core::scoring::constraints Namespace Reference

Classes
class	AmbiguousConstraint
	Nested constraint where only the one with lowest energy is considered. More...
class	AmbiguousNMRConstraint
class	AmbiguousNMRDistanceConstraint
class	AngleConstraint
	An Angular Constraint. More...
class	AtomPairConstraint
struct	XYZs
class	AtomToAxisConstraint
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	BasePairConstraint
class	AtomPairConstraintCreator
	Constraint creator for the AtomPairConstraint constraint. More...
class	NamedAtomPairConstraintCreator
	Constraint creator for the NamedAtomPairConstraint constraint. More...
class	BasePairConstraintCreator
	Constraint creator for the BasePairConstraint constraint. More...
class	AngleConstraintCreator
	Constraint creator for the AngleConstraint constraint. More...
class	DihedralConstraintCreator
	Constraint creator for the DihedralConstraint constraint. More...
class	DihedralPairConstraintCreator
	Constraint creator for DihedralPairConstraint. More...
class	BigBinConstraintCreator
	Constraint creator for the BigBinConstraint constraint. More...
class	MultiConstraintCreator
	Constraint creator for the MultiConstraint constraint. More...
class	AmbiguousConstraintCreator
	Constraint creator for the AmbiguousConstraint constraint. More...
class	KofNConstraintCreator
	Constraint creator for the KofNConstraint constraint. More...
class	CoordinateConstraintCreator
	Constraint creator for the CoordinateConstraint constraint. More...
class	LocalCoordinateConstraintCreator
	Constraint creator for the LocalCoordinateConstraint constraint. More...
class	AmbiguousNMRDistanceConstraintCreator
	Constraint creator for the AmbiguousNMRDistanceConstraint constraint. More...
class	AmbiguousNMRConstraintCreator
	Constraint creator for the AmbiguousNMRConstraint constraint. More...
class	SiteConstraintCreator
	Constraint creator for the SiteConstraint constraint. More...
class	SiteConstraintResiduesCreator
	Constraint creator for the SiteConstraintResidues constraint. More...
class	FabConstraintCreator
	Constraint creator for the FabConstraint constraint. More...
class	NamedAngleConstraintCreator
	Constraint creator for the NamedAngleConstraint. 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	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	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	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	FabConstraint
class	KofNConstraint
class	LocalCoordinateConstraint
class	MembraneSpanConstraint
	This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
class	MembraneSpanTermZConstraint
	This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
class	MultiConstraint
class	NamedAngleConstraint
class	Obsolet_NamedAtomPairConstraint
class	NamedAtomPairConstraint
class	NamedDihedralConstraint
class	NonResidueTypeConstraint
	This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
class	ResidueCouplingConstraint
	This class favors a particular residue identity at two particular positions by adding the scaled tensor value to the energy map. 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	RTConstraint
class	SequenceProfileConstraint
class	SequenceProfileConstraintCreator
	Constraint creator for the SequenceProfileConstraint constraint. More...
class	SiteConstraint
class	SiteConstraintResidues

Typedefs
typedef utility::pointer::shared_ptr< AmbiguousConstraint >	AmbiguousConstraintOP
typedef utility::pointer::shared_ptr< AmbiguousConstraint const >	AmbiguousConstraintCOP
typedef utility::pointer::shared_ptr< AmbiguousNMRConstraint >	AmbiguousNMRConstraintOP
typedef utility::pointer::shared_ptr< AmbiguousNMRConstraint const >	AmbiguousNMRConstraintCOP
typedef utility::pointer::shared_ptr< AmbiguousNMRDistanceConstraint >	AmbiguousNMRDistanceConstraintOP
typedef utility::pointer::shared_ptr< AmbiguousNMRDistanceConstraint const >	AmbiguousNMRDistanceConstraintCOP
typedef utility::vector1< core::id::NamedAtomID >	NamedAtoms
typedef utility::pointer::shared_ptr< AngleConstraint >	AngleConstraintOP
typedef utility::pointer::shared_ptr< AngleConstraint const >	AngleConstraintCOP
typedef utility::pointer::shared_ptr< AtomPairConstraint >	AtomPairConstraintOP
typedef utility::pointer::shared_ptr< AtomPairConstraint const >	AtomPairConstraintCOP
typedef utility::pointer::shared_ptr< AtomToAxisConstraint >	AtomToAxisConstraintOP
typedef utility::pointer::shared_ptr< AtomToAxisConstraint const >	AtomToAxisConstraintCOP
using	XYZ = numeric::xyzVector< core::Real >
typedef utility::pointer::shared_ptr< BackboneStubConstraint >	BackboneStubConstraintOP
typedef utility::pointer::shared_ptr< BackboneStubConstraint const >	BackboneStubConstraintCOP
typedef utility::vector1< BackboneStubConstraintOP >	BackboneStubConstraintOPs
typedef utility::vector1< BackboneStubConstraintCOP >	BackboneStubConstraintCOPs
typedef utility::pointer::shared_ptr< BackboneStubLinearConstraint >	BackboneStubLinearConstraintOP
typedef utility::pointer::shared_ptr< BackboneStubLinearConstraint const >	BackboneStubLinearConstraintCOP
typedef utility::vector1< BackboneStubLinearConstraintOP >	BackboneStubLinearConstraintOPs
typedef utility::vector1< BackboneStubLinearConstraintCOP >	BackboneStubLinearConstraintCOPs
typedef utility::pointer::shared_ptr< BasePairConstraint >	BasePairConstraintOP
typedef utility::pointer::shared_ptr< BasePairConstraint const >	BasePairConstraintCOP
typedef utility::pointer::shared_ptr< BigBinConstraint >	BigBinConstraintOP
typedef utility::pointer::shared_ptr< BigBinConstraint const >	BigBinConstraintCOP
typedef utility::pointer::shared_ptr< BoundFunc >	BoundFuncOP
typedef utility::pointer::shared_ptr< BoundFunc const >	BoundFuncCOP
typedef utility::pointer::shared_ptr< ConstantConstraint >	ConstantConstraintOP
typedef utility::pointer::shared_ptr< ConstantConstraint const >	ConstantConstraintCOP
typedef utility::pointer::shared_ptr< Constraint >	ConstraintOP
typedef utility::pointer::shared_ptr< Constraint const >	ConstraintCOP
typedef utility::vector1< ConstraintOP >	ConstraintOPs
typedef utility::vector1< ConstraintCOP >	ConstraintCOPs
typedef utility::pointer::shared_ptr< ConstraintCreator >	ConstraintCreatorOP
typedef utility::pointer::shared_ptr< ConstraintCreator const >	ConstraintCreatorCOP
typedef utility::pointer::shared_ptr< CstEnergyContainer >	CstEnergyContainerOP
typedef utility::pointer::shared_ptr< CstEnergyContainer const >	CstEnergyContainerCOP
typedef utility::pointer::shared_ptr< ConstraintGraph >	ConstraintGraphOP
typedef utility::pointer::shared_ptr< ConstraintGraph const >	ConstraintGraphCOP
typedef utility::pointer::shared_ptr< Constraints >	ConstraintsOP
typedef utility::pointer::shared_ptr< Constraints const >	ConstraintsCOP
typedef utility::pointer::shared_ptr< ConstraintsEnergy >	ConstraintsEnergyOP
typedef utility::pointer::shared_ptr< ConstraintsEnergy const >	ConstraintsEnergyCOP
typedef utility::pointer::shared_ptr< ResidueConstraints >	ResidueConstraintsOP
typedef utility::pointer::shared_ptr< ResidueConstraints const >	ResidueConstraintsCOP
typedef utility::pointer::shared_ptr< ConstraintSet >	ConstraintSetOP
typedef utility::pointer::shared_ptr< ConstraintSet const >	ConstraintSetCOP
typedef utility::pointer::shared_ptr< CoordinateConstraint >	CoordinateConstraintOP
typedef utility::pointer::shared_ptr< CoordinateConstraint const >	CoordinateConstraintCOP
typedef utility::pointer::shared_ptr< CstMinimizationData >	CstMinimizationDataOP
typedef utility::pointer::shared_ptr< CstMinimizationData const >	CstMinimizationDataCOP
typedef utility::pointer::shared_ptr< DihedralConstraint >	DihedralConstraintOP
typedef utility::pointer::shared_ptr< DihedralConstraint const >	DihedralConstraintCOP
typedef utility::pointer::shared_ptr< DOF_Constraint >	DOF_ConstraintOP
typedef utility::pointer::shared_ptr< DOF_Constraint const >	DOF_ConstraintCOP
typedef utility::vector1< DOF_ConstraintOP >	DOF_ConstraintOPs
typedef utility::vector1< DOF_ConstraintCOP >	DOF_ConstraintCOPs
typedef utility::pointer::shared_ptr< FabConstraint >	FabConstraintOP
typedef utility::pointer::shared_ptr< FabConstraint const >	FabConstraintCOP
typedef utility::pointer::shared_ptr< KofNConstraint >	KofNConstraintOP
typedef utility::pointer::shared_ptr< KofNConstraint const >	KofNConstraintCOP
typedef utility::pointer::shared_ptr< LocalCoordinateConstraint >	LocalCoordinateConstraintOP
typedef utility::pointer::shared_ptr< LocalCoordinateConstraint const >	LocalCoordinateConstraintCOP
typedef utility::pointer::shared_ptr< MembraneSpanConstraint >	MembraneSpanConstraintOP
typedef utility::pointer::shared_ptr< MembraneSpanConstraint const >	MembraneSpanConstraintCOP
typedef utility::pointer::shared_ptr< MembraneSpanTermZConstraint >	MembraneSpanTermZConstraintOP
typedef utility::pointer::shared_ptr< MembraneSpanTermZConstraint const >	MembraneSpanTermZConstraintCOP
typedef utility::pointer::shared_ptr< MultiConstraint >	MultiConstraintOP
typedef utility::pointer::shared_ptr< MultiConstraint const >	MultiConstraintCOP
typedef utility::pointer::shared_ptr< NamedAngleConstraint >	NamedAngleConstraintOP
typedef utility::pointer::shared_ptr< NamedAngleConstraint const >	NamedAngleConstraintCOP
typedef utility::pointer::shared_ptr< NamedAtomPairConstraint >	NamedAtomPairConstraintOP
typedef utility::pointer::shared_ptr< NamedAtomPairConstraint const >	NamedAtomPairConstraintCOP
typedef utility::pointer::shared_ptr< Obsolet_NamedAtomPairConstraint >	Obsolet_NamedAtomPairConstraintOP
typedef utility::pointer::shared_ptr< Obsolet_NamedAtomPairConstraint const >	Obsolet_NamedAtomPairConstraintCOP
typedef utility::pointer::shared_ptr< NamedDihedralConstraint >	NamedDihedralConstraintOP
typedef utility::pointer::shared_ptr< NamedDihedralConstraint const >	NamedDihedralConstraintCOP
typedef utility::pointer::shared_ptr< NonResidueTypeConstraint >	NonResidueTypeConstraintOP
typedef utility::pointer::shared_ptr< NonResidueTypeConstraint const >	NonResidueTypeConstraintCOP
typedef utility::pointer::shared_ptr< ResidueCouplingConstraint >	ResidueCouplingConstraintOP
typedef utility::pointer::shared_ptr< ResidueCouplingConstraint const >	ResidueCouplingConstraintCOP
typedef numeric::MathNTensor< double, 4 >	CouplingTensor
typedef utility::pointer::shared_ptr< CouplingTensor >	CouplingTensorOP
typedef utility::pointer::shared_ptr< const CouplingTensor >	CouplingTensorCOP
typedef utility::pointer::shared_ptr< std::vector< int > >	indexListOP
typedef utility::pointer::shared_ptr< const std::vector< int > >	indexListCOP
typedef utility::pointer::shared_ptr< ResidueTypeConstraint >	ResidueTypeConstraintOP
typedef utility::pointer::shared_ptr< ResidueTypeConstraint const >	ResidueTypeConstraintCOP
typedef utility::pointer::shared_ptr< ResidueTypeLinkingConstraint >	ResidueTypeLinkingConstraintOP
typedef utility::pointer::shared_ptr< ResidueTypeLinkingConstraint const >	ResidueTypeLinkingConstraintCOP
typedef utility::pointer::shared_ptr< RTConstraint >	RTConstraintOP
typedef utility::pointer::shared_ptr< RTConstraint const >	RTConstraintCOP
typedef utility::pointer::shared_ptr< SequenceProfileConstraint >	SequenceProfileConstraintOP
typedef utility::pointer::shared_ptr< SequenceProfileConstraint const >	SequenceProfileConstraintCOP
typedef utility::pointer::shared_ptr< SiteConstraint >	SiteConstraintOP
typedef utility::pointer::shared_ptr< SiteConstraint const >	SiteConstraintCOP
typedef utility::pointer::shared_ptr< SiteConstraintResidues >	SiteConstraintResiduesOP
typedef utility::pointer::shared_ptr< SiteConstraintResidues const >	SiteConstraintResiduesCOP

Functions
bool	cst_eq (Constraint const &cst1, Constraint const &cst2)
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	TR ("core.scoring.constraints.AngleConstraint")
core::Real	distance_from_line (XYZ const &p, XYZ const &x1, XYZ const &x2)
XYZ	closest_point_on_line (XYZ const &p, XYZ const &x1, XYZ const &x2)
XYZ	closest_point_on_line (XYZs const &xyzs)
static basic::Tracer	tr ("core.scoring.constraints.BackboneStubConstraint")
std::map< std::string, core::id::AtomID >	auto_detect_atoms (pose::Pose const &pose, Size const seqpos)
static basic::Tracer	TR ("core.scoring.constraints.BackboneStubLinearConstraint")
core::chemical::rna::BaseEdge	get_edge_from_char (char const c)
std::ostream &	operator<< (std::ostream &out, Constraint const &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.scoring.constraints")
static basic::Tracer	TR ("core.scoring.constraints")
static basic::Tracer	TR ("core.scoring.constraints")
static basic::Tracer	TR ("core.scoring.constraints.KofNConstraint")
static basic::Tracer	TR ("core.scoring.constraints.MembraneSpanConstraint")
static basic::Tracer	TR ("core.scoring.constraints.MembraneSpanTermZConstraint")
std::ostream &	operator<< (std::ostream &out, Obsolet_NamedAtomPairConstraint const &cst)
static basic::Tracer	TR ("core.scoring.constraints.NamedDihedralConstraint")
static basic::Tracer	non_residue_type_constraint_tracer ("core.scoring.constraints.NonResidueTypeConstraint")
static basic::Tracer	TR ("core.scoring.constraints.ResidueCouplingConstraint")
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 basic::Tracer	tr ("core.scoring.constraints.util")
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 ()
std::string	get_cst_file_option (utility::options::OptionCollection const &options)
void	options_for_get_cst_file_option (utility::options::OptionKeyList &opts)
	companion function for get_cst_file_option More...
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 ()
std::string	get_cst_fa_file_option (utility::options::OptionCollection const &options)
void	options_for_get_cst_fa_file_option (utility::options::OptionKeyList &opts)
	companion function for get_cst_file_option More...
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)
void	print_atom_pair_constraints (pose::Pose const &pose, std::ostream &out=std::cout)
	example of how to go through a pose constraint set and print out stuff. More...
void	map_constraints_from_original_pose (core::pose::Pose const &original_pose, core::pose::Pose &pose)
	map constraints to new atom numbers after, e.g. variants change. requires pose to have same number of residues. More...

Typedef Documentation

AmbiguousConstraintCOP

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

AmbiguousConstraintOP

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

AmbiguousNMRConstraintCOP

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

AmbiguousNMRConstraintOP

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

AmbiguousNMRDistanceConstraintCOP

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

AmbiguousNMRDistanceConstraintOP

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

AngleConstraintCOP

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

AngleConstraintOP

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

AtomPairConstraintCOP

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

AtomPairConstraintOP

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

AtomToAxisConstraintCOP

typedef utility::pointer::shared_ptr< AtomToAxisConstraint const > core::scoring::constraints::AtomToAxisConstraintCOP

AtomToAxisConstraintOP

typedef utility::pointer::shared_ptr< AtomToAxisConstraint > core::scoring::constraints::AtomToAxisConstraintOP

BackboneStubConstraintCOP

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

BackboneStubConstraintCOPs

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

BackboneStubConstraintOP

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

BackboneStubConstraintOPs

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

BackboneStubLinearConstraintCOP

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

BackboneStubLinearConstraintCOPs

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

BackboneStubLinearConstraintOP

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

BackboneStubLinearConstraintOPs

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

BasePairConstraintCOP

typedef utility::pointer::shared_ptr< BasePairConstraint const > core::scoring::constraints::BasePairConstraintCOP

BasePairConstraintOP

typedef utility::pointer::shared_ptr< BasePairConstraint > core::scoring::constraints::BasePairConstraintOP

BigBinConstraintCOP

typedef utility::pointer::shared_ptr< BigBinConstraint const > core::scoring::constraints::BigBinConstraintCOP

BigBinConstraintOP

typedef utility::pointer::shared_ptr< BigBinConstraint > core::scoring::constraints::BigBinConstraintOP

BoundFuncCOP

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

BoundFuncOP

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

ConstantConstraintCOP

typedef utility::pointer::shared_ptr< ConstantConstraint const > core::scoring::constraints::ConstantConstraintCOP

ConstantConstraintOP

typedef utility::pointer::shared_ptr< ConstantConstraint > core::scoring::constraints::ConstantConstraintOP

ConstraintCOP

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

ConstraintCOPs

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

ConstraintCreatorCOP

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

ConstraintCreatorOP

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

ConstraintGraphCOP

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

ConstraintGraphOP

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

ConstraintOP

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

ConstraintOPs

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

ConstraintsCOP

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

ConstraintsEnergyCOP

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

ConstraintsEnergyOP

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

ConstraintSetCOP

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

ConstraintSetOP

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

ConstraintsOP

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

CoordinateConstraintCOP

typedef utility::pointer::shared_ptr< CoordinateConstraint const > core::scoring::constraints::CoordinateConstraintCOP

CoordinateConstraintOP

typedef utility::pointer::shared_ptr< CoordinateConstraint > core::scoring::constraints::CoordinateConstraintOP

CouplingTensor

typedef numeric::MathNTensor< double, 4 > core::scoring::constraints::CouplingTensor

CouplingTensorCOP

typedef utility::pointer::shared_ptr< const CouplingTensor > core::scoring::constraints::CouplingTensorCOP

CouplingTensorOP

typedef utility::pointer::shared_ptr< CouplingTensor > core::scoring::constraints::CouplingTensorOP

CstEnergyContainerCOP

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

CstEnergyContainerOP

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

CstMinimizationDataCOP

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

CstMinimizationDataOP

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

DihedralConstraintCOP

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

DihedralConstraintOP

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

DOF_ConstraintCOP

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

DOF_ConstraintCOPs

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

DOF_ConstraintOP

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

DOF_ConstraintOPs

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

FabConstraintCOP

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

FabConstraintOP

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

indexListCOP

typedef utility::pointer::shared_ptr< const std::vector<int> > core::scoring::constraints::indexListCOP

indexListOP

typedef utility::pointer::shared_ptr< std::vector<int> > core::scoring::constraints::indexListOP

KofNConstraintCOP

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

KofNConstraintOP

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

LocalCoordinateConstraintCOP

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

LocalCoordinateConstraintOP

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

MembraneSpanConstraintCOP

typedef utility::pointer::shared_ptr< MembraneSpanConstraint const > core::scoring::constraints::MembraneSpanConstraintCOP

MembraneSpanConstraintOP

typedef utility::pointer::shared_ptr< MembraneSpanConstraint > core::scoring::constraints::MembraneSpanConstraintOP

MembraneSpanTermZConstraintCOP

typedef utility::pointer::shared_ptr< MembraneSpanTermZConstraint const > core::scoring::constraints::MembraneSpanTermZConstraintCOP

MembraneSpanTermZConstraintOP

typedef utility::pointer::shared_ptr< MembraneSpanTermZConstraint > core::scoring::constraints::MembraneSpanTermZConstraintOP

MultiConstraintCOP

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

MultiConstraintOP

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

NamedAngleConstraintCOP

typedef utility::pointer::shared_ptr< NamedAngleConstraint const > core::scoring::constraints::NamedAngleConstraintCOP

NamedAngleConstraintOP

typedef utility::pointer::shared_ptr< NamedAngleConstraint > core::scoring::constraints::NamedAngleConstraintOP

NamedAtomPairConstraintCOP

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

NamedAtomPairConstraintOP

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

NamedAtoms

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

NamedDihedralConstraintCOP

typedef utility::pointer::shared_ptr< NamedDihedralConstraint const > core::scoring::constraints::NamedDihedralConstraintCOP

NamedDihedralConstraintOP

typedef utility::pointer::shared_ptr< NamedDihedralConstraint > core::scoring::constraints::NamedDihedralConstraintOP

NonResidueTypeConstraintCOP

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

NonResidueTypeConstraintOP

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

Obsolet_NamedAtomPairConstraintCOP

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

Obsolet_NamedAtomPairConstraintOP

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

ResidueConstraintsCOP

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

ResidueConstraintsOP

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

ResidueCouplingConstraintCOP

typedef utility::pointer::shared_ptr< ResidueCouplingConstraint const > core::scoring::constraints::ResidueCouplingConstraintCOP

ResidueCouplingConstraintOP

typedef utility::pointer::shared_ptr< ResidueCouplingConstraint > core::scoring::constraints::ResidueCouplingConstraintOP

ResidueTypeConstraintCOP

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

ResidueTypeConstraintOP

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

ResidueTypeLinkingConstraintCOP

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

ResidueTypeLinkingConstraintOP

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

RTConstraintCOP

typedef utility::pointer::shared_ptr< RTConstraint const > core::scoring::constraints::RTConstraintCOP

RTConstraintOP

typedef utility::pointer::shared_ptr< RTConstraint > core::scoring::constraints::RTConstraintOP

SequenceProfileConstraintCOP

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

SequenceProfileConstraintOP

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

SiteConstraintCOP

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

SiteConstraintOP

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

SiteConstraintResiduesCOP

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

SiteConstraintResiduesOP

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

XYZ

using core::scoring::constraints::XYZ = typedef numeric::xyzVector< core::Real >

Function Documentation

add_constraint_to_residue_constraints()

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().

add_constraints_from_cmdline()

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().

Referenced by protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::cluster::GatherPosesMover::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), and protocols::loop_modeling::LoopProtocol::start_protocol().

add_constraints_from_cmdline_to_pose()

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(), and get_cst_file_option().

Referenced by add_constraints_from_cmdline(), protocols::mpi_refinement::MultiObjective::add_objective_function_info(), protocols::loop_grower::LoopGrower::add_user_csts(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::medal::MedalMover::apply(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), protocols::star::setup_constraints(), and protocols::jobdist::universal_main().

add_constraints_from_cmdline_to_scorefxn()

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, and core::scoring::ScoreFunction::set_weight().

Referenced by add_constraints_from_cmdline(), protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators(), protocols::loop_grower::LoopGrower::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::backrub::BackrubProtocol::finalize_setup(), protocols::floppy_tail::FloppyTailMover::FloppyTailMover(), protocols::flxbb::FlxbbDesign_main(), protocols::relax::generate_relax_from_cmd(), protocols::hydrate::Hydrate::Hydrate(), protocols::relax::LocalRelax::LocalRelax(), protocols::medal::MedalMover::score_function(), protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions(), and protocols::chemically_conjugated_docking::UBQ_GTPaseMover::UBQ_GTPaseMover().

add_coordinate_constraints() [1/2]

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(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::add_coordinatecst_for_hotspot_packing(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::stepwise::modeler::rna::minimize_with_constraints(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints().

add_coordinate_constraints() [2/2]

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::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), and core::conformation::Residue::xyz().

add_fa_constraints_from_cmdline()

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().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::relax(), and protocols::loop_modeling::LoopProtocol::start_protocol().

add_fa_constraints_from_cmdline_to_pose()

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(), and get_cst_fa_file_option().

Referenced by add_fa_constraints_from_cmdline(), protocols::mpi_refinement::MultiObjective::add_objective_function_info(), protocols::loop_grower::LoopGrower::add_user_csts(), protocols::backrub::BackrubProtocol::apply(), protocols::coupled_moves::CoupledMovesProtocol::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::md::CartesianMD::cst_on_pose_simple(), protocols::floppy_tail::FloppyTailMover::low_res(), protocols::mpi_refinement::WorkUnit_Relax::run(), protocols::jobdist::universal_main(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

add_fa_constraints_from_cmdline_to_scorefxn()

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, and core::scoring::ScoreFunction::set_weight().

Referenced by protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators(), add_fa_constraints_from_cmdline(), protocols::indel::IndelOptimizationMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::coupled_moves::CoupledMovesProtocol::configure_score_fxn(), protocols::backrub::BackrubProtocol::finalize_setup(), protocols::floppy_tail::FloppyTailMover::FloppyTailMover(), protocols::flxbb::FlxbbDesign_main(), protocols::relax::generate_relax_from_cmd(), protocols::hydrate::Hydrate::Hydrate(), protocols::hybridization::HybridizeProtocol::init(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::relax::LocalRelax::LocalRelax(), protocols::ncbb::NcbbDockDesignProtocol::NcbbDockDesignProtocol(), protocols::ncbb::oop::OopDockDesignProtocol::OopDockDesignProtocol(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::ncbb::SecStructFinder::SecStructFinder(), and protocols::glycan_docking::GlycanDockProtocol::setup_scorefxn().

auto_detect_atoms()

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

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), core::conformation::Residue::bonded_neighbor(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), tr(), and core::conformation::Residue::upper_connect_atom().

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

bin_by_seq_separation()

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

inline

Referenced by combine_constraints().

choose_effective_sequence_separation()

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(), core::conformation::membrane::in, and core::scoring::rg.

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::abinitio::abscript::ConstraintPreparer::prepare(), and protocols::constraints_additional::ConstraintEvaluator::prepare_pose().

closest_point_on_line() [1/2]

XYZ core::scoring::constraints::closest_point_on_line	(	XYZ const &	p,
		XYZ const &	x1,
		XYZ const &	x2
	)

Referenced by protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::features::SmotifFeatures::calculate_angles(), closest_point_on_line(), core::scoring::constraints::AtomToAxisConstraint::dist(), core::scoring::constraints::AtomToAxisConstraint::fill_f1_f2(), core::energy_methods::MPSpanAngleEnergy::find_helix_vector(), protocols::simple_filters::HelixHelixAngleFilter::find_helix_vector(), and core::scoring::constraints::AtomToAxisConstraint::score().

closest_point_on_line() [2/2]

XYZ core::scoring::constraints::closest_point_on_line

(

XYZs const &

xyzs

)

References core::scoring::constraints::XYZs::atom, core::scoring::constraints::XYZs::axis1, core::scoring::constraints::XYZs::axis2, and closest_point_on_line().

combinable()

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

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

Referenced by combine_constraints().

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(), core::conformation::membrane::in, core::conformation::membrane::out, core::scoring::rg, and tr().

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::abinitio::abscript::ConstraintPreparer::prepare(), and protocols::constraints_additional::ConstraintEvaluator::prepare_pose().

combine_NMR_atom_string()

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_CEN(), and core::scoring::constraints::AmbiguousNMRDistanceConstraint::show_def().

count_constraint()

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

References protocols::mean_field::max(), and tr().

Referenced by skip_redundant_constraints().

cst_eq()

bool core::scoring::constraints::cst_eq	(	Constraint const &	cst1,
		Constraint const &	cst2
	)

References core::scoring::constraints::Constraint::atom(), and core::scoring::constraints::Constraint::natoms().

Referenced by core::scoring::constraints::AmbiguousNMRConstraint::add_individual_constraint().

cull_violators()

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().

dexponential()

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_().

dgaussian()

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.

References core::simple_metrics::metrics::mean.

Referenced by core::scoring::func::SoedingFunc::compute_func(), core::scoring::func::MixtureFunc::dfunc_component(), core::scoring::disulfides::Cb_Distance_Func::func(), core::scoring::func::GaussianFunc::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().

distance_from_line()

core::Real core::scoring::constraints::distance_from_line	(	XYZ const &	p,
		XYZ const &	x1,
		XYZ const &	x2
	)

This can be sped up by using distances-squared

drop_constraints()

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

References core::conformation::membrane::in, core::conformation::membrane::out, and core::scoring::rg.

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), and protocols::abinitio::abscript::ConstraintPreparer::prepare().

exponential_deriv()

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().

gaussian_deriv()

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(), and core::simple_metrics::metrics::mean.

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

get_cst_fa_file_option() [1/2]

std::string core::scoring::constraints::get_cst_fa_file_option

(

)

Referenced by add_fa_constraints_from_cmdline_to_pose(), protocols::abinitio::AbrelaxApplication::fold(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), merge_fa_constraints_from_cmdline_to_pose(), protocols::topology_broker::ConstraintClaimer::new_decoy(), protocols::relax::Relax_main(), protocols::relax::WorkUnit_BatchRelax::run(), and protocols::glycan_docking::GlycanDockProtocol::setup_scorefxn().

get_cst_fa_file_option() [2/2]

std::string core::scoring::constraints::get_cst_fa_file_option

(

utility::options::OptionCollection const &

options

)

References core::scoring::rg, and tr().

get_cst_file_option() [1/2]

std::string core::scoring::constraints::get_cst_file_option

(

)

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

get_cst_file_option() [2/2]

std::string core::scoring::constraints::get_cst_file_option

(

utility::options::OptionCollection const &

options

)

References core::scoring::rg, and tr().

get_edge_from_char()

core::chemical::rna::BaseEdge core::scoring::constraints::get_edge_from_char ( char const  c )

inline

References core::chemical::rna::HOOGSTEEN, core::chemical::rna::SUGAR, and core::chemical::rna::WATSON_CRICK.

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

get_section_name()

std::string core::scoring::constraints::get_section_name

(

std::string

line

)

References protocols::loops::start.

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

is_aromatic() [1/2]

bool core::scoring::constraints::is_aromatic

(

core::chemical::AA

aa

)

References protocols::cluster::calibur::aa, core::chemical::aa_his, core::chemical::aa_phe, core::chemical::aa_trp, and core::chemical::aa_tyr.

is_aromatic() [2/2]

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

inline

References core::chemical::ResidueTypeBase::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().

keep_constraint()

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().

linear_interpolate()

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::func::EtableFunc::func().

logdgaussian()

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 core::simple_metrics::metrics::mean.

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

logdgaussian_deriv()

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.

References core::simple_metrics::metrics::mean.

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

map_constraints_from_original_pose()

void core::scoring::constraints::map_constraints_from_original_pose	(	pose::Pose const &	original_pose,
		pose::Pose &	pose
	)

map constraints to new atom numbers after, e.g. variants change. requires pose to have same number of residues.

References core::pose::Pose::annotated_sequence(), core::pose::Pose::constraint_set(), and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::stepwise::modeler::rna::bulge::BulgeApplyMover::apply(), protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover::apply(), and protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants().

merge_constraints_from_cmdline()

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().

merge_constraints_from_cmdline_to_pose()

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(), and get_cst_file_option().

Referenced by merge_constraints_from_cmdline().

merge_constraints_from_cmdline_to_scorefxn()

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().

Referenced by merge_constraints_from_cmdline().

merge_csts_to_scorefunction()

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().

merge_fa_constraints_from_cmdline()

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().

merge_fa_constraints_from_cmdline_to_pose()

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(), and get_cst_fa_file_option().

Referenced by merge_fa_constraints_from_cmdline().

merge_fa_constraints_from_cmdline_to_scorefxn()

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().

Referenced by merge_fa_constraints_from_cmdline().

non_residue_type_constraint_tracer()

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

static

operator<<() [1/3]

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

operator<<() [2/3]

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

References core::conformation::membrane::out, and core::scoring::constraints::Constraint::show().

operator<<() [3/3]

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

options_for_get_cst_fa_file_option()

void core::scoring::constraints::options_for_get_cst_fa_file_option

(

utility::options::OptionKeyList &

opts

)

companion function for get_cst_file_option

options_for_get_cst_file_option()

void core::scoring::constraints::options_for_get_cst_file_option

(

utility::options::OptionKeyList &

opts

)

companion function for get_cst_file_option

parse_NMR_name() [1/2]

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

References core::chemical::ResidueTypeBase::aa(), protocols::cluster::calibur::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::size().

parse_NMR_name() [2/2]

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

References protocols::cluster::calibur::aa, core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, and is_aromatic().

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

parse_NMR_name_old()

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

References core::chemical::ResidueTypeBase::aa(), protocols::cluster::calibur::aa, core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, core::chemical::ResidueType::atom_index(), is_aromatic(), core::pose::Pose::is_fullatom(), core::chemical::ResidueTypeBase::name3(), core::pose::named_atom_id_to_atom_id(), core::conformation::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and tr().

print_atom_pair_constraints()

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

example of how to go through a pose constraint set and print out stuff.

example of how to go through a pose constraint set and print out stuff.

References core::pose::Pose::constraint_set(), core::conformation::membrane::out, core::scoring::constraints::Constraint::show_def(), core::pose::Pose::size(), and core::scoring::constraints::Constraint::type().

remove_constraint_from_residue_constraints()

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().

remove_constraints_of_type() [1/2]

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().

Referenced by protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs().

remove_constraints_of_type() [2/2]

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

remove_nonbb_constraints()

void core::scoring::constraints::remove_nonbb_constraints

(

pose::Pose &

pose

)

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

Referenced by protocols::hybridization::HybridizeProtocol::apply().

requires_CB_mapping()

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

References core::chemical::ResidueTypeBase::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().

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(), core::conformation::membrane::in, keep_constraint(), core::conformation::membrane::out, protocols::rigid::random, core::scoring::rg, and tr().

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

TR() [1/13]

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

static

TR() [2/13]

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

static

TR() [3/13]

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

static

TR() [4/13]

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

static

Referenced by core::scoring::constraints::AngleConstraint::angle(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), core::scoring::constraints::DihedralPairConstraint::dihedral_diff(), core::scoring::constraints::SequenceProfileConstraint::dist(), core::scoring::constraints::AtomToAxisConstraint::dist(), core::scoring::constraints::DistancePairConstraint::distance_diff(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::constraints::SequenceProfileConstraint::read_def(), core::scoring::constraints::AngleConstraint::read_def(), core::scoring::constraints::FabConstraint::read_def(), core::scoring::constraints::KofNConstraint::read_def(), core::scoring::constraints::SiteConstraint::read_def(), core::scoring::constraints::SiteConstraintResidues::read_def(), core::scoring::constraints::DihedralConstraint::read_def(), core::scoring::constraints::DihedralPairConstraint::read_def(), core::scoring::constraints::DistancePairConstraint::read_def(), core::scoring::constraints::NamedAngleConstraint::read_def(), core::scoring::constraints::NamedDihedralConstraint::read_def(), core::scoring::constraints::SequenceProfileConstraint::remap_resid(), core::scoring::constraints::SequenceProfileConstraint::remapped_clone(), core::scoring::constraints::AtomToAxisConstraint::remapped_clone(), core::scoring::constraints::BackboneStubLinearConstraint::score(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), and core::scoring::constraints::NamedAngleConstraint::setup_for_scoring().

tr() [1/4]

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

static

Referenced by core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint(), auto_detect_atoms(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), combine_constraints(), combine_NMR_atom_string(), count_constraint(), cull_violators(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::constraints::RTConstraint::fill_f1_f2(), get_cst_fa_file_option(), get_cst_file_option(), core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), keep_constraint(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CEN(), merge_csts_to_scorefunction(), core::scoring::constraints::ConstraintSet::on_connection_change(), core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint(), core::scoring::constraints::ConstraintIO::parse_coordinate_constraint(), parse_NMR_name_old(), core::scoring::constraints::ConstraintIO::parse_residue(), core::scoring::constraints::ConstraintIO::read_constraints(), core::scoring::constraints::ConstraintIO::read_constraints_new(), core::scoring::constraints::ConstraintIO::read_cst_angles(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_bindingsites(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), core::scoring::constraints::CoordinateConstraint::read_def(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), core::scoring::constraints::BasePairConstraint::read_def(), core::scoring::constraints::MultiConstraint::read_def(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::read_def(), core::scoring::constraints::NamedAtomPairConstraint::read_def(), core::scoring::constraints::ConstraintIO::read_individual_constraint_new(), core::scoring::constraints::ConstraintSet::remap_residue_positions(), core::scoring::constraints::ConstraintSet::remove_constraint(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::constraints::NamedAtomPairConstraint::setup_for_scoring(), skip_redundant_constraints(), and core::scoring::constraints::LocalCoordinateConstraint::xyz_target().

TR() [5/13]

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

static

TR() [6/13]

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

static

TR() [7/13]

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

static

TR() [8/13]

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

static

TR() [9/13]

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

static

TR() [10/13]

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

static

TR() [11/13]

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

static

TR() [12/13]

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

static

TR() [13/13]

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

static

tr() [2/4]

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

static

tr() [3/4]

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

static

tr() [4/4]

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

static