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core::pack::dunbrack Namespace Reference

Classes

class  ChiSet
 
class  CoarseRotamer
 
class  CoarseRotamerSet
 
class  CoarseSingleResidueLibrary
 
class  DunbrackConstraint
 
class  DunbrackConstraintCreator
 Mover creator for the DunbrackConstraint constraint. More...
 
class  DunbrackEnergy
 
class  DunbrackEnergyCreator
 
class  DunbrackRotamerMeanSD
 forward declaration; default precision is DunbrackReal More...
 
class  PackedDunbrackRotamer
 forward declaration; default precision is DunbrackReal; More...
 
class  DunbrackRotamer
 forward declaration; default precision is DunbrackReal More...
 
class  DunbrackRotamerSampleData
 
class  RotamerBuildingData
 a simple class for passing data around in virtual function calls of the rotamer creating process. Derived classes will be simple containers for interpolated rotameric data that 1) has to be available to the derived class when building rotamers and 2) cannot be stored as member data in the derived class in a thread-safe manner. Derived classes of the RotamerBuildingData can be declared on the stack, passed into the RotamericSingleResidueDunbrackLibrary::build_chi_sets function, and then in the (virtual) chisamples_for_rotamer function, the derived classes may be downcast. More...
 
class  RotamerConstraint
 This class favors a particular rotamer at a particular position by reducing its Dunbrack energy. More...
 
class  RotamericSingleResidueDunbrackLibrary
 
class  RotamericData
 
class  SingleResidueRotamerLibrary
 
class  RotamerLibrary
 
class  RotamerLibraryScratchSpace
 
class  SemiRotamericSingleResidueDunbrackLibrary
 This class is meant to represent the non-rotameric chi observed in several amino acids (asn, asp, gln, glu, his, phe, trp, tyr ) which are rotameric for the chi closest to the backbone and non rotameric for exactly one chi angle. This non-rotameric chi (abv. nrchi) is the last chi for each of these 8 amino acids except tyrosine, where this chi is the last heavy-atom chi. The last chi on tyrosine governs a hydroxyl. Unlike in the fully rotameric residues, the last heavyatom chi in semi-rotameric residues do not "communicate" to the rotameric chi. That is, in the rotameric chi, the mean chi1 value is sensitive to the chi3 value. If the third diherdal switches from trans to g+, then chi1 would shift in response. Changes to the non-rotameric chi do not effect the rotameric chi. The data structure here is good for this model but no other. More...
 
class  BBDepNRChiSample
 P for precision. More...
 
class  BBIndNRChiSample
 
class  BBDepSemiRotamericData
 A class to hold rotamer building data on the stack and yet have it accessible to derived classes when invoking base class functions. An alternative would have been to store mutable member data in the Library class itself. This option, however, is not thread safe. This data is used by the SemiRotamericSRDL class for when building backbone dependent rotamers. More...
 
struct  BBDepScoreInterpData
 
class  BBIndSemiRotamericData
 A class to hold rotamer building data on the stack and yet have it accessible to derived classes when invoking base class functions. An alternative would have been to store mutable member data in the Library class itself. This option, however, is not thread safe. This data is used by the SemiRotamericSRDL class for when building backbone independent rotamers. More...
 
class  ProbSortClass
 
class  SingleLigandRotamerLibrary
 A fixed library of conformations for some residue type (doesn't have to be a ligand). More...
 
class  SingleResidueDunbrackLibraryConcrete
 
class  SingleResidueDunbrackLibrary
 

Typedefs

typedef
utility::pointer::owning_ptr
< ChiSet
ChiSetOP
 
typedef
utility::pointer::owning_ptr
< ChiSet const > 
ChiSetCOP
 
typedef
utility::pointer::owning_ptr
< CoarseRotamer
CoarseRotamerOP
 
typedef
utility::pointer::owning_ptr
< CoarseRotamer const > 
CoarseRotamerCOP
 
typedef
utility::pointer::owning_ptr
< CoarseRotamerSet
CoarseRotamerSetOP
 
typedef
utility::pointer::owning_ptr
< CoarseRotamerSet const > 
CoarseRotamerSetCOP
 
typedef
utility::pointer::owning_ptr
< CoarseSingleResidueLibrary
CoarseSingleResidueLibraryOP
 
typedef
utility::pointer::owning_ptr
< CoarseSingleResidueLibrary
const > 
CoarseSingleResidueLibraryCOP
 
typedef
utility::pointer::owning_ptr
< DunbrackConstraint
DunbrackConstraintOP
 
typedef
utility::pointer::owning_ptr
< DunbrackConstraint const > 
DunbrackConstraintCOP
 
typedef float DunbrackReal
 
typedef utility::vector1< SizeRotVector
 
typedef utility::vector1< RealChiVector
 
typedef utility::vector1< RealAngleVector
 
typedef
utility::pointer::owning_ptr
< RotamerConstraint
RotamerConstraintOP
 
typedef
utility::pointer::owning_ptr
< RotamerConstraint const > 
RotamerConstraintCOP
 
typedef
utility::pointer::owning_ptr
< RotamerLibrary
RotamerLibraryOP
 
typedef
utility::pointer::owning_ptr
< RotamerLibrary const > 
RotamerLibraryCOP
 
typedef
utility::pointer::owning_ptr
< SingleResidueRotamerLibrary
SingleResidueRotamerLibraryOP
 
typedef
utility::pointer::access_ptr
< SingleResidueRotamerLibrary
SingleResidueRotamerLibraryAP
 
typedef
utility::pointer::owning_ptr
< SingleResidueRotamerLibrary
const > 
SingleResidueRotamerLibraryCOP
 
typedef
utility::pointer::access_ptr
< SingleResidueRotamerLibrary
const > 
SingleResidueRotamerLibraryCAP
 
typedef
utility::pointer::owning_ptr
< SingleResidueDunbrackLibrary
SingleResidueDunbrackLibraryOP
 
typedef
utility::pointer::access_ptr
< SingleResidueDunbrackLibrary
SingleResidueDunbrackLibraryAP
 
typedef
utility::pointer::owning_ptr
< SingleResidueDunbrackLibrary
const > 
SingleResidueDunbrackLibraryCOP
 
typedef
utility::pointer::access_ptr
< SingleResidueDunbrackLibrary
const > 
SingleResidueDunbrackLibraryCAP
 
typedef utility::vector1
< conformation::ResidueOP
RotamerVector
 
typedef
utility::fixedsizearray1< Real,
DUNBRACK_MAX_SCTOR
Real4
 
typedef
utility::fixedsizearray1< Size,
DUNBRACK_MAX_SCTOR
Size4
 
typedef
utility::fixedsizearray1< Real,
DUNBRACK_MAX_BBTOR
Real3
 
typedef
utility::fixedsizearray1< Size,
DUNBRACK_MAX_BBTOR
Size3
 
typedef
utility::pointer::owning_ptr
< RotamerLibraryScratchSpace
RotamerLibraryScratchSpaceOP
 
typedef
utility::pointer::owning_ptr
< RotamerLibraryScratchSpace
const > 
RotamerLibraryScratchSpaceCOP
 
typedef
utility::pointer::owning_ptr
< SingleLigandRotamerLibrary
SingleLigandRotamerLibraryOP
 
typedef
utility::pointer::owning_ptr
< SingleLigandRotamerLibrary
const > 
SingleLigandRotamerLibraryCOP
 
typedef
utility::pointer::access_ptr
< SingleLigandRotamerLibrary
SingleLigandRotamerLibraryAP
 
typedef
utility::pointer::access_ptr
< SingleLigandRotamerLibrary
const > 
SingleLigandRotamerLibraryCAP
 

Functions

static basic::Tracer TR ("core.pack.dunbrack.DunbrackConstraint")
 
void bicubic_interpolation (Real v00, Real d2dx200, Real d2dy200, Real d4dx2y200, Real v01, Real d2dx201, Real d2dy201, Real d4dx2y201, Real v10, Real d2dx210, Real d2dy210, Real d4dx2y210, Real v11, Real d2dx211, Real d2dy211, Real d4dx2y211, Real dxp, Real dyp, Real binwx, Real binwy, Real &val, Real &dvaldx, Real &dvaldy)
 Interpolate in a grid with the values, and second derivatives given, and simultaneously evaluate the derivative. No option for working with periodic ranges. Instead, make sure that interpolation doesn't need to span > 180 degrees. More...
 
void tricubic_interpolation (Real v000, Real dvdx000, Real dvdy000, Real dvdz000, Real dvdxy000, Real dvdxz000, Real dvdyz000, Real dvdxyz000, Real v001, Real dvdx001, Real dvdy001, Real dvdz001, Real dvdxy001, Real dvdxz001, Real dvdyz001, Real dvdxyz001, Real v010, Real dvdx010, Real dvdy010, Real dvdz010, Real dvdxy010, Real dvdxz010, Real dvdyz010, Real dvdxyz010, Real v011, Real dvdx011, Real dvdy011, Real dvdz011, Real dvdxy011, Real dvdxz011, Real dvdyz011, Real dvdxyz011, Real v100, Real dvdx100, Real dvdy100, Real dvdz100, Real dvdxy100, Real dvdxz100, Real dvdyz100, Real dvdxyz100, Real v101, Real dvdx101, Real dvdy101, Real dvdz101, Real dvdxy101, Real dvdxz101, Real dvdyz101, Real dvdxyz101, Real v110, Real dvdx110, Real dvdy110, Real dvdz110, Real dvdxy110, Real dvdxz110, Real dvdyz110, Real dvdxyz110, Real v111, Real dvdx111, Real dvdy111, Real dvdz111, Real dvdxy111, Real dvdxz111, Real dvdyz111, Real dvdxyz111, Real dxp, Real dyp, Real dzp, Real binwx, Real binwy, Real binwz, Real &val, Real &dvaldx, Real &dvaldy, Real &dvaldz)
 
void interpolate_rotamers (DunbrackRotamer< FOUR > const &rot00, DunbrackRotamer< FOUR > const &rot10, DunbrackRotamer< FOUR > const &rot01, DunbrackRotamer< FOUR > const &rot11, Real phi_err, Real psi_err, Real binrange, Size nchi_aa, DunbrackRotamer< FOUR, Real > &interpolated_rotamer)
 
void expand_proton_chi_oldversion (pack::task::ExtraRotSample ex_samp_level, chemical::ResidueTypeCOP concrete_residue, Size proton_chi, utility::vector1< ChiSetOP > &chi_set_vector)
 
void expand_proton_chi (pack::task::ExtraRotSample ex_samp_level, chemical::ResidueTypeCOP concrete_residue, Size proton_chi, utility::vector1< ChiSetOP > &chi_set_vector)
 Should this be here? More...
 
template<Size S>
DunbrackRotamer< S, Realincrease_rotamer_precision (DunbrackRotamer< S, DunbrackReal > const &original_rotamer)
 
static basic::Tracer TR ("core.pack.dunbrack.RotamerConstraint")
 
void load_unboundrot (pose::Pose &pose)
 Convenience function adds constraints to the supplied pose based on the -unboundrot command line flag. More...
 
void load_unboundrot (pose::Pose &pose, core::pose::PoseCOPs const &unboundrot_poses)
 Convenience function adds constraints to the supplied pose based on the list of provided poses. More...
 
void rotamer_from_chi (conformation::Residue const &rsd, RotVector &rot)
 helper that'll determine the rotamer bins for a residue by asking its associated rotamer library for that information. More...
 
void rotamer_from_chi (chemical::ResidueType const &rsd_type, ChiVector const &chi, RotVector &rot)
 helper that'll determine the rotamer bins for a residue_type by asking its associated rotamer library for that information. Takes chi vector as input parameter. More...
 
void rotamer_from_chi_02 (ChiVector const &chi,chemical::AA const res,RotVector &rot)
 Do not bother calling this function if you're interested in staying up to date with changes in the rotamer library. Call rotamer_from_chi instead. It will eventually call this function iff dun10 is not set to true. More...
 
*void rotamer_from_chi_02 (Real4 const &chi, chemical::AA const res, Size nchi, Size4 &rot)
 
void read_dunbrack_library (RotamerLibrary &rotamer_library)
 
Real subtract_chi_angles (Real chi1, Real chi2, chemical::AA const &aa, int chino)
 Find the difference in angles between two chi values using hard-coded symmetry information for the symmetric amino acids. Disappears for 2010 library. More...
 
bool psc_compare (ProbSortClass left, ProbSortClass right)
 
static basic::Tracer TR ("core.pack.dunbrack.SingleLigandRotamerLibrary")
 
void dump_library (std::string filename, RotamerVector const &rotamers)
 
conformation::ResidueOP dup_residue (conformation::Residue const &existing, conformation::Residue const &conformer)
 Helper function for superposition. More...
 
static basic::Tracer SRDL_TR ("core.pack.dunbrack")
 

Variables

Size const ONE = 1
 
Size const TWO = 2
 
Size const THREE = 3
 
Size const FOUR = 4
 
 c
 DEPRICATED convert between the real-valued chi dihedrals and the rotamer well indices. More...
 
Size const DUNBRACK_MAX_BBTOR = 3
 
Size const DUNBRACK_MAX_SCTOR = 4
 
static const Real MIN_ROT_PROB = 1.e-8
 

Typedef Documentation

Low precision in Dunbrack rotamer library suggests no need to store chi dihedrals and standard deviations with 64 bits.

typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::Real3
typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_SCTOR > core::pack::dunbrack::Real4
typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::Size3
typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_SCTOR > core::pack::dunbrack::Size4

Function Documentation

void core::pack::dunbrack::bicubic_interpolation ( Real  v00,
Real  d2dx200,
Real  d2dy200,
Real  d4dx2y200,
Real  v01,
Real  d2dx201,
Real  d2dy201,
Real  d4dx2y201,
Real  v10,
Real  d2dx210,
Real  d2dy210,
Real  d4dx2y210,
Real  v11,
Real  d2dx211,
Real  d2dy211,
Real  d4dx2y211,
Real  dxp,
Real  dyp,
Real  binwx,
Real  binwy,
Real val,
Real dvaldx,
Real dvaldy 
)

Interpolate in a grid with the values, and second derivatives given, and simultaneously evaluate the derivative. No option for working with periodic ranges. Instead, make sure that interpolation doesn't need to span > 180 degrees.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers().

void core::pack::dunbrack::dump_library ( std::string  filename,
RotamerVector const &  rotamers 
)
conformation::ResidueOP core::pack::dunbrack::dup_residue ( conformation::Residue const &  existing,
conformation::Residue const &  conformer 
)

Helper function for superposition.

Helper function, combines existing's metadata with conformer's conformation.

References core::conformation::Residue::chain(), core::conformation::Residue::clone(), and core::conformation::Residue::seqpos().

Referenced by core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector().

void core::pack::dunbrack::expand_proton_chi ( pack::task::ExtraRotSample  ex_samp_level,
chemical::ResidueTypeCOP  concrete_residue,
Size  proton_chi,
utility::vector1< ChiSetOP > &  chi_set_vector 
)
void core::pack::dunbrack::expand_proton_chi_oldversion ( pack::task::ExtraRotSample  ex_samp_level,
chemical::ResidueTypeCOP  concrete_residue,
Size  proton_chi,
utility::vector1< ChiSetOP > &  chi_set_vector 
)
template<Size S>
DunbrackRotamer< S, Real > core::pack::dunbrack::increase_rotamer_precision ( DunbrackRotamer< S, DunbrackReal > const &  original_rotamer)
void core::pack::dunbrack::interpolate_rotamers ( DunbrackRotamer< FOUR > const &  rot00,
DunbrackRotamer< FOUR > const &  rot10,
DunbrackRotamer< FOUR > const &  rot01,
DunbrackRotamer< FOUR > const &  rot11,
Real  phi_err,
Real  psi_err,
Real  binrange,
Size  nchi_aa,
DunbrackRotamer< FOUR, Real > &  interpolated_rotamer 
)

interpolates the angles and the sdevs as Reals (doubles)

References core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::chi_mean(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::chi_sd(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotamer_probability(), and core::pack::dunbrack::DunbrackRotamer< S, P >::rotwell().

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbind(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples_bbind(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_bbind(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers().

void core::pack::dunbrack::load_unboundrot ( pose::Pose pose)
void core::pack::dunbrack::load_unboundrot ( pose::Pose pose,
core::pose::PoseCOPs const &  unboundrot_poses 
)
bool core::pack::dunbrack::psc_compare ( ProbSortClass  left,
ProbSortClass  right 
)
void core::pack::dunbrack::read_dunbrack_library ( RotamerLibrary &  rotamer_library)
void core::pack::dunbrack::rotamer_from_chi ( conformation::Residue const &  rsd,
RotVector &  rot 
)
void core::pack::dunbrack::rotamer_from_chi ( chemical::ResidueType const &  rsd_type,
ChiVector const &  chi,
RotVector &  rot 
)

helper that'll determine the rotamer bins for a residue_type by asking its associated rotamer library for that information. Takes chi vector as input parameter.

References core::pack::dunbrack::RotamerLibrary::get_instance(), and core::pack::dunbrack::RotamerLibrary::get_rsd_library().

void core::pack::dunbrack::rotamer_from_chi_02 ( ChiVector const &  chi,
chemical::AA const  res,
RotVector &  rot 
)

Do not bother calling this function if you're interested in staying up to date with changes in the rotamer library. Call rotamer_from_chi instead. It will eventually call this function iff dun10 is not set to true.

References DUNBRACK_MAX_SCTOR.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static().

void core::pack::dunbrack::rotamer_from_chi_02 ( Real4 const &  chi,
chemical::AA const  res,
Size  nchi,
Size4 &  rot 
)
static basic::Tracer core::pack::dunbrack::SRDL_TR ( "core.pack.dunbrack"  )
static
Real core::pack::dunbrack::subtract_chi_angles ( Real  chi1,
Real  chi2,
chemical::AA const &  aa,
int  chino 
)

Find the difference in angles between two chi values using hard-coded symmetry information for the symmetric amino acids. Disappears for 2010 library.

2002 Library hard code symmetry information.

References core::chemical::aa_asp, core::chemical::aa_glu, core::chemical::aa_phe, and core::chemical::aa_tyr.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), and protocols::features::RotamerFeatures::report_features().

static basic::Tracer core::pack::dunbrack::TR ( "core.pack.dunbrack.DunbrackConstraint"  )
static
static basic::Tracer core::pack::dunbrack::TR ( "core.pack.dunbrack.RotamerConstraint"  )
static
static basic::Tracer core::pack::dunbrack::TR ( "core.pack.dunbrack.SingleLigandRotamerLibrary"  )
static
void core::pack::dunbrack::tricubic_interpolation ( Real  v000,
Real  dvdx000,
Real  dvdy000,
Real  dvdz000,
Real  dvdxy000,
Real  dvdxz000,
Real  dvdyz000,
Real  dvdxyz000,
Real  v001,
Real  dvdx001,
Real  dvdy001,
Real  dvdz001,
Real  dvdxy001,
Real  dvdxz001,
Real  dvdyz001,
Real  dvdxyz001,
Real  v010,
Real  dvdx010,
Real  dvdy010,
Real  dvdz010,
Real  dvdxy010,
Real  dvdxz010,
Real  dvdyz010,
Real  dvdxyz010,
Real  v011,
Real  dvdx011,
Real  dvdy011,
Real  dvdz011,
Real  dvdxy011,
Real  dvdxz011,
Real  dvdyz011,
Real  dvdxyz011,
Real  v100,
Real  dvdx100,
Real  dvdy100,
Real  dvdz100,
Real  dvdxy100,
Real  dvdxz100,
Real  dvdyz100,
Real  dvdxyz100,
Real  v101,
Real  dvdx101,
Real  dvdy101,
Real  dvdz101,
Real  dvdxy101,
Real  dvdxz101,
Real  dvdyz101,
Real  dvdxyz101,
Real  v110,
Real  dvdx110,
Real  dvdy110,
Real  dvdz110,
Real  dvdxy110,
Real  dvdxz110,
Real  dvdyz110,
Real  dvdxyz110,
Real  v111,
Real  dvdx111,
Real  dvdy111,
Real  dvdz111,
Real  dvdxy111,
Real  dvdxz111,
Real  dvdyz111,
Real  dvdxyz111,
Real  dxp,
Real  dyp,
Real  dzp,
Real  binwx,
Real  binwy,
Real  binwz,
Real val,
Real dvaldx,
Real dvaldy,
Real dvaldz 
)

Variable Documentation

core::pack::dunbrack::c

DEPRICATED convert between the real-valued chi dihedrals and the rotamer well indices.

This code comes directly from Roland Dunbrack. In certain rare edge cases, floating point comparison breaks down (e.g. ! x >= 120.0 && ! x < 120.0 ) and Dunbrack's code leaves the rotamer well unassigned – a value of zero. I'm modifying the code to guarantee that the rotamer well is assigned, but so that Dunbrack's original form is still recognizable. e.g. if (x) a; if (y) b; if (z) c; now reads as: if (x) a; else if ( y ) b; else /*if (z)

Referenced by core::fragment::picking_old::vall::VallResidue::aa(), protocols::frag_picker::VallResidue::aa(), protocols::protein_interface_design::movers::Splice::add_sequence_constraints(), core::pose::Pose::annotated_sequence(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::jd2::parser::FragmentReader::apply(), protocols::sparta::ANN::applyVecNormalization(), protocols::motifs::bpdefs2map(), protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(), protocols::frag_picker::scores::InterbondAngleScore::cached_score(), protocols::sparta::PDB::calc_ElectricField(), protocols::evaluation::PCA::calc_fit_R(), protocols::toolbox::calc_fit_R(), core::scoring::sc::ShapeComplementarityCalculator::CalcNeighborDistance(), core::pose::carbohydrates::calculate_carbohydrate_phi(), core::scoring::FACTSPotential::calculate_GBpair_apprx(), core::sequence::AnnotatedSequence::calculate_map(), protocols::protein_interface_design::movers::Splice::ccd(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::chain(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::chain(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::chain(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::chain(), protocols::protein_interface_design::movers::AddChainBreak::change_foldtree(), core::pack::task::operation::RotamerExplosion::chi(), protocols::simple_moves::sidechain_moves::SetChiMover::chinum(), protocols::simple_moves::BBConRotMover::closure(), core::scoring::packstat::compute_cav_ball_clusters(), core::scoring::packstat::compute_cav_ball_neighbor_count(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), protocols::comparative_modeling::LoopRelaxMover::compute_rmsd(), protocols::idealize::IdealizeMover::constraints_only(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::coord_sdev(), core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesDihedral(), protocols::protein_interface_design::movers::ResidueBBDofs::cut_site(), protocols::pockets::dD_dv1(), protocols::pockets::dD_dv2(), protocols::pockets::dD_dv3(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::jumping::dis_get_ncac(), core::sequence::DP_Matrix::DP_Matrix(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), protocols::frag_picker::VallProvider::find_chunk(), protocols::pockets::Find_Closest_Intersect_SQ(), protocols::forge::methods::fixH(), protocols::forge::methods::fold_tree_from_pose(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), protocols::ligand_docking::Translate::gaussian_translate_ligand(), protocols::ligand_docking::generate_unique_name(), protocols::pockets::DelphiElectrostatics::get_electrostatics_energy(), core::kinematics::TreeVizBuilder::get_ft_node_bounds(), core::scoring::disulfides::RT_helper::get_ncac(), protocols::jumping::get_ncac(), protocols::toolbox::KClusterElement::get_ndx_list(), core::scoring::dna::DirectReadoutPotential::get_xy_bin(), core::scoring::dna::DirectReadoutPotential::get_z_bin(), protocols::sparta::PDB::getBondAngle(), core::scoring::SecondaryStructurePotential::identify_ss(), core::scoring::hbonds::HBondDatabase::initialize_HBPoly1D(), protocols::frag_picker::quota::QuotaCollector::insert(), protocols::frag_picker::quota::SecondaryStructurePool::insert(), protocols::frag_picker::GrabAllCollector::insert(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::insert(), protocols::frag_picker::quota::ABEGO_SS_Pool::insert(), protocols::evaluation::PCA::jacobi(), protocols::frag_picker::scores::RDCScore::jacobi(), protocols::toolbox::jacobi(), core::scoring::jacobi(), core::scoring::jacobi3(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), core::scoring::electron_density::KromerMann::KromerMann(), core::scoring::saxs::FormFactorManager::load_ff(), core::scoring::saxs::FormFactorManager::load_ff_from_db(), protocols::protein_interface_design::movers::Splice::locked_res_id(), protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd::make(), protocols::protein_interface_design::movers::PlacementAuctionMover::max_cb_cb_dist(), core::scoring::etable::MembEtable::modify_pot(), core::scoring::etable::Etable::modify_pot_one_pair(), protocols::pockets::PocketGrid::newSearch(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), core::sequence::AnnotatedSequence::one_letter_sequence(), protocols::frag_picker::operator<<(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::frag_picker::FragmentPicker::quota_protocol(), protocols::frag_picker::JCouplingIO::read(), protocols::frag_picker::scores::AtomPairConstraintsScore::read_constraints(), protocols::frag_picker::scores::DihedralConstraintsScore::read_constraints(), protocols::frag_picker::scores::InterbondAngleScore::read_constraints(), core::fragment::SecstructSRFD::read_data(), protocols::constraints_additional::SequenceCoupling1BDConstraint::read_def(), protocols::jumping::read_disulf_pairing_list(), protocols::frag_picker::read_fragment_candidates(), core::scoring::constraints::ConstraintIO::read_individual_constraint_new(), protocols::loops::read_loop_fragments(), core::scoring::dssp::read_pairing_list(), protocols::topology_broker::PseudocontactShiftEnergyController::read_tag(), protocols::rosetta_scripts::ParsedProtocol::report_call_order(), protocols::features::SaltBridgeFeatures::report_features(), protocols::hotspot_hashing::StubGenerator::residueStubOrientFrame(), protocols::evaluation::PCA::rotate_vec(), protocols::toolbox::rotate_vec(), protocols::sparta::ANN::set_input_code(), protocols::medal::setup_atom_pair_constraints(), core::fragment::picking_old::vall::VallResidue::ss(), protocols::frag_picker::VallResidue::ss(), protocols::frag_picker::VallResidue::ss_str(), protocols::protein_interface_design::star_fold_tree(), protocols::hotspot_hashing::stub_from_points(), protocols::hotspot_hashing::stub_to_points(), core::scoring::sc::MolecularSurfaceCalculator::SubDiv(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::svdcmp(), protocols::ligand_docking::Translate::uniform_translate_ligand(), protocols::match::Bool3DGridKinemageWriter::write_grid_to_kinemage(), and protocols::features::HBondFeatures::write_hbond_chem_types_table_schema().

Size const core::pack::dunbrack::DUNBRACK_MAX_BBTOR = 3
Size const core::pack::dunbrack::DUNBRACK_MAX_SCTOR = 4
Size const core::pack::dunbrack::FOUR = 4
const Real core::pack::dunbrack::MIN_ROT_PROB = 1.e-8
static
Size const core::pack::dunbrack::ONE = 1
Size const core::pack::dunbrack::THREE = 3
Size const core::pack::dunbrack::TWO = 2