constraint. More...

class	BigBinConstraint
	constraint on dihedral angle formed by 4 points More...

class	BoundFunc

class	PeriodicBoundFunc
	a variant of the bound func that is periodic More...

class	OffsetPeriodicBoundFunc
	a variant of the bound func that is periodic More...

class	CharmmPeriodicFunc
	function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) More...

class	CircularGeneral1D_Func
	Function that allows return of arbitrary FArrays – this time circularized. More...

class	CircularHarmonicFunc
	Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...

class	CircularPowerFunc
	Generalization of CircularCircularPowerFunc – other exponents allowed. More...

class	CircularSigmoidalFunc
	Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...

class	ConstantConstraint
	A Constant Constraint. More...

class	ConstantFunc
	Derived class of class Func representing a Constant distribution with a user-specified mean and standard deviation. More...

class	Constraint
	Actually a restraint, like a virtual rubber band between a pair of atoms. More...

class	ConstraintCreator
	Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...

class	CstResNeighbIterator

class	CstResNeighbConstIterator

class	CstEnergyContainer

class	ConstraintFactory

class	ConstraintRegistrator
	This templated class will register an instance of an ConstraintCreator (class T) with the ConstraintFactory. It will ensure that no ConstraintCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	ConstraintNode

class	ConstraintEdge

class	ConstraintGraph

class	ConstraintIO

class	Constraints

class	ConstraintsEnergy

class	ConstraintsEnergyCreator

class	ResidueConstraints

class	ConstraintSet

class	CoordinateConstraint

class	CountViolFunc

class	CstMinimizationData

class	DihedralConstraint
	constraint on dihedral angle formed by 4 points More...

class	DihedralPairConstraint
	constraint on dihedral angle formed by 4 points More...

class	DistancePairConstraint
	constraint on CA distance More...

class	DOF_Constraint
	This isn't quite a standard constraint since it acts on DOF's directly rather than on XYZ coordinates. More...

class	EtableFunc
	Class for representing arbitrarily defined functions. More...

class	FabConstraint

class	FadeFunc

class	FlatHarmonicFunc

class	FourPointsFunc
	A simple class that represents the coordinates of four points, pretending that they all belong to residue 1. The residue() method is not implemented and cause a utility_exit. More...

class	Func
	Func is an abstract base class representing a function used to define constraints, in which func(r) gives the constraint score for the given value r. More...

class	FuncFactory

class	GaussianFunc
	Derived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation. More...

class	HarmonicFunc

class	IdentityFunc

class	KarplusFunc
	Function that evaluates a J-coupling from dihedral angles in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...

class	KofNConstraint

class	LinearPenaltyFunction

class	LocalCoordinateConstraint

class	MinMultiHarmonicFunc

class	MixtureFunc
	Derived class of class Func representing a Mixture of several distinct functions. The function is of the form ln( g(r) / h(r) ), where g(r) is a mixture of a Gaussian and Exponential distributions, and h(r) is a Gaussian distribution. See methods and implementation for more information. More...

class	MultiConstraint

class	Obsolet_NamedAtomPairConstraint

class	NamedAtomPairConstraint

class	NonResidueTypeConstraint
	This class favors a particular residue identity at a particular position by reducing its res_type energy. More...

class	PeriodicFunc
	function of type y = ( k * cos(n * (x - x0) ) ) + C More...

class	ResidueTypeConstraint
	This class favors a particular residue identity at a particular position by reducing its res_type energy. More...

class	ResidueTypeLinkingConstraint
	This class favors a particular residue identity at a particular position by reducing its res_type energy. More...

class	ScalarWeightedFunc

class	SequenceProfileConstraint

class	SequenceProfileConstraintCreator
	Constraint creator for the SequenceProfileConstraint constraint. More...

class	SigmoidFunc

class	SiteConstraint

class	SiteConstraintResidues

class	SkipViolFunc

class	SoedingFunc
	Derived class of class Func representing a Soeding distribution with a user-specified mean and standard deviation. More...

class	SOGFunc
	Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation. More...

class	SOGFunc_Impl
	Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation. More...

class	SplineFunc

class	SquareWell2Func

class	SquareWellFunc

class	SumFunc

class	TopOutFunc

class	USOGFunc
	Unnormalized, unbounded sum of Gaussians constraint. More...

class	XYZ_Func
	just a simple class that takes an AtomID and returns a Vector (position) More...

class	ResidueXYZ

class	ResiduePairXYZ

class	ConformationXYZ

class	ChainbreakDistFunc

Typedefs
typedef utility::pointer::owning_ptr < AmberPeriodicFunc >	AmberPeriodicFuncOP

typedef utility::pointer::owning_ptr < AmberPeriodicFunc const >	AmberPeriodicFuncCOP

typedef utility::pointer::owning_ptr < AmbiguousConstraint >	AmbiguousConstraintOP

typedef utility::pointer::owning_ptr < AmbiguousConstraint const >	AmbiguousConstraintCOP

typedef utility::pointer::owning_ptr < AmbiguousNMRConstraint >	AmbiguousNMRConstraintOP

typedef utility::pointer::owning_ptr < AmbiguousNMRConstraint const >	AmbiguousNMRConstraintCOP

typedef utility::pointer::owning_ptr < AmbiguousNMRDistanceConstraint >	AmbiguousNMRDistanceConstraintOP

typedef utility::pointer::owning_ptr < AmbiguousNMRDistanceConstraint const >	AmbiguousNMRDistanceConstraintCOP

typedef utility::vector1 < core::id::NamedAtomID >	NamedAtoms

typedef utility::pointer::owning_ptr < AngleConstraint >	AngleConstraintOP

typedef utility::pointer::owning_ptr < AngleConstraint const >	AngleConstraintCOP

typedef utility::pointer::owning_ptr < AtomPairConstraint >	AtomPairConstraintOP

typedef utility::pointer::owning_ptr < AtomPairConstraint const >	AtomPairConstraintCOP

typedef utility::pointer::owning_ptr < BackboneStubConstraint >	BackboneStubConstraintOP

typedef utility::pointer::owning_ptr < BackboneStubConstraint const >	BackboneStubConstraintCOP

typedef utility::vector1 < BackboneStubConstraintOP >	BackboneStubConstraintOPs

typedef utility::vector1 < BackboneStubConstraintCOP >	BackboneStubConstraintCOPs

typedef utility::pointer::owning_ptr < BoundFunc >	BoundFuncOP

typedef utility::pointer::owning_ptr < BoundFunc const >	BoundFuncCOP

typedef utility::pointer::owning_ptr < CircularGeneral1D_Func >	CircularGeneral1D_FuncOP

typedef utility::pointer::owning_ptr < CircularGeneral1D_Func const >	CircularGeneral1D_FuncCOP

typedef utility::pointer::owning_ptr < CircularHarmonicFunc >	CircularHarmonicFuncOP

typedef utility::pointer::owning_ptr < CircularHarmonicFunc const >	CircularHarmonicFuncCOP

typedef utility::pointer::owning_ptr < CircularPowerFunc >	CircularPowerFuncOP

typedef utility::pointer::owning_ptr < CircularPowerFunc const >	CircularPowerFuncCOP

typedef utility::pointer::owning_ptr < CircularSigmoidalFunc >	CircularSigmoidalFuncOP

typedef utility::pointer::owning_ptr < CircularSigmoidalFunc const >	CircularSigmoidalFuncCOP

typedef utility::pointer::owning_ptr < ConstantFunc >	ConstantFuncOP

typedef utility::pointer::owning_ptr < Constraint >	ConstraintOP

typedef utility::pointer::owning_ptr < Constraint const >	ConstraintCOP

typedef utility::vector1 < ConstraintOP >	ConstraintOPs

typedef utility::vector1 < ConstraintCOP >	ConstraintCOPs

typedef utility::pointer::owning_ptr < ConstraintCreator >	ConstraintCreatorOP

typedef utility::pointer::owning_ptr < ConstraintCreator const >	ConstraintCreatorCOP

typedef utility::pointer::owning_ptr < CstEnergyContainer >	CstEnergyContainerOP

typedef utility::pointer::owning_ptr < CstEnergyContainer const >	CstEnergyContainerCOP

typedef utility::pointer::owning_ptr < ConstraintGraph >	ConstraintGraphOP

typedef utility::pointer::owning_ptr < ConstraintGraph const >	ConstraintGraphCOP

typedef utility::pointer::owning_ptr < Constraints >	ConstraintsOP

typedef utility::pointer::owning_ptr < Constraints const >	ConstraintsCOP

typedef utility::pointer::owning_ptr < ConstraintsEnergy >	ConstraintsEnergyOP

typedef utility::pointer::owning_ptr < ConstraintsEnergy const >	ConstraintsEnergyCOP

typedef utility::pointer::owning_ptr < ResidueConstraints >	ResidueConstraintsOP

typedef utility::pointer::owning_ptr < ResidueConstraints const >	ResidueConstraintsCOP

typedef utility::pointer::owning_ptr < ConstraintSet >	ConstraintSetOP

typedef utility::pointer::owning_ptr < ConstraintSet const >	ConstraintSetCOP

typedef utility::pointer::owning_ptr < CstMinimizationData >	CstMinimizationDataOP

typedef utility::pointer::owning_ptr < CstMinimizationData const >	CstMinimizationDataCOP

typedef utility::pointer::owning_ptr < DihedralConstraint >	DihedralConstraintOP

typedef utility::pointer::owning_ptr < DihedralConstraint const >	DihedralConstraintCOP

typedef utility::pointer::owning_ptr < DOF_Constraint >	DOF_ConstraintOP

typedef utility::pointer::owning_ptr < DOF_Constraint const >	DOF_ConstraintCOP

typedef utility::vector1 < DOF_ConstraintOP >	DOF_ConstraintOPs

typedef utility::vector1 < DOF_ConstraintCOP >	DOF_ConstraintCOPs

typedef utility::pointer::owning_ptr < EtableFunc >	EtableFuncOP

typedef utility::pointer::owning_ptr < FabConstraint >	FabConstraintOP

typedef utility::pointer::owning_ptr < FabConstraint const >	FabConstraintCOP

typedef utility::pointer::owning_ptr < FadeFunc >	FadeFuncOP

typedef utility::pointer::owning_ptr < FadeFunc const >	FadeFuncCOP

typedef utility::pointer::owning_ptr < FlatHarmonicFunc >	FlatHarmonicFuncOP

typedef utility::pointer::owning_ptr < FlatHarmonicFunc const >	FlatHarmonicFuncCOP

typedef utility::pointer::owning_ptr < FourPointsFunc >	FourPointsFuncOP

typedef utility::pointer::owning_ptr < FourPointsFunc const >	FourPointsFuncCOP

typedef utility::pointer::owning_ptr < Func >	FuncOP

typedef utility::pointer::owning_ptr < GaussianFunc >	GaussianFuncOP

typedef utility::pointer::owning_ptr < HarmonicFunc >	HarmonicFuncOP

typedef utility::pointer::owning_ptr < HarmonicFunc const >	HarmonicFuncCOP

typedef utility::pointer::owning_ptr < IdentityFunc >	IdentityFuncOP

typedef utility::pointer::owning_ptr < IdentityFunc const >	IdentityFuncCOP

typedef utility::pointer::owning_ptr < KarplusFunc >	KarplusFuncOP

typedef utility::pointer::owning_ptr < KarplusFunc const >	KarplusFuncCOP

typedef utility::pointer::owning_ptr < KofNConstraint >	KofNConstraintOP

typedef utility::pointer::owning_ptr < KofNConstraint const >	KofNConstraintCOP

typedef utility::pointer::owning_ptr < LocalCoordinateConstraint >	LocalCoordinateConstraintOP

typedef utility::pointer::owning_ptr < LocalCoordinateConstraint const >	LocalCoordinateConstraintCOP

typedef utility::pointer::owning_ptr < MinMultiHarmonicFunc >	MinMultiHarmonicFuncOP

typedef utility::pointer::owning_ptr < MinMultiHarmonicFunc const >	MinMultiHarmonicFuncCOP

typedef utility::pointer::owning_ptr < MixtureFunc >	MixtureFuncOP

typedef utility::pointer::owning_ptr < MultiConstraint >	MultiConstraintOP

typedef utility::pointer::owning_ptr < MultiConstraint const >	MultiConstraintCOP

typedef utility::pointer::owning_ptr < NamedAtomPairConstraint >	NamedAtomPairConstraintOP

typedef utility::pointer::owning_ptr < NamedAtomPairConstraint const >	NamedAtomPairConstraintCOP

typedef utility::pointer::owning_ptr < Obsolet_NamedAtomPairConstraint >	Obsolet_NamedAtomPairConstraintOP

typedef utility::pointer::owning_ptr < Obsolet_NamedAtomPairConstraint const >	Obsolet_NamedAtomPairConstraintCOP

typedef utility::pointer::owning_ptr < NonResidueTypeConstraint >	NonResidueTypeConstraintOP

typedef utility::pointer::owning_ptr < NonResidueTypeConstraint const >	NonResidueTypeConstraintCOP

typedef utility::pointer::owning_ptr < ResidueTypeConstraint >	ResidueTypeConstraintOP

typedef utility::pointer::owning_ptr < ResidueTypeConstraint const >	ResidueTypeConstraintCOP

typedef utility::pointer::owning_ptr < ResidueTypeLinkingConstraint >	ResidueTypeLinkingConstraintOP

typedef utility::pointer::owning_ptr < ResidueTypeLinkingConstraint const >	ResidueTypeLinkingConstraintCOP

typedef utility::pointer::owning_ptr < ScalarWeightedFunc >	ScalarWeightedFuncOP

typedef utility::pointer::owning_ptr < ScalarWeightedFunc const >	ScalarWeightedFuncCOP

typedef utility::pointer::owning_ptr < SequenceProfileConstraint >	SequenceProfileConstraintOP

typedef utility::pointer::owning_ptr < SequenceProfileConstraint const >	SequenceProfileConstraintCOP

typedef utility::pointer::owning_ptr < SiteConstraint >	SiteConstraintOP

typedef utility::pointer::owning_ptr < SiteConstraint const >	SiteConstraintCOP

typedef utility::pointer::owning_ptr < SiteConstraintResidues >	SiteConstraintResiduesOP

typedef utility::pointer::owning_ptr < SiteConstraintResidues const >	SiteConstraintResiduesCOP

typedef utility::pointer::owning_ptr < SoedingFunc >	SoedingFuncOP

typedef utility::pointer::owning_ptr < SOGFunc >	SOGFuncOP

typedef utility::pointer::owning_ptr < SOGFunc_Impl >	SOGFunc_ImplOP

typedef utility::pointer::owning_ptr < SplineFunc >	SplineFuncOP

typedef utility::pointer::owning_ptr < SplineFunc const >	SplineFuncCOP

typedef utility::pointer::owning_ptr < SquareWell2Func >	SquareWell2FuncOP

typedef utility::pointer::owning_ptr < SquareWell2Func const >	SquareWell2FuncCOP

typedef utility::pointer::owning_ptr < SquareWellFunc >	SquareWellFuncOP

typedef utility::pointer::owning_ptr < SquareWellFunc const >	SquareWellFuncCOP

typedef utility::pointer::owning_ptr < SumFunc >	SumFuncOP

typedef utility::pointer::owning_ptr < TopOutFunc >	TopOutFuncOP

typedef utility::pointer::owning_ptr < TopOutFunc const >	TopOutFuncCOP

typedef utility::pointer::owning_ptr < USOGFunc >	USOGFuncOP

typedef utility::pointer::owning_ptr < USOGFunc const >	USOGFuncCOP

Functions
bool	is_aromatic (pose::Pose const &pose, core::Size res)

bool	is_aromatic (core::chemical::AA aa)

void	parse_NMR_name (std::string name, core::Size res, core::chemical::AA aa, NamedAtoms &atoms)

void	parse_NMR_name (std::string name, core::Size res, AmbiguousNMRDistanceConstraint::Atoms &atoms, core::pose::Pose const &pose)

void	parse_NMR_name_old (std::string name, core::Size res, AmbiguousNMRDistanceConstraint::Atoms &atoms, core::pose::Pose const &pose)

bool	requires_CB_mapping (AmbiguousNMRDistanceConstraint::Atoms atoms, pose::Pose const &pose)

void	combine_NMR_atom_string (AmbiguousNMRDistanceConstraint::Atoms atoms, std::string &atom_str, pose::Pose const &pose)

static basic::Tracer	TRACER ("core.io.constraints")

static basic::Tracer	TR ("core.scoring.constraints.BackboneStubConstraint")

std::ostream &	operator<< (std::ostream &out, Constraint &cst)

std::string	get_section_name (std::string line)

static basic::Tracer	tr ("core.scoring.ConstraintsEnergy")

static basic::Tracer	tr ("core.scoring.ConstraintSet")

void	add_constraint_to_residue_constraints (int const seqpos, ConstraintCOP cst, ResidueConstraints &residue_constraints)
	helper, static More...

bool	remove_constraint_from_residue_constraints (int const seqpos, ConstraintCOP cst, ResidueConstraints &residue_constraints, bool object_comparison)
	helper, static More...

std::ostream &	operator<< (std::ostream &os, ConstraintSet const &set)

static basic::Tracer	TR ("core.io.constraints")

static basic::Tracer	TR ("core.io.constraints")

static basic::Tracer	TR ("core.io.constraints")

std::ostream &	operator<< (std::ostream &out, const Func &f)

static basic::Tracer	trMinMultiHarmonicFunc ("fragment.picking.scores.MinMultiHarmonicFunc")

std::ostream &	operator<< (std::ostream &out, Obsolet_NamedAtomPairConstraint const &cst)

static basic::Tracer	non_residue_type_constraint_tracer ("core.scoring.constraints.NonResidueTypeConstraint")

static basic::Tracer	TR ("core.scoring.constraints.ResidueTypeConstraint")

static basic::Tracer	TR ("core.scoring.constraints.ResidueTypeLinkingConstraint")

static basic::Tracer	TR ("core.scoring.constraints.SequenceProfileConstraint")

core::Real	readValueOrDie (std::istream &in)
	Reads and returns a single floating point value from the specified input stream, aborting if either the failbit or badbit is flipped. More...

static numeric::random::RandomGenerator	RG (42015512)

static basic::Tracer	tr ("core.scoring.constraints")

Real	logdgaussian (Real x, Real mean, Real sd, Real weight)
	Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...

Real	logdgaussian_deriv (Real x, Real mean, Real sd, Real)
	Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...

Real	dgaussian (Real x, Real mean, Real sd, Real weight)
	Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...

Real	gaussian_deriv (Real x, Real mean, Real sd, Real weight)
	Returns the weighted derivative of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...

Real	dexponential (Real x, Real anchor, Real rate, Real weight)
	Returns the weighted value of an exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10. More...

Real	exponential_deriv (Real x, Real anchor, Real rate, Real weight)
	Returns the weighted derivative of a log-exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10. More...

Real	linear_interpolate (Real const x_val, Real const x1, Real const x2, Real const y1, Real const y2)
	Estimates the y-value of the given x-value by interpolating between the given points (x1,y1) and (x2,y2) by using linear interpolation between the two points. More...

void	cull_violators (ConstraintCOPs const &target_list, ConstraintCOPs &culled_list, pose::Pose const &filter_pose, core::Real threshold)

std::string	get_cst_file_option ()

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

void	add_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)

void	add_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)

std::string	get_cst_fa_file_option ()

void	add_fa_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
	add constraints if specified by user using the -constraints::cst_fa_file flag. Setting appropriate weights for ScoreFunction is done elsewhere. More...

void	add_fa_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
	add constraints if specified by user. More...

void	add_fa_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
	add constraints if specified by user. More...

void	add_coordinate_constraints (core::pose::Pose &pose, core::Real const coord_sdev=10.0)
	handy function for tethering pose to starting coordinates. More...

bool	combinable (Constraint const &cst, utility::vector1< Size > exclude_res)

void	choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, ConstraintCOPs &in)
	combine constraints randomly into AmbiguousConstraints N -> 1 this greatly decreases the odds to have a wrong constraint More...

core::Size	bin_by_seq_separation (core::Size sep)

void	combine_constraints (ConstraintCOPs &in, core::Size combine_ratio, utility::vector1< bool > exclude_res, core::kinematics::ShortestPathInFoldTree const &sp_in)
	combine constraints randomly into AmbiguousConstraints N -> 1 this greatly decreases the odds to have a wrong constraint More...

void	count_constraint (ConstraintCOP cst, bool redundant, ObjexxFCL::FArray2D_int &count_matrix, Size influence_width, Size total_residue)

bool	keep_constraint (ConstraintCOP cst, bool redundant, ObjexxFCL::FArray2D_int &count_matrix, Size influence_width, Size total_residue)

void	skip_redundant_constraints (ConstraintCOPs &in, core::Size total_residue, core::Size influence_width=1)
	have at most one constraint per residue pair... More...

void	drop_constraints (ConstraintCOPs &in, core::Real drop_rate)

Typedef Documentation

typedef utility::pointer::owning_ptr< AmberPeriodicFunc const > core::scoring::constraints::AmberPeriodicFuncCOP

Definition at line 28 of file AmberPeriodicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< AmberPeriodicFunc > core::scoring::constraints::AmberPeriodicFuncOP

Definition at line 26 of file AmberPeriodicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< AmbiguousConstraint const > core::scoring::constraints::AmbiguousConstraintCOP

Definition at line 27 of file AmbiguousConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AmbiguousConstraint > core::scoring::constraints::AmbiguousConstraintOP

Definition at line 24 of file AmbiguousConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AmbiguousNMRConstraint const > core::scoring::constraints::AmbiguousNMRConstraintCOP

Definition at line 27 of file AmbiguousNMRConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AmbiguousNMRConstraint > core::scoring::constraints::AmbiguousNMRConstraintOP

Definition at line 24 of file AmbiguousNMRConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AmbiguousNMRDistanceConstraint const > core::scoring::constraints::AmbiguousNMRDistanceConstraintCOP

Definition at line 27 of file AmbiguousNMRDistanceConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AmbiguousNMRDistanceConstraint > core::scoring::constraints::AmbiguousNMRDistanceConstraintOP

Definition at line 24 of file AmbiguousNMRDistanceConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AngleConstraint const > core::scoring::constraints::AngleConstraintCOP

Definition at line 27 of file AngleConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AngleConstraint > core::scoring::constraints::AngleConstraintOP

Definition at line 24 of file AngleConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AtomPairConstraint const > core::scoring::constraints::AtomPairConstraintCOP

Definition at line 27 of file AtomPairConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< AtomPairConstraint > core::scoring::constraints::AtomPairConstraintOP

Definition at line 24 of file AtomPairConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< BackboneStubConstraint const > core::scoring::constraints::BackboneStubConstraintCOP

Definition at line 28 of file BackboneStubConstraint.fwd.hh.

typedef utility::vector1< BackboneStubConstraintCOP > core::scoring::constraints::BackboneStubConstraintCOPs

Definition at line 31 of file BackboneStubConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< BackboneStubConstraint > core::scoring::constraints::BackboneStubConstraintOP

Definition at line 25 of file BackboneStubConstraint.fwd.hh.

typedef utility::vector1< BackboneStubConstraintOP > core::scoring::constraints::BackboneStubConstraintOPs

Definition at line 30 of file BackboneStubConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< BoundFunc const > core::scoring::constraints::BoundFuncCOP

Definition at line 28 of file BoundConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< BoundFunc > core::scoring::constraints::BoundFuncOP

Definition at line 26 of file BoundConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< CircularGeneral1D_Func const > core::scoring::constraints::CircularGeneral1D_FuncCOP

Definition at line 28 of file CircularGeneral1D_Func.fwd.hh.

typedef utility::pointer::owning_ptr< CircularGeneral1D_Func > core::scoring::constraints::CircularGeneral1D_FuncOP

Definition at line 26 of file CircularGeneral1D_Func.fwd.hh.

typedef utility::pointer::owning_ptr< CircularHarmonicFunc const > core::scoring::constraints::CircularHarmonicFuncCOP

Definition at line 28 of file CircularHarmonicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< CircularHarmonicFunc > core::scoring::constraints::CircularHarmonicFuncOP

Definition at line 26 of file CircularHarmonicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< CircularPowerFunc const > core::scoring::constraints::CircularPowerFuncCOP

Definition at line 28 of file CircularPowerFunc.fwd.hh.

typedef utility::pointer::owning_ptr< CircularPowerFunc > core::scoring::constraints::CircularPowerFuncOP

Definition at line 26 of file CircularPowerFunc.fwd.hh.

typedef utility::pointer::owning_ptr< CircularSigmoidalFunc const > core::scoring::constraints::CircularSigmoidalFuncCOP

Definition at line 28 of file CircularSigmoidalFunc.fwd.hh.

typedef utility::pointer::owning_ptr< CircularSigmoidalFunc > core::scoring::constraints::CircularSigmoidalFuncOP

Definition at line 26 of file CircularSigmoidalFunc.fwd.hh.

typedef utility::pointer::owning_ptr< ConstantFunc > core::scoring::constraints::ConstantFuncOP

Definition at line 26 of file ConstantFunc.fwd.hh.

typedef utility::pointer::owning_ptr< Constraint const > core::scoring::constraints::ConstraintCOP

Definition at line 31 of file Constraint.fwd.hh.

typedef utility::vector1< ConstraintCOP > core::scoring::constraints::ConstraintCOPs

Definition at line 33 of file Constraint.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintCreator const > core::scoring::constraints::ConstraintCreatorCOP

Definition at line 29 of file ConstraintCreator.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintCreator > core::scoring::constraints::ConstraintCreatorOP

Definition at line 26 of file ConstraintCreator.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintGraph const > core::scoring::constraints::ConstraintGraphCOP

Definition at line 28 of file ConstraintGraph.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintGraph > core::scoring::constraints::ConstraintGraphOP

Definition at line 25 of file ConstraintGraph.fwd.hh.

typedef utility::pointer::owning_ptr< Constraint > core::scoring::constraints::ConstraintOP

Definition at line 28 of file Constraint.fwd.hh.

typedef utility::vector1< ConstraintOP > core::scoring::constraints::ConstraintOPs

Definition at line 32 of file Constraint.fwd.hh.

typedef utility::pointer::owning_ptr< Constraints const > core::scoring::constraints::ConstraintsCOP

Definition at line 25 of file Constraints.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintsEnergy const > core::scoring::constraints::ConstraintsEnergyCOP

Definition at line 28 of file ConstraintsEnergy.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintsEnergy > core::scoring::constraints::ConstraintsEnergyOP

Definition at line 25 of file ConstraintsEnergy.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintSet const > core::scoring::constraints::ConstraintSetCOP

Definition at line 29 of file ConstraintSet.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintSet > core::scoring::constraints::ConstraintSetOP

Definition at line 27 of file ConstraintSet.fwd.hh.

typedef utility::pointer::owning_ptr< Constraints > core::scoring::constraints::ConstraintsOP

Definition at line 23 of file Constraints.fwd.hh.

typedef utility::pointer::owning_ptr< CstEnergyContainer const > core::scoring::constraints::CstEnergyContainerCOP

Definition at line 30 of file ConstraintEnergyContainer.fwd.hh.

typedef utility::pointer::owning_ptr< CstEnergyContainer > core::scoring::constraints::CstEnergyContainerOP

Definition at line 27 of file ConstraintEnergyContainer.fwd.hh.

typedef utility::pointer::owning_ptr< CstMinimizationData const > core::scoring::constraints::CstMinimizationDataCOP

Definition at line 33 of file CstMinimizationData.hh.

typedef utility::pointer::owning_ptr< CstMinimizationData > core::scoring::constraints::CstMinimizationDataOP

Definition at line 31 of file CstMinimizationData.hh.

typedef utility::pointer::owning_ptr< DihedralConstraint const > core::scoring::constraints::DihedralConstraintCOP

Definition at line 27 of file DihedralConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< DihedralConstraint > core::scoring::constraints::DihedralConstraintOP

Definition at line 24 of file DihedralConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< DOF_Constraint const > core::scoring::constraints::DOF_ConstraintCOP

Definition at line 31 of file DOF_Constraint.fwd.hh.

typedef utility::vector1< DOF_ConstraintCOP > core::scoring::constraints::DOF_ConstraintCOPs

Definition at line 33 of file DOF_Constraint.fwd.hh.

typedef utility::pointer::owning_ptr< DOF_Constraint > core::scoring::constraints::DOF_ConstraintOP

Definition at line 28 of file DOF_Constraint.fwd.hh.

typedef utility::vector1< DOF_ConstraintOP > core::scoring::constraints::DOF_ConstraintOPs

Definition at line 32 of file DOF_Constraint.fwd.hh.

typedef utility::pointer::owning_ptr< EtableFunc > core::scoring::constraints::EtableFuncOP

Definition at line 26 of file EtableFunc.fwd.hh.

typedef utility::pointer::owning_ptr< FabConstraint const > core::scoring::constraints::FabConstraintCOP

Definition at line 29 of file FabConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< FabConstraint > core::scoring::constraints::FabConstraintOP

Definition at line 26 of file FabConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< FadeFunc const > core::scoring::constraints::FadeFuncCOP

Definition at line 28 of file FadeFunc.fwd.hh.

typedef utility::pointer::owning_ptr< FadeFunc > core::scoring::constraints::FadeFuncOP

Definition at line 26 of file FadeFunc.fwd.hh.

typedef utility::pointer::owning_ptr< FlatHarmonicFunc const > core::scoring::constraints::FlatHarmonicFuncCOP

Definition at line 28 of file FlatHarmonicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< FlatHarmonicFunc > core::scoring::constraints::FlatHarmonicFuncOP

Definition at line 26 of file FlatHarmonicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< FourPointsFunc const > core::scoring::constraints::FourPointsFuncCOP

Definition at line 27 of file FourPointsFunc.fwd.hh.

typedef utility::pointer::owning_ptr< FourPointsFunc > core::scoring::constraints::FourPointsFuncOP

Definition at line 24 of file FourPointsFunc.fwd.hh.

typedef utility::pointer::owning_ptr< Func > core::scoring::constraints::FuncOP

Definition at line 30 of file Func.fwd.hh.

typedef utility::pointer::owning_ptr< GaussianFunc > core::scoring::constraints::GaussianFuncOP

Definition at line 26 of file GaussianFunc.fwd.hh.

typedef utility::pointer::owning_ptr< HarmonicFunc const > core::scoring::constraints::HarmonicFuncCOP

Definition at line 28 of file HarmonicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< HarmonicFunc > core::scoring::constraints::HarmonicFuncOP

Definition at line 26 of file HarmonicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< IdentityFunc const > core::scoring::constraints::IdentityFuncCOP

Definition at line 28 of file IdentityFunc.fwd.hh.

typedef utility::pointer::owning_ptr< IdentityFunc > core::scoring::constraints::IdentityFuncOP

Definition at line 26 of file IdentityFunc.fwd.hh.

typedef utility::pointer::owning_ptr< KarplusFunc const > core::scoring::constraints::KarplusFuncCOP

Definition at line 28 of file KarplusFunc.fwd.hh.

typedef utility::pointer::owning_ptr< KarplusFunc > core::scoring::constraints::KarplusFuncOP

Definition at line 26 of file KarplusFunc.fwd.hh.

typedef utility::pointer::owning_ptr< KofNConstraint const > core::scoring::constraints::KofNConstraintCOP

Definition at line 28 of file KofNConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< KofNConstraint > core::scoring::constraints::KofNConstraintOP

Definition at line 25 of file KofNConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< LocalCoordinateConstraint const > core::scoring::constraints::LocalCoordinateConstraintCOP

Definition at line 48 of file LocalCoordinateConstraint.hh.

typedef utility::pointer::owning_ptr< LocalCoordinateConstraint > core::scoring::constraints::LocalCoordinateConstraintOP

Definition at line 46 of file LocalCoordinateConstraint.hh.

typedef utility::pointer::owning_ptr< MinMultiHarmonicFunc const > core::scoring::constraints::MinMultiHarmonicFuncCOP

Definition at line 27 of file MinMultiHarmonicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< MinMultiHarmonicFunc > core::scoring::constraints::MinMultiHarmonicFuncOP

Definition at line 25 of file MinMultiHarmonicFunc.fwd.hh.

typedef utility::pointer::owning_ptr< MixtureFunc > core::scoring::constraints::MixtureFuncOP

Definition at line 26 of file MixtureFunc.fwd.hh.

typedef utility::pointer::owning_ptr< MultiConstraint const > core::scoring::constraints::MultiConstraintCOP

Definition at line 27 of file MultiConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< MultiConstraint > core::scoring::constraints::MultiConstraintOP

Definition at line 24 of file MultiConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< NamedAtomPairConstraint const > core::scoring::constraints::NamedAtomPairConstraintCOP

Definition at line 27 of file NamedAtomPairConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< NamedAtomPairConstraint > core::scoring::constraints::NamedAtomPairConstraintOP

Definition at line 24 of file NamedAtomPairConstraint.fwd.hh.

typedef utility::vector1< core::id::NamedAtomID > core::scoring::constraints::NamedAtoms

Definition at line 213 of file AmbiguousNMRDistanceConstraint.hh.

typedef utility::pointer::owning_ptr< NonResidueTypeConstraint const > core::scoring::constraints::NonResidueTypeConstraintCOP

Definition at line 28 of file NonResidueTypeConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< NonResidueTypeConstraint > core::scoring::constraints::NonResidueTypeConstraintOP

Definition at line 26 of file NonResidueTypeConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< Obsolet_NamedAtomPairConstraint const > core::scoring::constraints::Obsolet_NamedAtomPairConstraintCOP

Definition at line 32 of file NamedAtomPairConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< Obsolet_NamedAtomPairConstraint > core::scoring::constraints::Obsolet_NamedAtomPairConstraintOP

Definition at line 29 of file NamedAtomPairConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueConstraints const > core::scoring::constraints::ResidueConstraintsCOP

Definition at line 25 of file ConstraintSet.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueConstraints > core::scoring::constraints::ResidueConstraintsOP

Definition at line 23 of file ConstraintSet.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueTypeConstraint const > core::scoring::constraints::ResidueTypeConstraintCOP

Definition at line 28 of file ResidueTypeConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueTypeConstraint > core::scoring::constraints::ResidueTypeConstraintOP

Definition at line 26 of file ResidueTypeConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueTypeLinkingConstraint const > core::scoring::constraints::ResidueTypeLinkingConstraintCOP

Definition at line 29 of file ResidueTypeLinkingConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueTypeLinkingConstraint > core::scoring::constraints::ResidueTypeLinkingConstraintOP

Definition at line 27 of file ResidueTypeLinkingConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< ScalarWeightedFunc const > core::scoring::constraints::ScalarWeightedFuncCOP

Definition at line 31 of file ScalarWeightedFunc.fwd.hh.

typedef utility::pointer::owning_ptr< ScalarWeightedFunc > core::scoring::constraints::ScalarWeightedFuncOP

Definition at line 29 of file ScalarWeightedFunc.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceProfileConstraint const > core::scoring::constraints::SequenceProfileConstraintCOP

Definition at line 25 of file SequenceProfileConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceProfileConstraint > core::scoring::constraints::SequenceProfileConstraintOP

Definition at line 23 of file SequenceProfileConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< SiteConstraint const > core::scoring::constraints::SiteConstraintCOP

Definition at line 28 of file SiteConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< SiteConstraint > core::scoring::constraints::SiteConstraintOP

Definition at line 25 of file SiteConstraint.fwd.hh.

typedef utility::pointer::owning_ptr< SiteConstraintResidues const > core::scoring::constraints::SiteConstraintResiduesCOP

Definition at line 28 of file SiteConstraintResidues.fwd.hh.

typedef utility::pointer::owning_ptr< SiteConstraintResidues > core::scoring::constraints::SiteConstraintResiduesOP

Definition at line 25 of file SiteConstraintResidues.fwd.hh.

typedef utility::pointer::owning_ptr< SoedingFunc > core::scoring::constraints::SoedingFuncOP

Definition at line 26 of file SoedingFunc.fwd.hh.

typedef utility::pointer::owning_ptr< SOGFunc_Impl > core::scoring::constraints::SOGFunc_ImplOP

Definition at line 26 of file SOGFunc_Impl.fwd.hh.

typedef utility::pointer::owning_ptr< SOGFunc > core::scoring::constraints::SOGFuncOP

Definition at line 26 of file SOGFunc.fwd.hh.

typedef utility::pointer::owning_ptr< SplineFunc const > core::scoring::constraints::SplineFuncCOP

Definition at line 26 of file SplineFunc.fwd.hh.

typedef utility::pointer::owning_ptr< SplineFunc > core::scoring::constraints::SplineFuncOP

Definition at line 24 of file SplineFunc.fwd.hh.

typedef utility::pointer::owning_ptr< SquareWell2Func const > core::scoring::constraints::SquareWell2FuncCOP

Definition at line 29 of file SquareWell2Func.fwd.hh.

typedef utility::pointer::owning_ptr< SquareWell2Func > core::scoring::constraints::SquareWell2FuncOP

Definition at line 27 of file SquareWell2Func.fwd.hh.

typedef utility::pointer::owning_ptr< SquareWellFunc const > core::scoring::constraints::SquareWellFuncCOP

Definition at line 28 of file SquareWellFunc.fwd.hh.

typedef utility::pointer::owning_ptr< SquareWellFunc > core::scoring::constraints::SquareWellFuncOP

Definition at line 26 of file SquareWellFunc.fwd.hh.

typedef utility::pointer::owning_ptr< SumFunc > core::scoring::constraints::SumFuncOP

Definition at line 30 of file SumFunc.fwd.hh.

typedef utility::pointer::owning_ptr< TopOutFunc const > core::scoring::constraints::TopOutFuncCOP

Definition at line 28 of file TopOutFunc.fwd.hh.

typedef utility::pointer::owning_ptr< TopOutFunc > core::scoring::constraints::TopOutFuncOP

Definition at line 26 of file TopOutFunc.fwd.hh.

typedef utility::pointer::owning_ptr<USOGFunc const> core::scoring::constraints::USOGFuncCOP

Definition at line 24 of file USOGFunc.fwd.hh.

typedef utility::pointer::owning_ptr<USOGFunc> core::scoring::constraints::USOGFuncOP

Definition at line 22 of file USOGFunc.fwd.hh.

Function Documentation

void core::scoring::constraints::add_constraint_to_residue_constraints	(	int const	seqpos,
		ConstraintCOP	cst,
		ResidueConstraints &	residue_constraints
	)

helper, static

Definition at line 480 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::find(), core::scoring::constraints::ResidueConstraints::has(), and core::scoring::constraints::ResidueConstraints::insert().

Referenced by core::scoring::constraints::ConstraintSet::add_constraint(), and core::scoring::constraints::ConstraintSet::add_residue_pair_constraint().

void core::scoring::constraints::add_constraints_from_cmdline	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction &	scorefxn_
	)

Definition at line 199 of file util.cc.

References add_constraints_from_cmdline_to_pose(), and add_constraints_from_cmdline_to_scorefxn().

Referenced by protocols::rbsegment_relax::AutoRBMover::apply(), protocols::cluster::GatherPosesMover::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), and OPT_1GRP_KEY().

void core::scoring::constraints::add_constraints_from_cmdline_to_pose ( core::pose::Pose & pose)

Definition at line 178 of file util.cc.

References core::pose::Pose::constraint_set(), get_cst_file_option(), core::scoring::constraints::ConstraintIO::get_instance(), and core::scoring::constraints::ConstraintIO::read_constraints().

Referenced by add_constraints_from_cmdline(), protocols::medal::MedalMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::star::setup_constraints(), and protocols::jobdist::universal_main().

void core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction & scorefxn_)

Definition at line 188 of file util.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, and core::scoring::ScoreFunction::set_weight().

Referenced by add_constraints_from_cmdline(), protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::floppy_tail::FloppyTailMover::FloppyTailMover(), protocols::flxbb::FlxbbDesign_main(), protocols::relax::generate_relax_from_cmd(), protocols::medal::MedalMover::score_function(), and protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions().

void core::scoring::constraints::add_coordinate_constraints	(	pose::Pose &	pose,
		Real const	coord_sdev
	)

handy function for tethering pose to starting coordinates.

Definition at line 252 of file util.cc.

References core::pose::Pose::constraint_set(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::rna::RNA_Minimizer::apply(), protocols::swa::protein::StepWiseProteinPoseMinimizer::apply(), protocols::swa::rna::minimize_with_constraints(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints(), and protocols::rna::RNA_LoopCloser::tight_minimize().

void core::scoring::constraints::add_fa_constraints_from_cmdline	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction &	scorefxn_
	)

add constraints if specified by user.

Definition at line 242 of file util.cc.

References add_fa_constraints_from_cmdline_to_pose(), and add_fa_constraints_from_cmdline_to_scorefxn().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), and protocols::abinitio::AbrelaxApplication::relax().

void core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose ( core::pose::Pose & pose)

add constraints if specified by user using the -constraints::cst_fa_file flag. Setting appropriate weights for ScoreFunction is done elsewhere.

add constraints if specified by user.

Definition at line 218 of file util.cc.

References core::pose::Pose::constraint_set(), get_cst_fa_file_option(), core::scoring::constraints::ConstraintIO::get_instance(), and core::scoring::constraints::ConstraintIO::read_constraints().

Referenced by add_fa_constraints_from_cmdline(), protocols::floppy_tail::FloppyTailMover::apply(), and protocols::jobdist::universal_main().

void core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction & scorefxn_)

add constraints if specified by user.

Definition at line 230 of file util.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, and core::scoring::ScoreFunction::set_weight().

Referenced by protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators(), add_fa_constraints_from_cmdline(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::floppy_tail::FloppyTailMover::FloppyTailMover(), protocols::flxbb::FlxbbDesign_main(), protocols::relax::generate_relax_from_cmd(), protocols::hybridization::HybridizeProtocol::init(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), and protocols::relax::WorkUnit_BatchRelax::run().

core::Size core::scoring::constraints::bin_by_seq_separation ( core::Size sep)

inline

Definition at line 300 of file util.cc.

Referenced by combine_constraints().

void core::scoring::constraints::choose_effective_sequence_separation	(	core::kinematics::ShortestPathInFoldTree const &	sp,
		ConstraintCOPs &	in
	)

combine constraints randomly into AmbiguousConstraints N -> 1 this greatly decreases the odds to have a wrong constraint

call this on your constraints if you have MultiConstraints before running Abinitio – already done by broker-type application

Definition at line 292 of file util.cc.

References core::scoring::constraints::Constraint::choose_effective_sequence_separation(), and RG().

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), and protocols::constraints_additional::ConstraintEvaluator::prepare_pose().

bool core::scoring::constraints::combinable	(	Constraint const &	cst,
		utility::vector1< Size >	exclude_res
	)

Definition at line 278 of file util.cc.

References core::scoring::constraints::Constraint::residues().

Referenced by combine_constraints().

void core::scoring::constraints::combine_constraints	(	ConstraintCOPs &	in,
		core::Size	combine_ratio,
		utility::vector1< bool >	exclude_res,
		core::kinematics::ShortestPathInFoldTree const &	sp_in
	)

combine constraints randomly into AmbiguousConstraints N -> 1 this greatly decreases the odds to have a wrong constraint

combine constraints randomly into Ambiguous constraints...

Definition at line 308 of file util.cc.

References bin_by_seq_separation(), combinable(), RG(), and tr().

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), and protocols::constraints_additional::ConstraintEvaluator::prepare_pose().

void core::scoring::constraints::combine_NMR_atom_string	(	AmbiguousNMRDistanceConstraint::Atoms	atoms,
		std::string &	atom_str,
		pose::Pose const &	pose
	)

Definition at line 649 of file AmbiguousNMRDistanceConstraint.cc.

References core::conformation::Residue::atom_name(), core::pose::Pose::residue(), and tr().

Referenced by core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CEN(), and core::scoring::constraints::AmbiguousNMRDistanceConstraint::show_def().

void core::scoring::constraints::count_constraint	(	ConstraintCOP	cst,
		bool	redundant,
		ObjexxFCL::FArray2D_int &	count_matrix,
		Size	influence_width,
		Size	total_residue
	)

Definition at line 371 of file util.cc.

References tr().

Referenced by skip_redundant_constraints().

void core::scoring::constraints::cull_violators	(	ConstraintCOPs const &	target_list,
		ConstraintCOPs &	culled_list,
		pose::Pose const &	filter_pose,
		core::Real	threshold
	)

Definition at line 151 of file util.cc.

References tr().

Referenced by protocols::abinitio::AbrelaxApplication::add_constraints().

Real core::scoring::constraints::dexponential	(	Real	x,
		Real	anchor,
		Real	rate,
		Real	weight
	)

Returns the weighted value of an exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10.

Returns the weighted value of an Exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10.

Definition at line 108 of file util.cc.

Referenced by core::scoring::constraints::MixtureFunc::dfunc_component(), and core::scoring::constraints::MixtureFunc::func_().

Real core::scoring::constraints::dgaussian	(	Real	x,
		Real	mean,
		Real	sd,
		Real	weight
	)

Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

Definition at line 77 of file util.cc.

Referenced by core::scoring::constraints::SoedingFunc::compute_func(), core::scoring::constraints::MixtureFunc::dfunc_component(), core::scoring::constraints::GaussianFunc::func(), core::scoring::disulfides::Cb_Distance_Func::func(), core::scoring::constraints::MixtureFunc::func_(), gaussian_deriv(), core::scoring::constraints::USOGFunc::gaussianScore(), core::scoring::constraints::SOGFunc_Impl::get_alt_score_(), and core::scoring::constraints::SOGFunc_Impl::prob_sum_of_gaussians().

void core::scoring::constraints::drop_constraints	(	ConstraintCOPs &	in,
		core::Real	drop_rate
	)

Definition at line 484 of file util.cc.

References RG().

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints().

Real core::scoring::constraints::exponential_deriv	(	Real	x,
		Real	anchor,
		Real	rate,
		Real	weight
	)

Returns the weighted derivative of a log-exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10.

Returns the weighted derivative of an Exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10.

Definition at line 123 of file util.cc.

Referenced by core::scoring::constraints::MixtureFunc::dfunc_component().

Real core::scoring::constraints::gaussian_deriv	(	Real	x,
		Real	mean,
		Real	sd,
		Real	weight
	)

Returns the weighted derivative of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

Returns the weighted derivative of a Gaussian distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

Definition at line 92 of file util.cc.

References dgaussian().

Referenced by core::scoring::constraints::GaussianFunc::dfunc(), and core::scoring::constraints::MixtureFunc::dfunc_component().

std::string core::scoring::constraints::get_cst_fa_file_option ( )

Definition at line 205 of file util.cc.

References RG(), and tr().

Referenced by add_fa_constraints_from_cmdline_to_pose(), protocols::abinitio::AbrelaxApplication::fold(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::topology_broker::ConstraintClaimer::new_decoy(), protocols::relax::Relax_main(), and protocols::relax::WorkUnit_BatchRelax::run().

std::string core::scoring::constraints::get_cst_file_option ( )

Definition at line 168 of file util.cc.

References RG(), and tr().

Referenced by protocols::abinitio::AbrelaxApplication::add_constraints(), add_constraints_from_cmdline_to_pose(), protocols::topology_broker::ConstraintClaimer::new_decoy(), and protocols::relax::Relax_main().

std::string core::scoring::constraints::get_section_name ( std::string line)

Definition at line 395 of file ConstraintIO.cc.

References protocols::loops::start.

Referenced by core::scoring::constraints::ConstraintIO::read_constraints().

bool core::scoring::constraints::is_aromatic	(	pose::Pose const &	pose,
		core::Size	res
	)

inline

Definition at line 92 of file AmbiguousNMRDistanceConstraint.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_phe, core::chemical::aa_trp, core::chemical::aa_tyr, and core::pose::Pose::residue_type().

Referenced by parse_NMR_name(), and parse_NMR_name_old().

bool core::scoring::constraints::is_aromatic ( core::chemical::AA aa)

Definition at line 99 of file AmbiguousNMRDistanceConstraint.cc.

References core::chemical::aa_his, core::chemical::aa_phe, core::chemical::aa_trp, and core::chemical::aa_tyr.

bool core::scoring::constraints::keep_constraint	(	ConstraintCOP	cst,
		bool	redundant,
		ObjexxFCL::FArray2D_int &	count_matrix,
		Size	influence_width,
		Size	total_residue
	)

Definition at line 395 of file util.cc.

References tr().

Referenced by skip_redundant_constraints().

Real core::scoring::constraints::linear_interpolate	(	Real const	x_val,
		Real const	x1,
		Real const	x2,
		Real const	y1,
		Real const	y2
	)

Estimates the y-value of the given x-value by interpolating between the given points (x1,y1) and (x2,y2) by using linear interpolation between the two points.

Definition at line 133 of file util.cc.

Referenced by protocols::medal::MedalMover::apply(), and core::scoring::constraints::EtableFunc::func().

Real core::scoring::constraints::logdgaussian	(	Real	x,
		Real	mean,
		Real	sd,
		Real	weight
	)

Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

Returns the log of the weighted value of a Gaussian distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

Definition at line 53 of file util.cc.

Referenced by core::scoring::constraints::GaussianFunc::func().

Real core::scoring::constraints::logdgaussian_deriv	(	Real	x,
		Real	mean,
		Real	sd,
		Real
	)

Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

Returns the log of the weighted value of a Gaussian distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10.

Definition at line 66 of file util.cc.

Referenced by core::scoring::constraints::GaussianFunc::dfunc().

static basic::Tracer core::scoring::constraints::non_residue_type_constraint_tracer ( "core.scoring.constraints.NonResidueTypeConstraint" )

static

std::ostream& core::scoring::constraints::operator<<	(	std::ostream &	out,
		const Func &	f
	)

Definition at line 87 of file Func.cc.

References core::scoring::constraints::Func::show().

std::ostream& core::scoring::constraints::operator<<	(	std::ostream &	out,
		Obsolet_NamedAtomPairConstraint const &	cst
	)

Definition at line 213 of file NamedAtomPairConstraint.cc.

References core::scoring::constraints::Obsolet_NamedAtomPairConstraint::atom1_, core::scoring::constraints::Obsolet_NamedAtomPairConstraint::atom2_, and core::scoring::constraints::Obsolet_NamedAtomPairConstraint::cst_.

std::ostream& core::scoring::constraints::operator<<	(	std::ostream &	out,
		Constraint &	cst
	)

inline

Definition at line 327 of file Constraint.hh.

References core::scoring::constraints::Constraint::show().

std::ostream & core::scoring::constraints::operator<<	(	std::ostream &	os,
		ConstraintSet const &	set
	)

Definition at line 982 of file ConstraintSet.cc.

References core::scoring::constraints::ConstraintSet::show().

void core::scoring::constraints::parse_NMR_name	(	std::string	name,
		core::Size	res,
		core::chemical::AA	aa,
		NamedAtoms &	atoms
	)

Definition at line 105 of file AmbiguousNMRDistanceConstraint.cc.

Referenced by core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint(), parse_NMR_name(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::read_def(), and protocols::noesy_assign::ResonanceList::read_from_stream().

void core::scoring::constraints::parse_NMR_name	(	std::string	name,
		core::Size	res,
		AmbiguousNMRDistanceConstraint::Atoms &	atoms,
		core::pose::Pose const &	pose
	)

Definition at line 342 of file AmbiguousNMRDistanceConstraint.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_his, core::pose::Pose::is_fullatom(), core::pose::named_atom_id_to_atom_id(), core::conformation::named_atom_id_to_atom_id(), parse_NMR_name(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void core::scoring::constraints::parse_NMR_name_old	(	std::string	name,
		core::Size	res,
		AmbiguousNMRDistanceConstraint::Atoms &	atoms,
		core::pose::Pose const &	pose
	)

Definition at line 377 of file AmbiguousNMRDistanceConstraint.cc.

core::Real core::scoring::constraints::readValueOrDie ( std::istream & in)

Reads and returns a single floating point value from the specified input stream, aborting if either the failbit or badbit is flipped.

Definition at line 107 of file USOGFunc.cc.

Referenced by core::scoring::constraints::USOGFunc::read_data().

bool core::scoring::constraints::remove_constraint_from_residue_constraints	(	int const	seqpos,
		ConstraintCOP	cst,
		ResidueConstraints &	residue_constraints,
		bool	object_comparison
	)

helper, static

Definition at line 542 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::erase(), core::scoring::constraints::ResidueConstraints::find(), and core::scoring::constraints::ResidueConstraints::has().

Referenced by core::scoring::constraints::ConstraintSet::remove_constraint(), and core::scoring::constraints::ConstraintSet::remove_residue_pair_constraint().

bool core::scoring::constraints::requires_CB_mapping	(	AmbiguousNMRDistanceConstraint::Atoms	atoms,
		pose::Pose const &	pose
	)

Definition at line 629 of file AmbiguousNMRDistanceConstraint.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_gly, core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_is_backbone(), and core::pose::Pose::residue_type().

Referenced by core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CEN().

static numeric::random::RandomGenerator core::scoring::constraints::RG ( 42015512 )

static

Referenced by choose_effective_sequence_separation(), combine_constraints(), drop_constraints(), get_cst_fa_file_option(), get_cst_file_option(), and skip_redundant_constraints().

void core::scoring::constraints::skip_redundant_constraints	(	ConstraintCOPs &	in,
		Size	total_residue,
		Size	influence_width
	)

have at most one constraint per residue pair...

Definition at line 421 of file util.cc.

References count_constraint(), keep_constraint(), protocols::rigid::random, RG(), and tr().

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::abinitio::IterativeBase::gen_noe_assignments(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::abinitio::IterativeBase::register_options(), protocols::abinitio::IterativeBase::replace_noesy_filter_constraints(), and protocols::abinitio::IterativeBase::restore_status().

static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.ResidueTypeLinkingConstraint" )

static

static basic::Tracer core::scoring::constraints::TR ( "core.io.constraints" )

static

static basic::Tracer core::scoring::constraints::TR ( "core.io.constraints" )

static

static basic::Tracer core::scoring::constraints::TR ( "core.io.constraints" )

static

static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.ResidueTypeConstraint" )

static

static basic::Tracer core::scoring::constraints::tr ( "core.scoring.constraints" )

static

static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.BackboneStubConstraint" )

static

static basic::Tracer core::scoring::constraints::tr ( "core.scoring.ConstraintSet" )

static

static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.SequenceProfileConstraint" )

static

static basic::Tracer core::scoring::constraints::tr ( "core.scoring.ConstraintsEnergy" )

static

static basic::Tracer core::scoring::constraints::TRACER ( "core.io.constraints" )

static

Referenced by core::scoring::constraints::AngleConstraint::read_def().

static basic::Tracer core::scoring::constraints::trMinMultiHarmonicFunc ( "fragment.picking.scores.MinMultiHarmonicFunc" )

static

Referenced by core::scoring::constraints::MinMultiHarmonicFunc::read_data().

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation