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Rosetta 3.5
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Rosetta 3.5
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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 |
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, Real > | increase_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 |
Definition at line 41 of file DunbrackRotamer.fwd.hh.
| typedef utility::pointer::owning_ptr< ChiSet const > core::pack::dunbrack::ChiSetCOP |
Definition at line 34 of file ChiSet.fwd.hh.
Definition at line 31 of file ChiSet.fwd.hh.
| typedef utility::vector1< Real > core::pack::dunbrack::ChiVector |
Definition at line 40 of file DunbrackRotamer.fwd.hh.
Definition at line 26 of file CoarseRotamer.fwd.hh.
Definition at line 24 of file CoarseRotamer.fwd.hh.
| typedef utility::pointer::owning_ptr< CoarseRotamerSet const > core::pack::dunbrack::CoarseRotamerSetCOP |
Definition at line 30 of file CoarseRotamer.fwd.hh.
Definition at line 28 of file CoarseRotamer.fwd.hh.
| typedef utility::pointer::owning_ptr< CoarseSingleResidueLibrary const > core::pack::dunbrack::CoarseSingleResidueLibraryCOP |
Definition at line 27 of file CoarseSingleResidueLibrary.fwd.hh.
| typedef utility::pointer::owning_ptr< CoarseSingleResidueLibrary > core::pack::dunbrack::CoarseSingleResidueLibraryOP |
Definition at line 24 of file CoarseSingleResidueLibrary.fwd.hh.
| typedef utility::pointer::owning_ptr< DunbrackConstraint const > core::pack::dunbrack::DunbrackConstraintCOP |
Definition at line 27 of file DunbrackConstraint.fwd.hh.
| typedef utility::pointer::owning_ptr< DunbrackConstraint > core::pack::dunbrack::DunbrackConstraintOP |
Definition at line 25 of file DunbrackConstraint.fwd.hh.
| typedef float core::pack::dunbrack::DunbrackReal |
Low precision in Dunbrack rotamer library suggests no need to store chi dihedrals and standard deviations with 64 bits.
Definition at line 37 of file DunbrackRotamer.fwd.hh.
| typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::Real3 |
Definition at line 37 of file RotamerLibraryScratchSpace.fwd.hh.
| typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_SCTOR > core::pack::dunbrack::Real4 |
Definition at line 34 of file RotamerLibraryScratchSpace.fwd.hh.
| typedef utility::pointer::owning_ptr< RotamerConstraint const > core::pack::dunbrack::RotamerConstraintCOP |
Definition at line 28 of file RotamerConstraint.fwd.hh.
Definition at line 26 of file RotamerConstraint.fwd.hh.
| typedef utility::pointer::owning_ptr< RotamerLibrary const > core::pack::dunbrack::RotamerLibraryCOP |
Definition at line 34 of file RotamerLibrary.fwd.hh.
Definition at line 32 of file RotamerLibrary.fwd.hh.
| typedef utility::pointer::owning_ptr< RotamerLibraryScratchSpace const > core::pack::dunbrack::RotamerLibraryScratchSpaceCOP |
Definition at line 44 of file RotamerLibraryScratchSpace.fwd.hh.
| typedef utility::pointer::owning_ptr< RotamerLibraryScratchSpace > core::pack::dunbrack::RotamerLibraryScratchSpaceOP |
Definition at line 41 of file RotamerLibraryScratchSpace.fwd.hh.
Definition at line 50 of file RotamerLibrary.fwd.hh.
| typedef utility::vector1< Size > core::pack::dunbrack::RotVector |
Definition at line 39 of file DunbrackRotamer.fwd.hh.
| typedef utility::pointer::access_ptr< SingleLigandRotamerLibrary > core::pack::dunbrack::SingleLigandRotamerLibraryAP |
Definition at line 33 of file SingleLigandRotamerLibrary.hh.
| typedef utility::pointer::access_ptr< SingleLigandRotamerLibrary const > core::pack::dunbrack::SingleLigandRotamerLibraryCAP |
Definition at line 34 of file SingleLigandRotamerLibrary.hh.
| typedef utility::pointer::owning_ptr< SingleLigandRotamerLibrary const > core::pack::dunbrack::SingleLigandRotamerLibraryCOP |
Definition at line 32 of file SingleLigandRotamerLibrary.hh.
| typedef utility::pointer::owning_ptr< SingleLigandRotamerLibrary > core::pack::dunbrack::SingleLigandRotamerLibraryOP |
Definition at line 30 of file SingleLigandRotamerLibrary.hh.
| typedef utility::pointer::access_ptr< SingleResidueDunbrackLibrary > core::pack::dunbrack::SingleResidueDunbrackLibraryAP |
Definition at line 45 of file RotamerLibrary.fwd.hh.
| typedef utility::pointer::access_ptr< SingleResidueDunbrackLibrary const > core::pack::dunbrack::SingleResidueDunbrackLibraryCAP |
Definition at line 47 of file RotamerLibrary.fwd.hh.
| typedef utility::pointer::owning_ptr< SingleResidueDunbrackLibrary const > core::pack::dunbrack::SingleResidueDunbrackLibraryCOP |
Definition at line 46 of file RotamerLibrary.fwd.hh.
| typedef utility::pointer::owning_ptr< SingleResidueDunbrackLibrary > core::pack::dunbrack::SingleResidueDunbrackLibraryOP |
Definition at line 43 of file RotamerLibrary.fwd.hh.
| typedef utility::pointer::access_ptr< SingleResidueRotamerLibrary > core::pack::dunbrack::SingleResidueRotamerLibraryAP |
Definition at line 38 of file RotamerLibrary.fwd.hh.
| typedef utility::pointer::access_ptr< SingleResidueRotamerLibrary const > core::pack::dunbrack::SingleResidueRotamerLibraryCAP |
Definition at line 41 of file RotamerLibrary.fwd.hh.
| typedef utility::pointer::owning_ptr< SingleResidueRotamerLibrary const > core::pack::dunbrack::SingleResidueRotamerLibraryCOP |
Definition at line 39 of file RotamerLibrary.fwd.hh.
| typedef utility::pointer::owning_ptr< SingleResidueRotamerLibrary > core::pack::dunbrack::SingleResidueRotamerLibraryOP |
Definition at line 36 of file RotamerLibrary.fwd.hh.
| typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::Size3 |
Definition at line 38 of file RotamerLibraryScratchSpace.fwd.hh.
| typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_SCTOR > core::pack::dunbrack::Size4 |
Definition at line 35 of file RotamerLibraryScratchSpace.fwd.hh.
| 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.
Definition at line 78 of file DunbrackRotamer.cc.
Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers().
| void core::pack::dunbrack::dump_library | ( | std::string | filename, |
| RotamerVector const & | rotamers | ||
| ) |
Definition at line 63 of file SingleLigandRotamerLibrary.cc.
References core::io::pdb::dump_pdb_residue().
| 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.
Definition at line 278 of file SingleLigandRotamerLibrary.cc.
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 | ||
| ) |
Should this be here?
olli – I think this is slightly simpler to read than the original version apl – needs to find a new residence
Definition at line 511 of file DunbrackRotamer.cc.
References core::pack::task::NO_EXTRA_CHI_SAMPLES.
Referenced by core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::build_rna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), and core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_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 | ||
| ) |
Definition at line 452 of file DunbrackRotamer.cc.
References core::pack::task::NO_EXTRA_CHI_SAMPLES.
| DunbrackRotamer< S, Real > core::pack::dunbrack::increase_rotamer_precision | ( | DunbrackRotamer< S, DunbrackReal > const & | original_rotamer) |
Definition at line 471 of file DunbrackRotamer.hh.
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 average_rotamers(), and find_most_frequent_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)
Definition at line 389 of file DunbrackRotamer.cc.
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) |
Convenience function adds constraints to the supplied pose based on the -unboundrot command line flag.
Definition at line 51 of file RotamerConstraint.cc.
References core::io::pdb::build_pose_from_pdb_as_is(), protocols::abinitio::filename(), core::io::serialization::size(), and TR().
Referenced by protocols::simple_moves::LoadUnboundRotMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::ligand_docking::LigandDockProtocol::apply(), protocols::ub_e2c::ubi_e2c_modeler::setup_packer_task(), protocols::antibody::AntibodyModeler::setup_packer_task(), protocols::antibody::CDRH3Modeler::setup_packer_task(), protocols::antibody::LoopRlxMover::setup_packer_task(), protocols::antibody2::setup_packer_task(), protocols::docking::DockingHighResLegacy::setup_packing(), and protocols::symmetric_docking::SymDockingHiRes::setup_packing().
| void core::pack::dunbrack::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.
Definition at line 72 of file RotamerConstraint.cc.
References core::pose::Pose::add_constraint(), core::pack::dunbrack::RotamerLibrary::get_instance(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::name(), core::pose::Pose::total_residue(), TR(), and core::conformation::Residue::type().
| bool core::pack::dunbrack::psc_compare | ( | ProbSortClass | left, |
| ProbSortClass | right | ||
| ) |
Definition at line 27 of file SemiRotamericSingleResidueDunbrackLibrary.cc.
References core::pack::dunbrack::ProbSortClass::probability_.
Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotamer_definitions().
| void core::pack::dunbrack::read_dunbrack_library | ( | RotamerLibrary & | rotamer_library) |
Definition at line 1775 of file RotamerLibrary.cc.
References core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries().
Referenced by core::pack::dunbrack::RotamerLibrary::get_instance().
| void core::pack::dunbrack::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.
Definition at line 121 of file RotamerLibrary.cc.
References core::conformation::Residue::aa(), core::conformation::Residue::chi(), core::pack::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::chemical::num_canonical_aas, rot(), and core::conformation::Residue::type().
Referenced by core::pack::dunbrack::RotamerConstraint::add_residue(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_rotamer_recovery(), protocols::comparative_modeling::rots_from_pose(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::rots_from_pose(), core::pack::dunbrack::DunbrackConstraint::score(), core::pack::dunbrack::RotamerConstraint::score(), and protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native().
| 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.
Definition at line 138 of file RotamerLibrary.cc.
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.
Definition at line 153 of file RotamerLibrary.cc.
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 | ||
| ) |
Definition at line 183 of file RotamerLibrary.cc.
References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_trp, core::chemical::aa_tyr, and core::chemical::num_canonical_aas.
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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.
Definition at line 251 of file SingleResidueDunbrackLibrary.cc.
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().
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Referenced by core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_binary(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_binary(), core::pack::dunbrack::SingleLigandRotamerLibrary::fill_missing_atoms(), core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::pack::dunbrack::SingleLigandRotamerLibrary::init_from_file(), load_unboundrot(), core::pack::dunbrack::RotamerConstraint::score(), core::pack::dunbrack::RotamerLibrary::write_binary_fa_dunbrack_libraries_02(), and core::pack::dunbrack::RotamerLibrary::write_binary_fa_dunbrack_libraries_10().
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| 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 | ||
| ) |
Definition at line 178 of file DunbrackRotamer.cc.
Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score().
| 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)
Definition at line 181 of file RotamerLibrary.cc.
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 |
Definition at line 31 of file RotamerLibraryScratchSpace.fwd.hh.
Referenced by core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbdep(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbind().
| Size const core::pack::dunbrack::DUNBRACK_MAX_SCTOR = 4 |
Definition at line 32 of file RotamerLibraryScratchSpace.fwd.hh.
Referenced by core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotameric_data(), rotamer_from_chi_02(), and core::pack::dunbrack::DunbrackRotamerSampleData::set_nchi().
| Size const core::pack::dunbrack::FOUR = 4 |
Definition at line 46 of file DunbrackRotamer.fwd.hh.
Referenced by protocols::features::RotamerFeatures::report_features().
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Definition at line 65 of file SingleResidueDunbrackLibrary.cc.
| Size const core::pack::dunbrack::ONE = 1 |
Definition at line 43 of file DunbrackRotamer.fwd.hh.
Referenced by protocols::features::RotamerFeatures::report_features().
| Size const core::pack::dunbrack::THREE = 3 |
Definition at line 45 of file DunbrackRotamer.fwd.hh.
Referenced by protocols::features::RotamerFeatures::report_features().
| Size const core::pack::dunbrack::TWO = 2 |
Definition at line 44 of file DunbrackRotamer.fwd.hh.
Referenced by protocols::features::RotamerFeatures::report_features().
1.8.4