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core::scoring::constraints Namespace Reference

Classes

class  AmberPeriodicFunc
 function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) More...
 
class  AmbiguousConstraint
 
class  AmbiguousNMRConstraint
 
class  AmbiguousNMRDistanceConstraint
 
class  AngleConstraint
 An Angular Constraint. More...
 
class  AtomPairConstraint
 
class  BackboneStubConstraint
 This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location. More...
 
class  AtomPairConstraintCreator
 Mover creator for the AtomPairConstraint constraint. More...
 
class  AngleConstraintCreator
 Mover creator for the AngleConstraint constraint. More...
 
class  DihedralConstraintCreator
 Mover creator for the DihedralConstraint constraint. More...
 
class  DihedralPairConstraintCreator
 Constraint creator for DihedralPairConstraint. More...
 
class  BigBinConstraintCreator
 Mover creator for the BigBinConstraint constraint. More...
 
class  MultiConstraintCreator
 Mover creator for the MultiConstraint constraint. More...
 
class  AmbiguousConstraintCreator
 Mover creator for the AmbiguousConstraint constraint. More...
 
class  KofNConstraintCreator
 Mover creator for the KofNConstraint constraint. More...
 
class  CoordinateConstraintCreator
 Mover creator for the CoordinateConstraint constraint. More...
 
class  LocalCoordinateConstraintCreator
 Mover creator for the LocalCoordinateConstraint constraint. More...
 
class  AmbiguousNMRDistanceConstraintCreator
 Mover creator for the AmbiguousNMRDistanceConstraint constraint. More...
 
class  AmbiguousNMRConstraintCreator
 Mover creator for the AmbiguousNMRConstraint constraint. More...
 
class  SiteConstraintCreator
 Mover creator for the SiteConstraint constraint. More...
 
class  SiteConstraintResiduesCreator
 Mover creator for the SiteConstraintResidues constraint. More...
 
class  FabConstraintCreator
 Mover creator for the FabConstraint constraint. More...
 
class  BigBinConstraint
 constraint on dihedral angle formed by 4 points More...
 
class  BoundFunc
 
class  PeriodicBoundFunc
 a variant of the bound func that is periodic More...
 
class  OffsetPeriodicBoundFunc
 a variant of the bound func that is periodic More...
 
class  CharmmPeriodicFunc
 function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) More...
 
class  CircularGeneral1D_Func
 Function that allows return of arbitrary FArrays – this time circularized. More...
 
class  CircularHarmonicFunc
 Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...
 
class  CircularPowerFunc
 Generalization of CircularCircularPowerFunc – other exponents allowed. More...
 
class  CircularSigmoidalFunc
 Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...
 
class  ConstantConstraint
 A Constant Constraint. More...
 
class  ConstantFunc
 Derived class of class Func representing a Constant distribution with a user-specified mean and standard deviation. More...
 
class  Constraint
 Actually a restraint, like a virtual rubber band between a pair of atoms. More...
 
class  ConstraintCreator
 Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...
 
class  CstResNeighbIterator
 
class  CstResNeighbConstIterator
 
class  CstEnergyContainer
 
class  ConstraintFactory
 
class  ConstraintRegistrator
 This templated class will register an instance of an ConstraintCreator (class T) with the ConstraintFactory. It will ensure that no ConstraintCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  ConstraintNode
 
class  ConstraintEdge
 
class  ConstraintGraph
 
class  ConstraintIO
 
class  Constraints
 
class  ConstraintsEnergy
 
class  ConstraintsEnergyCreator
 
class  ResidueConstraints
 
class  ConstraintSet
 
class  CoordinateConstraint
 
class  CountViolFunc
 
class  CstMinimizationData
 
class  DihedralConstraint
 constraint on dihedral angle formed by 4 points More...
 
class  DihedralPairConstraint
 constraint on dihedral angle formed by 4 points More...
 
class  DistancePairConstraint
 constraint on CA distance More...
 
class  DOF_Constraint
 This isn't quite a standard constraint since it acts on DOF's directly rather than on XYZ coordinates. More...
 
class  EtableFunc
 Class for representing arbitrarily defined functions. More...
 
class  FabConstraint
 
class  FadeFunc
 
class  FlatHarmonicFunc
 
class  FourPointsFunc
 A simple class that represents the coordinates of four points, pretending that they all belong to residue 1. The residue() method is not implemented and cause a utility_exit. More...
 
class  Func
 Func is an abstract base class representing a function used to define constraints, in which func(r) gives the constraint score for the given value r. More...
 
class  FuncFactory
 
class  GaussianFunc
 Derived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation. More...
 
class  HarmonicFunc
 
class  IdentityFunc
 
class  KarplusFunc
 Function that evaluates a J-coupling from dihedral angles in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...
 
class  KofNConstraint
 
class  LinearPenaltyFunction
 
class  LocalCoordinateConstraint
 
class  MinMultiHarmonicFunc
 
class  MixtureFunc
 Derived class of class Func representing a Mixture of several distinct functions. The function is of the form ln( g(r) / h(r) ), where g(r) is a mixture of a Gaussian and Exponential distributions, and h(r) is a Gaussian distribution. See methods and implementation for more information. More...
 
class  MultiConstraint
 
class  Obsolet_NamedAtomPairConstraint
 
class  NamedAtomPairConstraint
 
class  NonResidueTypeConstraint
 This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
 
class  PeriodicFunc
 function of type y = ( k * cos(n * (x - x0) ) ) + C More...
 
class  ResidueTypeConstraint
 This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
 
class  ResidueTypeLinkingConstraint
 This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
 
class  ScalarWeightedFunc
 
class  SequenceProfileConstraint
 
class  SequenceProfileConstraintCreator
 Constraint creator for the SequenceProfileConstraint constraint. More...
 
class  SigmoidFunc
 
class  SiteConstraint
 
class  SiteConstraintResidues
 
class  SkipViolFunc
 
class  SoedingFunc
 Derived class of class Func representing a Soeding distribution with a user-specified mean and standard deviation. More...
 
class  SOGFunc
 Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation. More...
 
class  SOGFunc_Impl
 Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation. More...
 
class  SplineFunc
 
class  SquareWell2Func
 
class  SquareWellFunc
 
class  SumFunc
 
class  TopOutFunc
 
class  USOGFunc
 Unnormalized, unbounded sum of Gaussians constraint. More...
 
class  XYZ_Func
 just a simple class that takes an AtomID and returns a Vector (position) More...
 
class  ResidueXYZ
 
class  ResiduePairXYZ
 
class  ConformationXYZ
 
class  ChainbreakDistFunc
 

Typedefs

typedef
utility::pointer::owning_ptr
< AmberPeriodicFunc
AmberPeriodicFuncOP
 
typedef
utility::pointer::owning_ptr
< AmberPeriodicFunc const > 
AmberPeriodicFuncCOP
 
typedef
utility::pointer::owning_ptr
< AmbiguousConstraint
AmbiguousConstraintOP
 
typedef
utility::pointer::owning_ptr
< AmbiguousConstraint const > 
AmbiguousConstraintCOP
 
typedef
utility::pointer::owning_ptr
< AmbiguousNMRConstraint
AmbiguousNMRConstraintOP
 
typedef
utility::pointer::owning_ptr
< AmbiguousNMRConstraint const > 
AmbiguousNMRConstraintCOP
 
typedef
utility::pointer::owning_ptr
< AmbiguousNMRDistanceConstraint
AmbiguousNMRDistanceConstraintOP
 
typedef
utility::pointer::owning_ptr
< AmbiguousNMRDistanceConstraint
const > 
AmbiguousNMRDistanceConstraintCOP
 
typedef utility::vector1
< core::id::NamedAtomID
NamedAtoms
 
typedef
utility::pointer::owning_ptr
< AngleConstraint
AngleConstraintOP
 
typedef
utility::pointer::owning_ptr
< AngleConstraint const > 
AngleConstraintCOP
 
typedef
utility::pointer::owning_ptr
< AtomPairConstraint
AtomPairConstraintOP
 
typedef
utility::pointer::owning_ptr
< AtomPairConstraint const > 
AtomPairConstraintCOP
 
typedef
utility::pointer::owning_ptr
< BackboneStubConstraint
BackboneStubConstraintOP
 
typedef
utility::pointer::owning_ptr
< BackboneStubConstraint const > 
BackboneStubConstraintCOP
 
typedef utility::vector1
< BackboneStubConstraintOP
BackboneStubConstraintOPs
 
typedef utility::vector1
< BackboneStubConstraintCOP
BackboneStubConstraintCOPs
 
typedef
utility::pointer::owning_ptr
< BoundFunc
BoundFuncOP
 
typedef
utility::pointer::owning_ptr
< BoundFunc const > 
BoundFuncCOP
 
typedef
utility::pointer::owning_ptr
< CircularGeneral1D_Func
CircularGeneral1D_FuncOP
 
typedef
utility::pointer::owning_ptr
< CircularGeneral1D_Func const > 
CircularGeneral1D_FuncCOP
 
typedef
utility::pointer::owning_ptr
< CircularHarmonicFunc
CircularHarmonicFuncOP
 
typedef
utility::pointer::owning_ptr
< CircularHarmonicFunc const > 
CircularHarmonicFuncCOP
 
typedef
utility::pointer::owning_ptr
< CircularPowerFunc
CircularPowerFuncOP
 
typedef
utility::pointer::owning_ptr
< CircularPowerFunc const > 
CircularPowerFuncCOP
 
typedef
utility::pointer::owning_ptr
< CircularSigmoidalFunc
CircularSigmoidalFuncOP
 
typedef
utility::pointer::owning_ptr
< CircularSigmoidalFunc const > 
CircularSigmoidalFuncCOP
 
typedef
utility::pointer::owning_ptr
< ConstantFunc
ConstantFuncOP
 
typedef
utility::pointer::owning_ptr
< Constraint
ConstraintOP
 
typedef
utility::pointer::owning_ptr
< Constraint const > 
ConstraintCOP
 
typedef utility::vector1
< ConstraintOP
ConstraintOPs
 
typedef utility::vector1
< ConstraintCOP
ConstraintCOPs
 
typedef
utility::pointer::owning_ptr
< ConstraintCreator
ConstraintCreatorOP
 
typedef
utility::pointer::owning_ptr
< ConstraintCreator const > 
ConstraintCreatorCOP
 
typedef
utility::pointer::owning_ptr
< CstEnergyContainer
CstEnergyContainerOP
 
typedef
utility::pointer::owning_ptr
< CstEnergyContainer const > 
CstEnergyContainerCOP
 
typedef
utility::pointer::owning_ptr
< ConstraintGraph
ConstraintGraphOP
 
typedef
utility::pointer::owning_ptr
< ConstraintGraph const > 
ConstraintGraphCOP
 
typedef
utility::pointer::owning_ptr
< Constraints
ConstraintsOP
 
typedef
utility::pointer::owning_ptr
< Constraints const > 
ConstraintsCOP
 
typedef
utility::pointer::owning_ptr
< ConstraintsEnergy
ConstraintsEnergyOP
 
typedef
utility::pointer::owning_ptr
< ConstraintsEnergy const > 
ConstraintsEnergyCOP
 
typedef
utility::pointer::owning_ptr
< ResidueConstraints
ResidueConstraintsOP
 
typedef
utility::pointer::owning_ptr
< ResidueConstraints const > 
ResidueConstraintsCOP
 
typedef
utility::pointer::owning_ptr
< ConstraintSet
ConstraintSetOP
 
typedef
utility::pointer::owning_ptr
< ConstraintSet const > 
ConstraintSetCOP
 
typedef
utility::pointer::owning_ptr
< CstMinimizationData
CstMinimizationDataOP
 
typedef
utility::pointer::owning_ptr
< CstMinimizationData const > 
CstMinimizationDataCOP
 
typedef
utility::pointer::owning_ptr
< DihedralConstraint
DihedralConstraintOP
 
typedef
utility::pointer::owning_ptr
< DihedralConstraint const > 
DihedralConstraintCOP
 
typedef
utility::pointer::owning_ptr
< DOF_Constraint
DOF_ConstraintOP
 
typedef
utility::pointer::owning_ptr
< DOF_Constraint const > 
DOF_ConstraintCOP
 
typedef utility::vector1
< DOF_ConstraintOP
DOF_ConstraintOPs
 
typedef utility::vector1
< DOF_ConstraintCOP
DOF_ConstraintCOPs
 
typedef
utility::pointer::owning_ptr
< EtableFunc
EtableFuncOP
 
typedef
utility::pointer::owning_ptr
< FabConstraint
FabConstraintOP
 
typedef
utility::pointer::owning_ptr
< FabConstraint const > 
FabConstraintCOP
 
typedef
utility::pointer::owning_ptr
< FadeFunc
FadeFuncOP
 
typedef
utility::pointer::owning_ptr
< FadeFunc const > 
FadeFuncCOP
 
typedef
utility::pointer::owning_ptr
< FlatHarmonicFunc
FlatHarmonicFuncOP
 
typedef
utility::pointer::owning_ptr
< FlatHarmonicFunc const > 
FlatHarmonicFuncCOP
 
typedef
utility::pointer::owning_ptr
< FourPointsFunc
FourPointsFuncOP
 
typedef
utility::pointer::owning_ptr
< FourPointsFunc const > 
FourPointsFuncCOP
 
typedef
utility::pointer::owning_ptr
< Func
FuncOP
 
typedef
utility::pointer::owning_ptr
< GaussianFunc
GaussianFuncOP
 
typedef
utility::pointer::owning_ptr
< HarmonicFunc
HarmonicFuncOP
 
typedef
utility::pointer::owning_ptr
< HarmonicFunc const > 
HarmonicFuncCOP
 
typedef
utility::pointer::owning_ptr
< IdentityFunc
IdentityFuncOP
 
typedef
utility::pointer::owning_ptr
< IdentityFunc const > 
IdentityFuncCOP
 
typedef
utility::pointer::owning_ptr
< KarplusFunc
KarplusFuncOP
 
typedef
utility::pointer::owning_ptr
< KarplusFunc const > 
KarplusFuncCOP
 
typedef
utility::pointer::owning_ptr
< KofNConstraint
KofNConstraintOP
 
typedef
utility::pointer::owning_ptr
< KofNConstraint const > 
KofNConstraintCOP
 
typedef
utility::pointer::owning_ptr
< LocalCoordinateConstraint
LocalCoordinateConstraintOP
 
typedef
utility::pointer::owning_ptr
< LocalCoordinateConstraint
const > 
LocalCoordinateConstraintCOP
 
typedef
utility::pointer::owning_ptr
< MinMultiHarmonicFunc
MinMultiHarmonicFuncOP
 
typedef
utility::pointer::owning_ptr
< MinMultiHarmonicFunc const > 
MinMultiHarmonicFuncCOP
 
typedef
utility::pointer::owning_ptr
< MixtureFunc
MixtureFuncOP
 
typedef
utility::pointer::owning_ptr
< MultiConstraint
MultiConstraintOP
 
typedef
utility::pointer::owning_ptr
< MultiConstraint const > 
MultiConstraintCOP
 
typedef
utility::pointer::owning_ptr
< NamedAtomPairConstraint
NamedAtomPairConstraintOP
 
typedef
utility::pointer::owning_ptr
< NamedAtomPairConstraint
const > 
NamedAtomPairConstraintCOP
 
typedef
utility::pointer::owning_ptr
< Obsolet_NamedAtomPairConstraint
Obsolet_NamedAtomPairConstraintOP
 
typedef
utility::pointer::owning_ptr
< Obsolet_NamedAtomPairConstraint
const > 
Obsolet_NamedAtomPairConstraintCOP
 
typedef
utility::pointer::owning_ptr
< NonResidueTypeConstraint
NonResidueTypeConstraintOP
 
typedef
utility::pointer::owning_ptr
< NonResidueTypeConstraint
const > 
NonResidueTypeConstraintCOP
 
typedef
utility::pointer::owning_ptr
< ResidueTypeConstraint
ResidueTypeConstraintOP
 
typedef
utility::pointer::owning_ptr
< ResidueTypeConstraint const > 
ResidueTypeConstraintCOP
 
typedef
utility::pointer::owning_ptr
< ResidueTypeLinkingConstraint
ResidueTypeLinkingConstraintOP
 
typedef
utility::pointer::owning_ptr
< ResidueTypeLinkingConstraint
const > 
ResidueTypeLinkingConstraintCOP
 
typedef
utility::pointer::owning_ptr
< ScalarWeightedFunc
ScalarWeightedFuncOP
 
typedef
utility::pointer::owning_ptr
< ScalarWeightedFunc const > 
ScalarWeightedFuncCOP
 
typedef
utility::pointer::owning_ptr
< SequenceProfileConstraint
SequenceProfileConstraintOP
 
typedef
utility::pointer::owning_ptr
< SequenceProfileConstraint
const > 
SequenceProfileConstraintCOP
 
typedef
utility::pointer::owning_ptr
< SiteConstraint
SiteConstraintOP
 
typedef
utility::pointer::owning_ptr
< SiteConstraint const > 
SiteConstraintCOP
 
typedef
utility::pointer::owning_ptr
< SiteConstraintResidues
SiteConstraintResiduesOP
 
typedef
utility::pointer::owning_ptr
< SiteConstraintResidues const > 
SiteConstraintResiduesCOP
 
typedef
utility::pointer::owning_ptr
< SoedingFunc
SoedingFuncOP
 
typedef
utility::pointer::owning_ptr
< SOGFunc
SOGFuncOP
 
typedef
utility::pointer::owning_ptr
< SOGFunc_Impl
SOGFunc_ImplOP
 
typedef
utility::pointer::owning_ptr
< SplineFunc
SplineFuncOP
 
typedef
utility::pointer::owning_ptr
< SplineFunc const > 
SplineFuncCOP
 
typedef
utility::pointer::owning_ptr
< SquareWell2Func
SquareWell2FuncOP
 
typedef
utility::pointer::owning_ptr
< SquareWell2Func const > 
SquareWell2FuncCOP
 
typedef
utility::pointer::owning_ptr
< SquareWellFunc
SquareWellFuncOP
 
typedef
utility::pointer::owning_ptr
< SquareWellFunc const > 
SquareWellFuncCOP
 
typedef
utility::pointer::owning_ptr
< SumFunc
SumFuncOP
 
typedef
utility::pointer::owning_ptr
< TopOutFunc
TopOutFuncOP
 
typedef
utility::pointer::owning_ptr
< TopOutFunc const > 
TopOutFuncCOP
 
typedef
utility::pointer::owning_ptr
< USOGFunc
USOGFuncOP
 
typedef
utility::pointer::owning_ptr
< USOGFunc const > 
USOGFuncCOP
 

Functions

bool is_aromatic (pose::Pose const &pose, core::Size res)
 
bool is_aromatic (core::chemical::AA aa)
 
void parse_NMR_name (std::string name, core::Size res, core::chemical::AA aa, NamedAtoms &atoms)
 
void parse_NMR_name (std::string name, core::Size res, AmbiguousNMRDistanceConstraint::Atoms &atoms, core::pose::Pose const &pose)
 
void parse_NMR_name_old (std::string name, core::Size res, AmbiguousNMRDistanceConstraint::Atoms &atoms, core::pose::Pose const &pose)
 
bool requires_CB_mapping (AmbiguousNMRDistanceConstraint::Atoms atoms, pose::Pose const &pose)
 
void combine_NMR_atom_string (AmbiguousNMRDistanceConstraint::Atoms atoms, std::string &atom_str, pose::Pose const &pose)
 
static basic::Tracer TRACER ("core.io.constraints")
 
static basic::Tracer TR ("core.scoring.constraints.BackboneStubConstraint")
 
std::ostream & operator<< (std::ostream &out, Constraint &cst)
 
std::string get_section_name (std::string line)
 
static basic::Tracer tr ("core.scoring.ConstraintsEnergy")
 
static basic::Tracer tr ("core.scoring.ConstraintSet")
 
void add_constraint_to_residue_constraints (int const seqpos, ConstraintCOP cst, ResidueConstraints &residue_constraints)
 helper, static More...
 
bool remove_constraint_from_residue_constraints (int const seqpos, ConstraintCOP cst, ResidueConstraints &residue_constraints, bool object_comparison)
 helper, static More...
 
std::ostream & operator<< (std::ostream &os, ConstraintSet const &set)
 
static basic::Tracer TR ("core.io.constraints")
 
static basic::Tracer TR ("core.io.constraints")
 
static basic::Tracer TR ("core.io.constraints")
 
std::ostream & operator<< (std::ostream &out, const Func &f)
 
static basic::Tracer trMinMultiHarmonicFunc ("fragment.picking.scores.MinMultiHarmonicFunc")
 
std::ostream & operator<< (std::ostream &out, Obsolet_NamedAtomPairConstraint const &cst)
 
static basic::Tracer non_residue_type_constraint_tracer ("core.scoring.constraints.NonResidueTypeConstraint")
 
static basic::Tracer TR ("core.scoring.constraints.ResidueTypeConstraint")
 
static basic::Tracer TR ("core.scoring.constraints.ResidueTypeLinkingConstraint")
 
static basic::Tracer TR ("core.scoring.constraints.SequenceProfileConstraint")
 
core::Real readValueOrDie (std::istream &in)
 Reads and returns a single floating point value from the specified input stream, aborting if either the failbit or badbit is flipped. More...
 
static
numeric::random::RandomGenerator 
RG (42015512)
 
static basic::Tracer tr ("core.scoring.constraints")
 
Real logdgaussian (Real x, Real mean, Real sd, Real weight)
 Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real logdgaussian_deriv (Real x, Real mean, Real sd, Real)
 Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real dgaussian (Real x, Real mean, Real sd, Real weight)
 Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real gaussian_deriv (Real x, Real mean, Real sd, Real weight)
 Returns the weighted derivative of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real dexponential (Real x, Real anchor, Real rate, Real weight)
 Returns the weighted value of an exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real exponential_deriv (Real x, Real anchor, Real rate, Real weight)
 Returns the weighted derivative of a log-exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real linear_interpolate (Real const x_val, Real const x1, Real const x2, Real const y1, Real const y2)
 Estimates the y-value of the given x-value by interpolating between the given points (x1,y1) and (x2,y2) by using linear interpolation between the two points. More...
 
void cull_violators (ConstraintCOPs const &target_list, ConstraintCOPs &culled_list, pose::Pose const &filter_pose, core::Real threshold)
 
std::string get_cst_file_option ()
 
void add_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
 
void add_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
 
void add_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
 
std::string get_cst_fa_file_option ()
 
void add_fa_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
 add constraints if specified by user using the -constraints::cst_fa_file flag. Setting appropriate weights for ScoreFunction is done elsewhere. More...
 
void add_fa_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
 add constraints if specified by user. More...
 
void add_fa_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
 add constraints if specified by user. More...
 
void add_coordinate_constraints (core::pose::Pose &pose, core::Real const coord_sdev=10.0)
 handy function for tethering pose to starting coordinates. More...
 
bool combinable (Constraint const &cst, utility::vector1< Size > exclude_res)
 
void choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, ConstraintCOPs &in)
 combine constraints randomly into AmbiguousConstraints N -> 1 this greatly decreases the odds to have a wrong constraint More...
 
core::Size bin_by_seq_separation (core::Size sep)
 
void combine_constraints (ConstraintCOPs &in, core::Size combine_ratio, utility::vector1< bool > exclude_res, core::kinematics::ShortestPathInFoldTree const &sp_in)
 combine constraints randomly into AmbiguousConstraints N -> 1 this greatly decreases the odds to have a wrong constraint More...
 
void count_constraint (ConstraintCOP cst, bool redundant, ObjexxFCL::FArray2D_int &count_matrix, Size influence_width, Size total_residue)
 
bool keep_constraint (ConstraintCOP cst, bool redundant, ObjexxFCL::FArray2D_int &count_matrix, Size influence_width, Size total_residue)
 
void skip_redundant_constraints (ConstraintCOPs &in, core::Size total_residue, core::Size influence_width=1)
 have at most one constraint per residue pair... More...
 
void drop_constraints (ConstraintCOPs &in, core::Real drop_rate)
 

Typedef Documentation

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

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

add constraints if specified by user.

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

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

void core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction scorefxn_)
core::Size core::scoring::constraints::bin_by_seq_separation ( core::Size  sep)
inline

Referenced by combine_constraints().

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

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

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

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

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), 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(), RG(), and tr().

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

void core::scoring::constraints::combine_NMR_atom_string ( AmbiguousNMRDistanceConstraint::Atoms  atoms,
std::string &  atom_str,
pose::Pose const &  pose 
)
void core::scoring::constraints::count_constraint ( ConstraintCOP  cst,
bool  redundant,
ObjexxFCL::FArray2D_int &  count_matrix,
Size  influence_width,
Size  total_residue 
)

References tr().

Referenced by skip_redundant_constraints().

void core::scoring::constraints::cull_violators ( ConstraintCOPs const &  target_list,
ConstraintCOPs culled_list,
pose::Pose const &  filter_pose,
core::Real  threshold 
)
Real core::scoring::constraints::dexponential ( Real  x,
Real  anchor,
Real  rate,
Real  weight 
)

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

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

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

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

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

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

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

References dgaussian().

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

std::string core::scoring::constraints::get_cst_fa_file_option ( )
std::string core::scoring::constraints::get_cst_file_option ( )
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::constraints::EtableFunc::func().

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

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

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

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

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

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

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

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

static basic::Tracer core::scoring::constraints::non_residue_type_constraint_tracer ( "core.scoring.constraints.NonResidueTypeConstraint"  )
static
std::ostream& core::scoring::constraints::operator<< ( std::ostream &  out,
const Func &  f 
)
std::ostream& core::scoring::constraints::operator<< ( std::ostream &  out,
Obsolet_NamedAtomPairConstraint const &  cst 
)
std::ostream& core::scoring::constraints::operator<< ( std::ostream &  out,
Constraint &  cst 
)
inline
std::ostream & core::scoring::constraints::operator<< ( std::ostream &  os,
ConstraintSet const &  set 
)
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 
)
core::Real core::scoring::constraints::readValueOrDie ( std::istream &  in)

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

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

bool core::scoring::constraints::remove_constraint_from_residue_constraints ( int const  seqpos,
ConstraintCOP  cst,
ResidueConstraints residue_constraints,
bool  object_comparison 
)
bool core::scoring::constraints::requires_CB_mapping ( AmbiguousNMRDistanceConstraint::Atoms  atoms,
pose::Pose const &  pose 
)
static numeric::random::RandomGenerator core::scoring::constraints::RG ( 42015512  )
static
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.ResidueTypeLinkingConstraint"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.io.constraints"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.io.constraints"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.io.constraints"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.ResidueTypeConstraint"  )
static
static basic::Tracer core::scoring::constraints::tr ( "core.scoring.constraints"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.BackboneStubConstraint"  )
static
static basic::Tracer core::scoring::constraints::tr ( "core.scoring.ConstraintSet"  )
static
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.SequenceProfileConstraint"  )
static
static basic::Tracer core::scoring::constraints::tr ( "core.scoring.ConstraintsEnergy"  )
static

Referenced by core::scoring::constraints::ConstraintSet::add_constraint(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint(), combine_constraints(), combine_NMR_atom_string(), count_constraint(), cull_violators(), get_cst_fa_file_option(), get_cst_file_option(), keep_constraint(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CEN(), 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::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::Func::read_data(), core::scoring::constraints::CoordinateConstraint::read_def(), core::scoring::constraints::MultiConstraint::read_def(), core::scoring::constraints::NamedAtomPairConstraint::read_def(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::read_def(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::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::NamedAtomPairConstraint::setup_for_scoring(), skip_redundant_constraints(), and core::scoring::constraints::LocalCoordinateConstraint::xyz_target().

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