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core::scoring::constraints Namespace Reference

Classes

class  AmbiguousConstraint
 Nested constraint where only the one with lowest energy is considered. More...
 
class  AmbiguousConstraintCreator
 Constraint creator for the AmbiguousConstraint constraint. More...
 
class  AmbiguousNMRConstraint
 
class  AmbiguousNMRConstraintCreator
 Constraint creator for the AmbiguousNMRConstraint constraint. More...
 
class  AmbiguousNMRDistanceConstraint
 
class  AmbiguousNMRDistanceConstraintCreator
 Constraint creator for the AmbiguousNMRDistanceConstraint constraint. More...
 
class  AngleConstraint
 An Angular Constraint. More...
 
class  AngleConstraintCreator
 Constraint creator for the AngleConstraint constraint. More...
 
class  AtomPairConstraint
 
class  AtomPairConstraintCreator
 Constraint 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  BasePairConstraint
 
class  BasePairConstraintCreator
 Constraint creator for the BasePairConstraint constraint. More...
 
class  BigBinConstraint
 constraint on dihedral angle formed by 4 points More...
 
class  BigBinConstraintCreator
 Constraint 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
 Constraint 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
 Constraint 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
 Constraint creator for the FabConstraint constraint. More...
 
class  KofNConstraint
 
class  KofNConstraintCreator
 Constraint creator for the KofNConstraint constraint. More...
 
class  LocalCoordinateConstraint
 
class  LocalCoordinateConstraintCreator
 Constraint creator for the LocalCoordinateConstraint constraint. More...
 
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  MultiConstraintCreator
 Constraint creator for the MultiConstraint constraint. More...
 
class  NamedAngleConstraint
 
class  NamedAngleConstraintCreator
 Constraint creator for the NamedAngleConstraint. More...
 
class  NamedAtomPairConstraint
 
class  NamedAtomPairConstraintCreator
 Constraint creator for the NamedAtomPairConstraint constraint. More...
 
class  NamedDihedralConstraint
 
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  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  SiteConstraintCreator
 Constraint creator for the SiteConstraint constraint. More...
 
class  SiteConstraintResidues
 
class  SiteConstraintResiduesCreator
 Constraint creator for the SiteConstraintResidues constraint. More...
 

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
< 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")
 
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

typedef utility::pointer::shared_ptr< AmbiguousConstraint const > core::scoring::constraints::AmbiguousConstraintCOP
typedef utility::pointer::shared_ptr< AngleConstraint const > core::scoring::constraints::AngleConstraintCOP
typedef utility::pointer::shared_ptr< AngleConstraint > core::scoring::constraints::AngleConstraintOP
typedef utility::pointer::shared_ptr< AtomPairConstraint const > core::scoring::constraints::AtomPairConstraintCOP
typedef utility::pointer::shared_ptr< BasePairConstraint const > core::scoring::constraints::BasePairConstraintCOP
typedef utility::pointer::shared_ptr< BigBinConstraint const > core::scoring::constraints::BigBinConstraintCOP
typedef utility::pointer::shared_ptr< BigBinConstraint > core::scoring::constraints::BigBinConstraintOP
typedef utility::pointer::shared_ptr< BoundFunc const > core::scoring::constraints::BoundFuncCOP
typedef utility::pointer::shared_ptr< BoundFunc > core::scoring::constraints::BoundFuncOP
typedef utility::pointer::shared_ptr< ConstantConstraint const > core::scoring::constraints::ConstantConstraintCOP
typedef utility::pointer::shared_ptr< Constraint const > core::scoring::constraints::ConstraintCOP
typedef utility::pointer::shared_ptr< ConstraintCreator const > core::scoring::constraints::ConstraintCreatorCOP
typedef utility::pointer::shared_ptr< ConstraintCreator > core::scoring::constraints::ConstraintCreatorOP
typedef utility::pointer::shared_ptr< ConstraintGraph const > core::scoring::constraints::ConstraintGraphCOP
typedef utility::pointer::shared_ptr< ConstraintGraph > core::scoring::constraints::ConstraintGraphOP
typedef utility::pointer::shared_ptr< Constraint > core::scoring::constraints::ConstraintOP
typedef utility::pointer::shared_ptr< Constraints const > core::scoring::constraints::ConstraintsCOP
typedef utility::pointer::shared_ptr< ConstraintsEnergy const > core::scoring::constraints::ConstraintsEnergyCOP
typedef utility::pointer::shared_ptr< ConstraintsEnergy > core::scoring::constraints::ConstraintsEnergyOP
typedef utility::pointer::shared_ptr< ConstraintSet const > core::scoring::constraints::ConstraintSetCOP
typedef utility::pointer::shared_ptr< ConstraintSet > core::scoring::constraints::ConstraintSetOP
typedef utility::pointer::shared_ptr< Constraints > core::scoring::constraints::ConstraintsOP
typedef utility::pointer::shared_ptr< CoordinateConstraint const > core::scoring::constraints::CoordinateConstraintCOP
typedef numeric::MathNTensor< double, 4 > core::scoring::constraints::CouplingTensor
typedef utility::pointer::shared_ptr< const CouplingTensor > core::scoring::constraints::CouplingTensorCOP
typedef utility::pointer::shared_ptr< CouplingTensor > core::scoring::constraints::CouplingTensorOP
typedef utility::pointer::shared_ptr< CstEnergyContainer const > core::scoring::constraints::CstEnergyContainerCOP
typedef utility::pointer::shared_ptr< CstMinimizationData const > core::scoring::constraints::CstMinimizationDataCOP
typedef utility::pointer::shared_ptr< DihedralConstraint const > core::scoring::constraints::DihedralConstraintCOP
typedef utility::pointer::shared_ptr< DOF_Constraint const > core::scoring::constraints::DOF_ConstraintCOP
typedef utility::pointer::shared_ptr< DOF_Constraint > core::scoring::constraints::DOF_ConstraintOP
typedef utility::pointer::shared_ptr< FabConstraint const > core::scoring::constraints::FabConstraintCOP
typedef utility::pointer::shared_ptr< FabConstraint > core::scoring::constraints::FabConstraintOP
typedef utility::pointer::shared_ptr< const std::vector<int> > core::scoring::constraints::indexListCOP
typedef utility::pointer::shared_ptr< std::vector<int> > core::scoring::constraints::indexListOP
typedef utility::pointer::shared_ptr< KofNConstraint const > core::scoring::constraints::KofNConstraintCOP
typedef utility::pointer::shared_ptr< KofNConstraint > core::scoring::constraints::KofNConstraintOP
typedef utility::pointer::shared_ptr< MultiConstraint const > core::scoring::constraints::MultiConstraintCOP
typedef utility::pointer::shared_ptr< MultiConstraint > core::scoring::constraints::MultiConstraintOP
typedef utility::pointer::shared_ptr< NamedAngleConstraint const > core::scoring::constraints::NamedAngleConstraintCOP
typedef utility::pointer::shared_ptr< ResidueConstraints const > core::scoring::constraints::ResidueConstraintsCOP
typedef utility::pointer::shared_ptr< ResidueTypeConstraint const > core::scoring::constraints::ResidueTypeConstraintCOP
typedef utility::pointer::shared_ptr< RTConstraint const > core::scoring::constraints::RTConstraintCOP
typedef utility::pointer::shared_ptr< RTConstraint > core::scoring::constraints::RTConstraintOP
typedef utility::pointer::shared_ptr< SiteConstraint const > core::scoring::constraints::SiteConstraintCOP
typedef utility::pointer::shared_ptr< SiteConstraint > core::scoring::constraints::SiteConstraintOP

Function Documentation

void core::scoring::constraints::add_constraint_to_residue_constraints ( int const  seqpos,
ConstraintCOP  cst,
ResidueConstraints residue_constraints 
)
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::rbsegment_relax::AutoRBMover::apply(), protocols::cluster::GatherPosesMover::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), and protocols::loop_modeling::LoopProtocol::start_protocol().

void core::scoring::constraints::add_constraints_from_cmdline_to_pose ( core::pose::Pose pose)
void core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction scorefxn_)
void core::scoring::constraints::add_coordinate_constraints ( pose::Pose pose,
Real const  coord_sdev,
bool  include_sc 
)
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 
)
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::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::relax(), and protocols::loop_modeling::LoopProtocol::start_protocol().

void core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose ( core::pose::Pose pose)
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::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::loop_grower::LoopGrower::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(), and protocols::ncbb::SecStructFinder::SecStructFinder().

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

Referenced by combine_constraints().

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

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

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

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

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

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

void core::scoring::constraints::combine_NMR_atom_string ( AmbiguousNMRDistanceConstraint::Atoms  atoms,
std::string &  atom_str,
pose::Pose const &  pose 
)
void core::scoring::constraints::count_constraint ( ConstraintCOP  cst,
bool  redundant,
ObjexxFCL::FArray2D_int &  count_matrix,
Size  influence_width,
Size  total_residue 
)
bool core::scoring::constraints::cst_eq ( Constraint const &  cst1,
Constraint const &  cst2 
)
void core::scoring::constraints::cull_violators ( ConstraintCOPs const &  target_list,
ConstraintCOPs culled_list,
pose::Pose const &  filter_pose,
core::Real  threshold 
)
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 
)
void core::scoring::constraints::drop_constraints ( ConstraintCOPs in,
core::Real  drop_rate 
)
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 ( )
std::string core::scoring::constraints::get_cst_fa_file_option ( utility::options::OptionCollection const &  options)

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

std::string core::scoring::constraints::get_cst_file_option ( )
std::string core::scoring::constraints::get_cst_file_option ( utility::options::OptionCollection const &  options)

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

core::chemical::rna::BaseEdge core::scoring::constraints::get_edge_from_char ( char const  c)
inline
std::string core::scoring::constraints::get_section_name ( std::string  line)
bool core::scoring::constraints::is_aromatic ( pose::Pose const &  pose,
core::Size  res 
)
inline
bool core::scoring::constraints::is_aromatic ( core::chemical::AA  aa)
bool core::scoring::constraints::keep_constraint ( ConstraintCOP  cst,
bool  redundant,
ObjexxFCL::FArray2D_int &  count_matrix,
Size  influence_width,
Size  total_residue 
)

References tr().

Referenced by skip_redundant_constraints().

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

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

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

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

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

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

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

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.

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

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

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

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().

Referenced by merge_constraints_from_cmdline().

void core::scoring::constraints::merge_csts_to_scorefunction ( core::Real const  weight,
core::scoring::ScoreFunction 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(), and get_cst_fa_file_option().

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().

Referenced by merge_fa_constraints_from_cmdline().

static basic::Tracer core::scoring::constraints::non_residue_type_constraint_tracer ( "core.scoring.constraints.NonResidueTypeConstraint"  )
static
std::ostream & core::scoring::constraints::operator<< ( std::ostream &  out,
Constraint const &  cst 
)
std::ostream& core::scoring::constraints::operator<< ( std::ostream &  out,
Obsolet_NamedAtomPairConstraint const &  cst 
)
std::ostream & core::scoring::constraints::operator<< ( std::ostream &  os,
ConstraintSet const &  set 
)
void core::scoring::constraints::options_for_get_cst_fa_file_option ( utility::options::OptionKeyList &  opts)

companion function 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

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 
)
void core::scoring::constraints::parse_NMR_name_old ( std::string  name,
core::Size  res,
AmbiguousNMRDistanceConstraint::Atoms &  atoms,
core::pose::Pose const &  pose 
)
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::scoring::constraints::Constraint::show_def(), core::pose::Pose::size(), and core::scoring::constraints::Constraint::type().

bool core::scoring::constraints::remove_constraint_from_residue_constraints ( int const  seqpos,
ConstraintCOP  cst,
ResidueConstraints residue_constraints,
bool  object_comparison 
)
void core::scoring::constraints::remove_constraints_of_type ( core::pose::Pose pose,
std::string const &  type 
)
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().

void core::scoring::constraints::remove_nonbb_constraints ( pose::Pose pose)
bool core::scoring::constraints::requires_CB_mapping ( AmbiguousNMRDistanceConstraint::Atoms  atoms,
pose::Pose const &  pose 
)
void core::scoring::constraints::skip_redundant_constraints ( ConstraintCOPs in,
Size  total_residue,
Size  influence_width 
)
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.ResidueCouplingConstraint"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.ResidueTypeConstraint"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.ResidueTypeLinkingConstraint"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints"  )
static
static basic::Tracer core::scoring::constraints::tr ( "core.scoring.constraints.util"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.MembraneSpanTermZConstraint"  )
static
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::DistancePairConstraint::distance_diff(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::constraints::DistancePairConstraint::read_def(), core::scoring::constraints::DihedralPairConstraint::read_def(), core::scoring::constraints::DihedralConstraint::read_def(), core::scoring::constraints::SiteConstraintResidues::read_def(), core::scoring::constraints::SiteConstraint::read_def(), core::scoring::constraints::FabConstraint::read_def(), core::scoring::constraints::AngleConstraint::read_def(), core::scoring::constraints::KofNConstraint::read_def(), core::scoring::constraints::SequenceProfileConstraint::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::BackboneStubLinearConstraint::score(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), and core::scoring::constraints::NamedAngleConstraint::setup_for_scoring().

static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.BackboneStubLinearConstraint"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.NamedDihedralConstraint"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.MembraneSpanConstraint"  )
static
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::BasePairConstraint::read_def(), core::scoring::constraints::MultiConstraint::read_def(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::read_def(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), core::scoring::constraints::CoordinateConstraint::read_def(), core::scoring::constraints::NamedAtomPairConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::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().

static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.SequenceProfileConstraint"  )
static
static basic::Tracer core::scoring::constraints::tr ( "core.scoring.ConstraintSet"  )
static
static basic::Tracer core::scoring::constraints::tr ( "core.scoring.ConstraintsEnergy"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.KofNConstraint"  )
static