Classes
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	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	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	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	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	SquareWellFunc
class	SumFunc
class	TopOutFunc
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 < 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::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 < 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 < 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 < 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 < 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
Functions
bool	is_aromatic (pose::Pose const &pose, core::Size res)
void	parse_NMR_name (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
bool	remove_constraint_from_residue_constraints (int const seqpos, ConstraintCOP cst, ResidueConstraints &residue_constraints, bool object_comparison)
	helper, static
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")
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.
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.
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.
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.
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.
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.
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.
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
void	add_fa_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
	add constraints if specified by user.
void	add_fa_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
	add constraints if specified by user.
void	add_coordinate_constraints (core::pose::Pose &pose)
	handy function for tethering pose to starting coordinates.
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
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
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...

Typedef Documentation

Function Documentation

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

helper, static

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().

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

References add_constraints_from_cmdline_to_pose(), and add_constraints_from_cmdline_to_scorefxn().

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

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

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::star::setup_constraints(), and protocols::jobdist::universal_main().

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

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::flxbb::FlxbbDesign_main(), protocols::relax::generate_relax_from_cmd(), and protocols::medal::MedalMover::score_function().

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

handy function for tethering pose to starting coordinates.

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::swa::protein::StepWiseProteinPoseMinimizer::apply(), protocols::rna::RNA_Minimizer::apply(), protocols::swa::rna::minimize_with_constraints(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints().

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

add constraints if specified by user.

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

add constraints if specified by user.

-constraints::cst_fa_file flag. Setting appropriate weights for ScoreFunction is done elsewhere.

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(), 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.

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::flxbb::FlxbbDesign_main(), protocols::relax::generate_relax_from_cmd(), protocols::comparative_modeling::hybridize::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]

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

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

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

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

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...

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

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

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

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

Referenced by core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CB(), 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
	)

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
	)

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.

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.

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

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.

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.

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 ( )

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(), and protocols::relax::Relax_main().

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

References RG(), and tr().

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

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

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

bool core::scoring::constraints::is_aromatic	(	pose::Pose const &	pose,
		core::Size	res
	)		`[inline]`

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 core::scoring::hackelec::HackElecEnergyAroAro::evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergyAroAll::evaluate_rotamer_background_energies(), and parse_NMR_name().

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

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.

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.

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.

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,
		Obsolet_NamedAtomPairConstraint const &	cst
	)

std::ostream& core::scoring::constraints::operator<<	(	std::ostream &	out,
		Constraint &	cst
	)		`[inline]`

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

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

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

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

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

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

helper, static

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().

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

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_CB().

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

Referenced by choose_effective_sequence_separation(), combine_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...

References count_constraint(), keep_constraint(), core::scoring::constraints::MultiConstraint::member_constraints(), protocols::rigid::random, RG(), and tr().

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

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

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

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

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

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