Rosetta 3.4
Classes | Typedefs | Functions
core::scoring::constraints Namespace Reference

Classes

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

Typedefs

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

Functions

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

Typedef Documentation


Function Documentation

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

add constraints if specified by user.

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

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

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

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

Referenced by combine_constraints().

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

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

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

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

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

bool core::scoring::constraints::combinable ( Constraint const &  cst,
utility::vector1< Size exclude_res 
)
void core::scoring::constraints::combine_constraints ( ConstraintCOPs in,
core::Size  combine_ratio,
utility::vector1< bool exclude_res,
core::kinematics::ShortestPathInFoldTree const &  sp_in 
)

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

combine constraints randomly into Ambiguous constraints...

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

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

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

References tr().

Referenced by skip_redundant_constraints().

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

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

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

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

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

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

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

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

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

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

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

static basic::Tracer core::scoring::constraints::non_residue_type_constraint_tracer ( "core.scoring.constraints.NonResidueTypeConstraint"  ) [static]
std::ostream& core::scoring::constraints::operator<< ( std::ostream &  out,
Obsolet_NamedAtomPairConstraint const &  cst 
)
std::ostream& core::scoring::constraints::operator<< ( std::ostream &  out,
Constraint &  cst 
) [inline]
std::ostream& core::scoring::constraints::operator<< ( std::ostream &  out,
const Func &  f 
)
void core::scoring::constraints::parse_NMR_name ( std::string  name,
core::Size  res,
AmbiguousNMRDistanceConstraint::Atoms &  atoms,
core::pose::Pose const &  pose 
)
bool core::scoring::constraints::remove_constraint_from_residue_constraints ( int const  seqpos,
ConstraintCOP  cst,
ResidueConstraints residue_constraints,
bool  object_comparison 
)
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.scoring.ConstraintSet"  ) [static]
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.SequenceProfileConstraint"  ) [static]
static basic::Tracer core::scoring::constraints::TR ( "core.io.constraints"  ) [static]
static basic::Tracer core::scoring::constraints::tr ( "core.scoring.ConstraintsEnergy"  ) [static]

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_CB(), 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(), 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::NamedAtomPairConstraint::read_def(), core::scoring::constraints::MultiConstraint::read_def(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), core::scoring::constraints::CoordinateConstraint::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::tr ( "core.scoring.constraints"  ) [static]
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.ResidueTypeConstraint"  ) [static]
static basic::Tracer core::scoring::constraints::TR ( "core.scoring.constraints.BackboneStubConstraint"  ) [static]
static basic::Tracer core::scoring::constraints::TRACER ( "core.io.constraints"  ) [static]
static basic::Tracer core::scoring::constraints::trMinMultiHarmonicFunc ( "fragment.picking.scores.MinMultiHarmonicFunc"  ) [static]
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