Classes
class	AmbiguousConstraint

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

class	AmbiguousNMRConstraint

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

class	AmbiguousNMRDistanceConstraint

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

class	AngleConstraint
	An Angular Constraint. More...

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

class	AtomPairConstraint

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

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

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

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

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

class	BoundFunc

class	ConstantConstraint
	A Constant Constraint. 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	ConstraintEdge

class	ConstraintFactory

class	ConstraintGraph

class	ConstraintIO

class	ConstraintNode

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	Constraints

class	ConstraintsEnergy

class	ConstraintsEnergyCreator

class	ConstraintSet

class	CoordinateConstraint

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

class	CstEnergyContainer

class	CstMinimizationData

class	CstResNeighbConstIterator

class	CstResNeighbIterator

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

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

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

class	DihedralPairConstraintCreator
	Constraint creator for DihedralPairConstraint. 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	FabConstraint

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

class	KofNConstraint

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

class	LocalCoordinateConstraint

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

class	MultiConstraint

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

class	NamedAtomPairConstraint

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

class	Obsolet_NamedAtomPairConstraint

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

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

class	ResidueConstraints

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	SequenceProfileConstraint

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

class	SiteConstraint

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

class	SiteConstraintResidues

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

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::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 < BackboneStubLinearConstraint >	BackboneStubLinearConstraintOP

typedef utility::pointer::owning_ptr < BackboneStubLinearConstraint const >	BackboneStubLinearConstraintCOP

typedef utility::vector1 < BackboneStubLinearConstraintOP >	BackboneStubLinearConstraintOPs

typedef utility::vector1 < BackboneStubLinearConstraintCOP >	BackboneStubLinearConstraintCOPs

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

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

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 < FabConstraint >	FabConstraintOP

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

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 < 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 < 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

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)

std::map< std::string, core::id::AtomID >	auto_detect_atoms (pose::Pose const &pose, Size const seqpos)

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

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

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)

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

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. 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	merge_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
	merge cmdline constraints to pre-existing constraints More...

void	merge_csts_to_scorefunction (core::Real const weight, core::scoring::ScoreFunction &scorefxn_)

void	merge_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
	merge cmdline constraints to pre-existing constraints - only adds to ZERO weights; previously nonzero constraint weights are unmodified and a warning is issued More...

void	merge_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
	merge cmdline constraints to pre-existing constraints More...

void	merge_fa_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
	merge cmdline constraints to pre-existing constraints More...

void	merge_fa_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
	merge cmdline constraints to pre-existing constraints - only adds to ZERO weights; previously nonzero constraint weights are unmodified and a warning is issued More...

void	merge_fa_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
	merge cmdline constraints to pre-existing constraints More...

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

void	add_coordinate_constraints (core::pose::Pose &pose, core::Size const start_res, core::Size const end_res, core::Real const coord_sdev=10.0, bool include_sc=true)
	Add coordinate constraints for starting coordinates, start:end residues, inclusive. More...

void	remove_constraints_of_type (core::pose::Pose &pose, std::string const type)
	Remove all constraints of a given type from a pose. More...

void	remove_constraints_of_type (core::pose::Pose &pose, std::string const type, core::Size const start_res, core::Size const end_res)
	Remove all constraints of a given type from a pose that involve start_res to end_res. Useful for coordinate/dihedral constraints. More...

void	remove_nonbb_constraints (pose::Pose &pose)

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)

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

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

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

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

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

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

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

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

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.util")

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< BackboneStubLinearConstraint const > core::scoring::constraints::BackboneStubLinearConstraintCOP

typedef utility::vector1< BackboneStubLinearConstraintCOP > core::scoring::constraints::BackboneStubLinearConstraintCOPs

typedef utility::pointer::owning_ptr< BackboneStubLinearConstraint > core::scoring::constraints::BackboneStubLinearConstraintOP

typedef utility::vector1< BackboneStubLinearConstraintOP > core::scoring::constraints::BackboneStubLinearConstraintOPs

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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(), 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_
	)

add constraints from command line to SCOREFUNCTION AND POSE BOTH, if cst file is supplied by user. Overwrites any constraints present in either. Assumed to be "centroid constraints" using cst_file & cst_weight (will work fine with fa constraints, but uses the not-fa command line options).

References add_constraints_from_cmdline_to_pose(), and add_constraints_from_cmdline_to_scorefxn().

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

add constraints from command line to POSE ONLY, if cst file is supplied by user. Overwrites any constraints already in the Pose. Assumed to be "centroid constraints" using the cst_file flag (will work fine with fa constraints, but uses the not-fa command line option).

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

Referenced by add_constraints_from_cmdline().

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

add constraints from command line to SCOREFUNCTION ONLY, if cst file is supplied by user. Overwrites any constraint weights already in the scorefunction. Assumed to be "centroid constraints" using the cst_weight flag (will work fine with fa constraints, but uses the not-fa command line option).

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

Referenced by add_constraints_from_cmdline().

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

handy function for tethering pose to starting coordinates.

References core::pose::Pose::constraint_set(), core::pose::Pose::fold_tree(), core::conformation::Residue::last_backbone_atom(), nres, core::pose::Pose::residue(), core::kinematics::FoldTree::root(), and core::pose::Pose::total_residue().

void core::scoring::constraints::add_coordinate_constraints	(	pose::Pose &	pose,
		core::Size const	start_res,
		core::Size const	end_res,
		Real const	coord_sdev,
		bool	include_sc
	)

Add coordinate constraints for starting coordinates, start:end residues, inclusive.

References core::pose::Pose::constraint_set(), core::pose::Pose::fold_tree(), core::conformation::Residue::last_backbone_atom(), core::pose::Pose::residue(), and core::kinematics::FoldTree::root().

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

add constraints if specified by user.

add constraints from command line to SCOREFUNCTION AND POSE BOTH, if cst file is supplied by user. Overwrites any constraints present in either. Assumed to be "fullatom constraints" because it uses the cst_fa_file & cst_fa_weight flags, but will work with centroids otherwise.

References add_fa_constraints_from_cmdline_to_pose(), and add_fa_constraints_from_cmdline_to_scorefxn().

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

add constraints if specified by user.

add constraints from command line to POSE ONLY, if cst file is supplied by user. Overwrites any constraints already in the Pose. Assumed to be "fullatom constraints" using the cst_fa_file flag (will work fine with centroid constraints otherwise)

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

Referenced by add_fa_constraints_from_cmdline().

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

add constraints if specified by user.

add constraints from command line to SCOREFUNCTION ONLY, if cst file is supplied by user. Overwrites any constraint weights already in the scorefunction. Assumed to be "fullatom constraints" because it uses the cst_fa_weight flag, but will work with centroids otherwise.

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

Referenced by add_fa_constraints_from_cmdline().

std::map< std::string, core::id::AtomID > core::scoring::constraints::auto_detect_atoms	(	pose::Pose const &	pose,
		Size const	seqpos
	)

References j, core::pose::Pose::residue(), and tr.

Referenced by core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint().

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(), cst, and RG.

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

References core::scoring::constraints::Constraint::residues(), and runtime_assert.

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(), out, random_permutation(), RG, and tr.

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(), basic::NOESY_ASSIGN_NMR_STRING, 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
	)

References j, and 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.

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

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

References out, RG, and numeric::random::RandomGenerator::uniform().

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::func::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::func::GaussianFunc::dfunc(), and core::scoring::func::MixtureFunc::dfunc_component().

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

References option, numeric::random::RandomGenerator::random_range(), RG, and tr.

Referenced by add_fa_constraints_from_cmdline_to_pose(), and merge_fa_constraints_from_cmdline_to_pose().

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

References option, numeric::random::RandomGenerator::random_range(), RG, and tr.

Referenced by add_constraints_from_cmdline_to_pose(), and merge_constraints_from_cmdline_to_pose().

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

References start.

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 parse_NMR_name(), and parse_NMR_name_old().

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

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
	)

References j, and 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.

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.

References log().

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

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

merge cmdline constraints to pre-existing constraints

perform both pose and scorefunction updates in merge mode for centroid flags -cst_file and -cst_weight

References merge_constraints_from_cmdline_to_pose(), and merge_constraints_from_cmdline_to_scorefxn().

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

merge cmdline constraints to pre-existing constraints

merge centroid constraints from commandline (cst_file) to pose: read the user-specified constraints file, and merge those to the Pose's ConstraintSet. Creates a ConstraintSet normally, then merges it to the Pose's set.

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

Referenced by merge_constraints_from_cmdline().

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

merge cmdline constraints to pre-existing constraints - only adds to ZERO weights; previously nonzero constraint weights are unmodified and a warning is issued

"merge" constraint weights for scorefunction. I don't know what "merge" means here, so it will only modify the zero weights; nonzero weights are untouched. Reads -cst_weight from command line, and sets nonzero constraint weights to the new value

References merge_csts_to_scorefunction(), option, and user.

Referenced by merge_constraints_from_cmdline().

void core::scoring::constraints::merge_csts_to_scorefunction	(	core::Real const	weight,
		core::scoring::ScoreFunction &	scorefxn_
	)

weight merging helper function - only sets previously-nonzero weights!

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

Referenced by merge_constraints_from_cmdline_to_scorefxn(), and merge_fa_constraints_from_cmdline_to_scorefxn().

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

merge cmdline constraints to pre-existing constraints

perform both pose and scorefunction updates in merge mode for centroid flags -cst_fa_file and -cst_fa_weight

References merge_fa_constraints_from_cmdline_to_pose(), and merge_fa_constraints_from_cmdline_to_scorefxn().

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

merge cmdline constraints to pre-existing constraints

merge fullatom constraints from commandline (cst_fa_file) to pose: read the user-specified constraints file, and merge those to the Pose's ConstraintSet. Creates a ConstraintSet normally, then merges it to the Pose's set.

FA constraints (merge mode)

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

Referenced by merge_fa_constraints_from_cmdline().

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

merge cmdline constraints to pre-existing constraints - only adds to ZERO weights; previously nonzero constraint weights are unmodified and a warning is issued

"merge" constraint weights for scorefunction. I don't know what "merge" means here, so it will only modify the zero weights; nonzero weights are untouched. Reads -cst_fa_weight from command line, and sets nonzero constraint weights to the new value

References merge_csts_to_scorefunction(), option, and user.

Referenced by merge_fa_constraints_from_cmdline().

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

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

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

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

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
	)

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

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(), runtime_assert, 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
	)

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(), and core::scoring::constraints::ConstraintSet::remove_residue_pair_constraint().

void core::scoring::constraints::remove_constraints_of_type	(	core::pose::Pose &	pose,
		std::string const	type
	)

Remove all constraints of a given type from a pose.

References core::pose::Pose::constraint_set(), and core::pose::Pose::remove_constraint().

void core::scoring::constraints::remove_constraints_of_type	(	core::pose::Pose &	pose,
		std::string const	type,
		core::Size const	start_res,
		core::Size const	end_res
	)

Remove all constraints of a given type from a pose that involve start_res to end_res. Useful for coordinate/dihedral constraints.

References core::pose::Pose::constraint_set(), core::pose::Pose::remove_constraint(), and residues.

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

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

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(), basic::NOESY_ASSIGN_REQUIRES_CB_MAPPING, core::pose::Pose::residue_type(), and runtime_assert.

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

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(), j, keep_constraint(), out, random_permutation(), RG, and tr.

Variable Documentation

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

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().

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

static

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

static

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

static

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

static

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

static

basic::Tracer core::scoring::constraints::TR("core.scoring.constraints.BackboneStubLinearConstraint")

static

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

static

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

static

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

static

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

static

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

static

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

static

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

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation