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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
 A class who's size is known at compile time. A vector of these objects will occupy a perfectly contiguous region of memory, with no extra space allocated for pointers. These objects may be rapidly allocated and deallocated on the stack. More...
class  DunbrackRotamer
class  PackedDunbrackRotamer
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  RotamericData
class  RotamericSingleResidueDunbrackLibrary
class  SingleResidueRotamerLibrary
class  RotamerLibrary
class  RotamerLibraryScratchSpace
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...
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  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  SingleLigandRotamerLibrary
 A fixed library of conformations for some residue type (doesn't have to be a ligand). More...
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 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::ResidueTypeCAP concrete_residue, Size proton_chi, utility::vector1< ChiSetOP > &chi_set_vector)
void expand_proton_chi (pack::task::ExtraRotSample ex_samp_level, chemical::ResidueTypeCAP concrete_residue, Size proton_chi, utility::vector1< ChiSetOP > &chi_set_vector)
 Should this be here?
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.
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.
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.
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.
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 dun08 is not set to true.
*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 2008 library.
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.
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.
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::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::ResidueTypeCAP  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::ResidueTypeCAP  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,
core::pose::PoseCOPs const &  unboundrot_poses 
)
void core::pack::dunbrack::load_unboundrot ( pose::Pose pose)
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 dun08 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 2008 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().

static basic::Tracer core::pack::dunbrack::TR ( "core.pack.dunbrack.RotamerConstraint"  ) [static]
static basic::Tracer core::pack::dunbrack::TR ( "core.pack.dunbrack.SingleLigandRotamerLibrary"  ) [static]
static basic::Tracer core::pack::dunbrack::TR ( "core.pack.dunbrack.DunbrackConstraint"  ) [static]

Variable Documentation

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 protocols::frag_picker::VallResidue::aa(), core::fragment::picking_old::vall::VallResidue::aa(), 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::InterbondAngleScore::cached_score(), protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(), protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::sparta::PDB::calc_ElectricField(), protocols::toolbox::calc_fit_R(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::chain(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::chain(), protocols::protein_interface_design::movers::AddChainBreak::change_foldtree(), core::pack::task::operation::RotamerExplosion::chi(), 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::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::PlaidFingerprint::Find_Intersect(), 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::generate_unique_name(), protocols::jumping::get_ncac(), protocols::toolbox::KClusterElement::get_ndx_list(), core::scoring::methods::get_restag(), protocols::sparta::PDB::getBondAngle(), core::scoring::hbonds::HBondDatabase::initialize_HBPoly1D(), protocols::frag_picker::quota::SecondaryStructurePool::insert(), protocols::frag_picker::quota::QuotaCollector::insert(), protocols::frag_picker::quota::ABEGO_SS_Pool::insert(), protocols::frag_picker::GrabAllCollector::insert(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::insert(), 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::frag_picker::scores::MakeFragmentAllAtomCrmsd::make(), protocols::protein_interface_design::movers::PlacementAuctionMover::max_cb_cb_dist(), protocols::pockets::PocketGrid::newSearch(), core::sequence::AnnotatedSequence::one_letter_sequence(), protocols::frag_picker::operator<<(), protocols::frag_picker::FragmentPicker::quota_protocol(), protocols::frag_picker::JCouplingIO::read(), 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::toolbox::rotate_vec(), protocols::pockets::PocketGrid::searchD1(), protocols::pockets::PocketGrid::searchD2(), protocols::pockets::PocketGrid::searchD3(), protocols::pockets::PocketGrid::searchD4(), protocols::pockets::PocketGrid::searchX(), protocols::pockets::PocketGrid::searchY(), protocols::pockets::PocketGrid::searchZ(), protocols::sparta::ANN::set_input_code(), protocols::medal::setup_atom_pair_constraints(), protocols::frag_picker::VallResidue::ss(), core::fragment::picking_old::vall::VallResidue::ss(), protocols::frag_picker::VallResidue::ss_str(), protocols::protein_interface_design::star_fold_tree(), and protocols::match::Bool3DGridKinemageWriter::write_grid_to_kinemage().

const Real core::pack::dunbrack::MIN_ROT_PROB = 1.e-8 [static]
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