Classes |
class | AmbiguousConstraint |
class | AmbiguousNMRConstraint |
class | AmbiguousNMRDistanceConstraint |
class | AngleConstraint |
| An Angular Constraint. More...
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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...
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class | AtomPairConstraintCreator |
| Mover creator for the AtomPairConstraint constraint. More...
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class | AngleConstraintCreator |
| Mover creator for the AngleConstraint constraint. More...
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class | DihedralConstraintCreator |
| Mover creator for the DihedralConstraint constraint. More...
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class | DihedralPairConstraintCreator |
| Constraint creator for DihedralPairConstraint. More...
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class | BigBinConstraintCreator |
| Mover creator for the BigBinConstraint constraint. More...
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class | MultiConstraintCreator |
| Mover creator for the MultiConstraint constraint. More...
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class | AmbiguousConstraintCreator |
| Mover creator for the AmbiguousConstraint constraint. More...
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class | KofNConstraintCreator |
| Mover creator for the KofNConstraint constraint. More...
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class | CoordinateConstraintCreator |
| Mover creator for the CoordinateConstraint constraint. More...
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class | LocalCoordinateConstraintCreator |
| Mover creator for the LocalCoordinateConstraint constraint. More...
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class | AmbiguousNMRDistanceConstraintCreator |
| Mover creator for the AmbiguousNMRDistanceConstraint constraint. More...
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class | AmbiguousNMRConstraintCreator |
| Mover creator for the AmbiguousNMRConstraint constraint. More...
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class | SiteConstraintCreator |
| Mover creator for the SiteConstraint constraint. More...
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class | BigBinConstraint |
| constraint on dihedral angle formed by 4 points More...
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class | BoundFunc |
class | PeriodicBoundFunc |
| a variant of the bound func that is periodic More...
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class | OffsetPeriodicBoundFunc |
| a variant of the bound func that is periodic More...
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class | CharmmPeriodicFunc |
| function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) More...
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class | CircularGeneral1D_Func |
| Function that allows return of arbitrary FArrays -- this time circularized. More...
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class | CircularHarmonicFunc |
| Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...
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class | CircularPowerFunc |
| Generalization of CircularCircularPowerFunc -- other exponents allowed. More...
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class | CircularSigmoidalFunc |
| Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints. More...
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class | ConstantConstraint |
| A Constant Constraint. More...
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class | ConstantFunc |
| Derived class of class Func representing a Constant distribution with a user-specified mean and standard deviation. More...
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class | Constraint |
| Actually a *restraint*, like a virtual rubber band between a pair of atoms. More...
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class | ConstraintCreator |
| Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...
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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...
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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...
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class | DihedralPairConstraint |
| constraint on dihedral angle formed by 4 points More...
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class | DOF_Constraint |
| This isn't quite a standard constraint since it acts on DOF's directly rather than on XYZ coordinates. More...
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class | EtableFunc |
| Class for representing arbitrarily defined functions. More...
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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...
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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...
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class | FuncFactory |
class | GaussianFunc |
| Derived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation. More...
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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...
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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...
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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...
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class | PeriodicFunc |
| function of type y = ( k * cos(n * (x - x0) ) ) + C More...
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class | ResidueTypeConstraint |
| This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
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class | ResidueTypeLinkingConstraint |
| This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
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class | ScalarWeightedFunc |
class | SequenceProfileConstraint |
class | SequenceProfileConstraintCreator |
| Constraint creator for the SequenceProfileConstraint constraint. More...
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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...
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class | SOGFunc |
| Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation. More...
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class | SOGFunc_Impl |
| Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation. More...
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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...
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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...
|