Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Public Attributes | Protected Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > Class Template Reference

#include <RotamericSingleResidueDunbrackLibrary.hh>

Inheritance diagram for core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >:
Inheritance graph
[legend]

Public Types

typedef
SingleResidueDunbrackLibrary 
parent
 
- Public Types inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
typedef chemical::AA AA
 

Public Member Functions

 RotamericSingleResidueDunbrackLibrary (chemical::ResidueType const &rt, bool dun02, bool use_bicubic, bool entropy_correction, core::Real prob_buried, core::Real prob_nonburied, bool const reduced_resolution_library=false)
 Creator. More...
 
 ~RotamericSingleResidueDunbrackLibrary () override throw ()
 
Real rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch) const override
 Virtual functions required by the base classes. More...
 
Real rotamer_energy_deriv (conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch) const override
 
Real best_rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const override
 Returns the energy of the lowest-energy rotamer accessible to the given residue (based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue's current rotamer (local optimum); otherwise, consider all rotamers (global optimum). More...
 
void assign_random_rotamer_with_bias (conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const override
 Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center is true, then push the rotamer off from the center; for chi angles with a normal distribution, the perturbation is taken from a Gaussian random number with a standard deviation matching the chi angle's standard deviation. For chi angles that are not normally distributed, the behavior is open to the derived classe's interpretation. More...
 
void fill_rotamer_vector (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, rotamers::RotamerVector &rotamers) const override
 
utility::vector1
< DunbrackRotamerSampleData
get_all_rotamer_samples (Real5 bbs) const override
 Return all of the rotamer sample data given a particular backbone bin. For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe. More...
 
virtual Real get_probability_for_rotamer (utility::fixedsizearray1< Real, N > bbs, Size rot_ind) const
 
virtual DunbrackRotamerSampleData get_rotamer (utility::fixedsizearray1< Real, N > bbs, Size rot_ind) const
 
Real get_probability_for_rotamer (Real phi, Real psi, Size rot_ind) const override
 Return the probability for a particular rotamer where rotamers are indexed in order of decreasing probability (or something very close to decreasing probability). More...
 
DunbrackRotamerSampleData get_rotamer (Real phi, Real psi, Size rot_ind) const override
 
Size nchi () const override
 The number of chi represented by the library. More...
 
Size nbb () const override
 the number of backbone dihedrals represented by the library More...
 
Size n_rotamer_bins () const override
 
void write_to_file (utility::io::ozstream &out) const override
 
void write_to_binary (utility::io::ozstream &out) const override
 
void read_from_binary (utility::io::izstream &in) override
 
bool operator== (SingleResidueRotamerLibrary const &) const override
 Comparison operator, mainly intended to use in ASCII/binary comparsion tests Values tested should parallel those used in the read_from_binary() function. More...
 
void get_rotamer_from_chi (ChiVector const &chi, RotVector &rot) const override
 Convert a vector of chi angles (degrees) into a integer vector of rotamer wells. Derived class should be consistent, but may be arbitrary in how wells divide angle space. More...
 
std::string read_from_file (utility::io::izstream &in, bool first_line_three_letter_code_already_read)
 Read from input stream; stream may contain data for other amino acids. Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it's already been extracted from the input stream). Return the empty string if no other amino acid is specified. More...
 
Size find_another_representative_for_unlikely_rotamer (conformation::Residue const &rsd, pose::Pose const &pose, Size4 &rotwell) const
 
void interpolate_rotamers (conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, Size packed_rotno, PackedDunbrackRotamer< T, N, Real > &interpolated_rotamer) const
 
void get_bb_bins (utility::fixedsizearray1< Real, N > const &bbs, utility::fixedsizearray1< Size, N > &bb_bin, utility::fixedsizearray1< Size, N > &bb_bin_next, utility::fixedsizearray1< Real, N > &bb_alpha) const
 
void get_bb_bins (utility::fixedsizearray1< Real, N > const &bbs, utility::fixedsizearray1< Size, N > &bb_bin) const
 
void get_bb_bins (utility::vector1< core::Real > const &bbs, utility::vector1< core::Size > &bb_bin) const
 Version for external, non-template classes to access. More...
 
- Public Member Functions inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
SingleResidueDunbrackLibraryoperator= (SingleResidueDunbrackLibrary const &other)=delete
 
 SingleResidueDunbrackLibrary (SingleResidueDunbrackLibrary const &)=delete
 
 SingleResidueDunbrackLibrary (chemical::ResidueType const &rt, Size const n_rotameric_chi, bool dun02, bool use_bicubic, bool dun_entropy_correction, core::Real prob_buried, core::Real prob_nonburied)
 c-tor More...
 
virtual Size memory_usage_in_bytes () const
 Virtual functions the derived classes must implement. More...
 
void set_n_chi_bins (utility::vector1< Size > const &)
 Tell the base class the number of chi bins for each rotameric chi dimension. More...
 
Size rotwell_2_rotno (utility::vector1< Size > const &rotwell) const
 Conversion functions. More...
 
Size rotwell_2_rotno (Size4 const &rotwell) const
 Convert from the rotamer bin indices for each chi to the (non-compact) "rotamer number". More...
 
Size rotno_2_packed_rotno (Size const rotno) const
 Convert from the rotamer number to the compacted "packed rotamer number". Returns 0 if rotno has no corresponding packed rotno. More...
 
Size rotwell_2_packed_rotno (utility::vector1< Size > const &rotwell) const
 Convert from the rotamer bin indices for each chi to the compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno. More...
 
Size rotwell_2_packed_rotno (Size4 const &rotwell) const
 Convert from the rotamer bin indices for each chi to the compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno. More...
 
void packed_rotno_2_rotwell (Size const packed_rotno, utility::vector1< Size > &rotwell) const
 Convert from the packed rotamer number to the rotamer well. More...
 
void packed_rotno_2_rotwell (Size const packed_rotno, Size4 &rotwell) const
 
utility::vector1< Size > const & packed_rotno_2_rotwell (Size const packed_rotno) const
 
void rotno_2_rotwell (Size const rotno, utility::vector1< Size > &rotwell) const
 Convert from the rotamer number to the rotamer well. More...
 
Size bin_rotameric_chi (Real chi, Size which_chi) const
 , Turns out, when non-rotameric chi are taken out of the picture, all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function. More...
 
void bin_angle (Real const angle_start, Real const angle_step, Real const ASSERT_ONLY(angle_range), Size const nbins, Real const ang, Size &bin_lower, Size &bin_upper, Real &angle_alpha) const
 
void bin_angle (Real const angle_start, utility::vector1< core::Size > const &bin_equivs, Real const angle_step, Real const ASSERT_ONLY(angle_range), Size const nbins, Real const ang, Size &bin_lower, Size &bin_upper, Real &angle_alpha) const
 
AA aa () const
 The amino acid this library is representing. More...
 
Real probability_to_accumulate_while_building_rotamers (bool buried) const
 When creating rotamer, what position in the CDF should one build until? Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful. More...
 
void prob_to_accumulate (Real, Real)
 setters for accumulation probability cutoff (to support externally-controlled option dependence) More...
 
void prob_to_accumulate_buried (Real)
 
void prob_to_accumulate_nonburied (Real)
 
bool operator== (rotamers::SingleResidueRotamerLibrary const &) const override
 Comparison operator, mainly intended to use in ASCII/binary comparsion tests Values tested should parallel those used in the read_from_binary() function. More...
 
- Public Member Functions inherited from core::pack::rotamers::SingleResidueRotamerLibrary
 SingleResidueRotamerLibrary ()
 
 ~SingleResidueRotamerLibrary () override
 
virtual utility::vector1
< utility::vector1< core::Real > > 
compute_proton_chi_samplings (chemical::ResidueType const &concrete_residue, pack::task::ResidueLevelTask const &rlt, bool buried) const
 Return a vector (indexed by proton_chi number) of vectors of dihedral values to use in proton chi sampling. More...
 
virtual utility::vector1
< dunbrack::ChiSetOP
expand_proton_chis (utility::vector1< utility::vector1< core::Real > > const &sampling, chemical::ResidueType const &concrete_residue, core::Size max_rotamers=5000) const
 Given a vector of vectors of dihedrals to sample on proton chis, Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.) More...
 
virtual void bump_filter (RotamerVector &rotamers, core::Size resid, scoring::ScoreFunction const &sf, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) const
 Filter a RotamerVector by "bump energy" of a rotamer: All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector "rotamers" will be modified "in-place". More...
 
virtual core::PackerEnergy bump_check (core::conformation::ResidueCOP rotamer, core::Size resid, scoring::ScoreFunction const &sf, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) const
 Computes the "bump energy" of a rotamer: the bump energy is the sum of rotamer's interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization. More...
 
virtual core::Size current_rotamer (RotamerVector &rotamers, core::Size resid, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const
 Adds the current rotamer to rotamer vector, if the Rotlib supports it. More...
 
virtual void emergency_rotamer (RotamerVector &rotamers, core::Size resid, pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const
 Generate an "emergency rotamer" if we don't have any. More...
 
RotamerVector virtual_sidechain (RotamerVector const &rotamers, core::Size resid, pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const
 Add a virtualized sidechain to the rotamer vector if settings call for it. More...
 

Public Attributes

utility::fixedsizearray1< Size, N > N_BB_BINS
 
utility::fixedsizearray1< Real, N > BB_BINRANGE
 
utility::fixedsizearray1
< utility::vector1< core::Size >
, N > 
BIN_EQUIVALENTS
 
utility::fixedsizearray1
< std::function< Real(conformation::Residue
const &rsd, pose::Pose const
&pose) >, N > 
IVs
 

Protected Member Functions

void initialize_bicubic_splines ()
 
void increment_tensor_index_recursively (utility::fixedsizearray1< Size,(N+1) > &bb_bin, utility::fixedsizearray1< Size,(N+1) > const &bb_bin_maxes, core::Size const recursion_level) const
 Given a RotamericSingleResidueDunbrackLibrary of type T (probably core::Real) and with N backbone dihedrals, a vector of coordinates in the backbone bins tensor, and a vector of sizes for the dimensions of the backbone bins tensor, increment the coordinate in a manner that ensures that all bins can be iterated over. More...
 
void get_rotamer_from_chi_static_voronoi (ChiVector const &chi, core::Size &rot, core::conformation::Residue const &rsd, core::pose::Pose const &pose) const
 Given chi values and a pose residue, return indices specifying the nearest rotamer well centre. More...
 
void get_rotamer_from_chi_static (ChiVector const &chi, Size4 &rot) const
 When given a statically sized fixedsizearray, use this method. More...
 
void get_rotamer_from_chi_static (Real4 const &chi, Size4 &rot) const
 When given a statically sized fixedsizearray, use this method. More...
 
ObjexxFCL::FArray2D
< PackedDunbrackRotamer< T, N >
> const & 
rotamers () const
 Read and write access for derived classes and parser class. More...
 
ObjexxFCL::FArray2D
< PackedDunbrackRotamer< T, N > > & 
rotamers ()
 
ObjexxFCL::FArray2D< Size > const & packed_rotno_2_sorted_rotno () const
 
ObjexxFCL::FArray2D< Size > & packed_rotno_2_sorted_rotno ()
 
Size memory_usage_static () const override
 Worker functions. More...
 
Size memory_usage_dynamic () const override
 
Real eval_rotameric_energy_deriv (conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const
 Evaluates the score and chi-deviation penalty for the rotameric chi (in this class, that means all the chi) and stores the answers in the scratch object. If eval_deriv is true, then at the end of this function, scratch contains up-to-date dchidevpen_dbb, dchidevpen_dchi, chimean, chisd, chidev, chidevpen, dchimean_d(phi/psi), dchisd_d(phi/psi) rotwell and rotprob data. More...
 
void interpolate_rotamers (RotamerLibraryScratchSpace &scratch, Size packed_rotno, utility::fixedsizearray1< Size, N > const &bb_bin, utility::fixedsizearray1< Size, N > const &bb_bin_next, utility::fixedsizearray1< Real, N > const &bb_alpha, PackedDunbrackRotamer< T, N, Real > &interpolated_rotamer, ChiVector const &chi=ChiVector(T, 0.0), bool const use_chi=false) const
 
Size make_conditional_packed_rotno_index (Size const original_bb_index, Size const bb_index, Size const packed_rotno, ChiVector const &chi, bool const use_chi) const
 Given the index of a rotamer in the current backbone bin, find the closest rotamer index in another backbone bin. More...
 
void assign_random_rotamer (conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center, Size &packed_rotno) const
 Assigns random chi angles and returns the packed_rotno for the chosen random rotamer. More...
 
void assign_chi_for_interpolated_rotamer (PackedDunbrackRotamer< T, N, Real > const &interpolated_rotamer, conformation::Residue const &rsd, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const
 
void correct_termini_derivatives (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
 
Real get_phi_from_rsd (conformation::Residue const &rsd) const override
 
Real get_psi_from_rsd (conformation::Residue const &rsd) const override
 
utility::fixedsizearray1< Real, N > get_IVs_from_rsd (conformation::Residue const &rsd, pose::Pose const &pose) const
 
Real get_IV_from_rsd (core::Size bbn, conformation::Residue const &rsd, pose::Pose const &pose) const
 
template<class P >
DunbrackRotamer< T, N, P > packed_rotamer_2_regular_rotamer (PackedDunbrackRotamer< T, N, P > const &packedrot) const
 
void enumerate_chi_sets (chemical::ResidueType const &rsd_type, pack::task::PackerTask const &task, Size const seqpos, bool buried, RotamericData< T, N > const &rotamer_data, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, utility::vector1< ChiSetOP > &chi_set_vector) const
 This member function constructs a list of all combinations of chi angles for a rotamer sample. It relies on a virtual function chisamples_for_rotamer_chi that may be overridden by derived classes. With a list of samples for each chi, this function then enumerates all combinations. More...
 
virtual void chisamples_for_rotamer_and_chi (chemical::ResidueType const &rsd_type, pack::task::ResidueLevelTask const &rtask, bool buried, Size const chi_index, RotamericData< T, N > const &rotamer_data, utility::vector1< Real > const &extra_steps, utility::vector1< Real > &total_chi, utility::vector1< int > &total_rot, utility::vector1< Real > &total_ex_steps, utility::vector1< Real > &chisample_prob) const
 Used in tandem with enumerate_chi_sets, this function pushes back chi sample data into the four input vectors: the 1. chi value sample,. More...
 
void create_rotamers_from_chisets (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< ChiSetOP > const &chi_set_vector, rotamers::RotamerVector &rotamers) const
 Once all the chi have been enumerated, building the rotamers is a trivial task. This function is protected so that derived classes may simply enumerate their chi and then invoke this function. This arguably should be moved into the SingleResidueRotamerLibrary base class. More...
 
void setup_entropy_correction ()
 
void setup_entropy_correction () const
 
- Protected Member Functions inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
bool dun02 () const
 Read access for the derived class. More...
 
bool use_bicubic () const
 Read access for the derived class. More...
 
bool dun_entropy_correction () const
 Read access for the derived class. More...
 
utility::vector1< Size > const & n_chi_bins () const
 Read access to the n_chi_bins_ vector. More...
 
void mark_rotwell_exists (utility::vector1< Size > const &rotwell)
 The base class needs to be informed about which rotamer wells exist in order to create the rotwell to packed rot conversion data. set_chi_nbins must be called first. More...
 
void declare_all_existing_rotwells_encountered ()
 After the derived class has marked all the rotwells that do exist, the base class will create the rotwell to packerot conversion data. More...
 
Size n_packed_rots () const
 The number of existing rotamers. More...
 
Size n_possible_rots () const
 The number of possible rotamers – product of the chi_nbins_ array. More...
 

Private Member Functions

void build_rotamers (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, rotamers::RotamerVector &rotamers, PackedDunbrackRotamer< T, N, Real > const &interpolated_rotamer) const
 After an interpolated rotamer has been created, this method appends new rotamers to the vector of rotamers, taking extra samples at designated chi intervals if instructed to do so in the extra_chi_steps argument. More...
 
void verify_phipsi_bins (Real phi, Real psi, Size const phibin, Size const psibin, Size const phibin_next, Size const psibin_next) const
 
void verify_bb_bins (utility::fixedsizearray1< Real, N > const &bbs, utility::fixedsizearray1< Size, N > const &bb_bin, utility::fixedsizearray1< Size, N > const &bb_bin_next) const
 

Private Attributes

ObjexxFCL::FArray2D
< PackedDunbrackRotamer< T, N > > 
rotamers_
 
ObjexxFCL::FArray2D< Sizepacked_rotno_2_sorted_rotno_
 
utility::fixedsizearray1
< ObjexxFCL::FArray1D< Real >,(1
<< N) > 
ShannonEntropy_n_derivs_
 
bool peptoid_ = false
 AMW: one peptoid flag needed. More...
 
bool peptoid_is_achiral_ = true
 VKM: no, two, dammit! More...
 
bool canonical_aa_
 Is this a canonical amino acid? More...
 
bool canonicals_use_voronoi_
 Should canonicals use Voronoi-based detection of nearest rotamer well (true), or hard-coded definitions (false)? More...
 
bool noncanonicals_use_voronoi_
 Should noncanonicals use Voronoi-based detection of nearest rotamer well (true), or hard-coded definitions (false)? More...
 
bool correct_rotamer_well_order_on_read_
 If true, the order of rotamer wells is auto-corrected from the input rotamer file. False by default – shouldn't be necessary any more, with voronoi-based rotamer interpolation. More...
 

Friends

class RotamericSingleResidueDunbrackLibraryParser
 
class SingleResidueDunbrackLibrary
 

Additional Inherited Members

- Static Public Member Functions inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
static void n_rotamer_bins_for_aa (chemical::ResidueType const &rt, RotVector &rot, bool const dun02=false)
 Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType and store it in rot. More...
 
static void n_rotamer_bins_for_aa (chemical::AA const aa, RotVector &rot)
 
static void n_rotameric_bins_for_aa (chemical::AA const aa, RotVector &rot, bool dun02)
 
static void n_rotamer_bins_for_aa_02 (chemical::AA const aa, RotVector &rot)
 
- Static Public Attributes inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
static Real const PEPTIDE_NEUTRAL_PHI = -90
 constants More...
 
static Real const PEPTIDE_NEUTRAL_PSI = 130
 
static Real const PEPTOID_NEUTRAL_OMG = 180
 A good omega, phi, and psi values to use for terminal peptoid residues where they cannont be completely defined. More...
 
static Real const PEPTOID_NEUTRAL_PHI = -90
 
static Real const PEPTOID_NEUTRAL_PSI = 180
 
static Real const ANGLE_DELTA
 Precision measures for comparsions. More...
 
static Real const PROB_DELTA
 
static Real const ENERGY_DELTA
 
static Real const COEF_DELTA
 

Member Typedef Documentation

Constructor & Destructor Documentation

template<Size T, Size N>
core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary ( chemical::ResidueType const &  rt,
bool  dun02,
bool  use_bicubic,
bool  entropy_correction,
core::Real  prob_buried,
core::Real  prob_nonburied,
bool const  reduced_resolution_library = false 
)

Creator.

No default ctor RotamericSingleResidueDunbrackLibrary();

References core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::BB_BINRANGE, core::conformation::Residue::chain(), core::chemical::CTERM_CONNECT, core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_aramid(), core::conformation::Residue::is_lower_terminus(), core::chemical::ResidueType::is_meta_aramid(), core::chemical::ResidueType::is_ortho_aramid(), core::chemical::ResidueType::is_para_aramid(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::is_post_methylene_meta_aramid(), core::chemical::ResidueType::is_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_post_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_para_aramid(), core::chemical::ResidueTypeBase::is_protein(), protocols::stepwise::modeler::is_protein(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::IVs, core::chemical::ResidueType::lower_connect_id(), core::conformation::Residue::mainchain_torsions(), core::chemical::element::N, core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::N_BB_BINS, core::chemical::NTERM_CONNECT, core::pack::dunbrack::SingleResidueDunbrackLibrary::PEPTIDE_NEUTRAL_PHI, core::pack::dunbrack::SingleResidueDunbrackLibrary::PEPTIDE_NEUTRAL_PSI, core::pack::dunbrack::SingleResidueDunbrackLibrary::PEPTOID_NEUTRAL_OMG, core::pack::dunbrack::SingleResidueDunbrackLibrary::PEPTOID_NEUTRAL_PHI, core::pack::dunbrack::SingleResidueDunbrackLibrary::PEPTOID_NEUTRAL_PSI, core::conformation::Residue::residue_connection_partner(), and core::conformation::Residue::type().

Member Function Documentation

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::assign_chi_for_interpolated_rotamer ( PackedDunbrackRotamer< T, N, Real > const &  interpolated_rotamer,
conformation::Residue const &  rsd,
numeric::random::RandomGenerator &  RG,
ChiVector new_chi_angles,
bool  perturb_from_rotamer_center 
) const
protected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::assign_random_rotamer ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
RotamerLibraryScratchSpace scratch,
numeric::random::RandomGenerator &  RG,
ChiVector new_chi_angles,
bool  perturb_from_rotamer_center,
Size packed_rotno 
) const
protected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::assign_random_rotamer_with_bias ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
RotamerLibraryScratchSpace scratch,
numeric::random::RandomGenerator &  RG,
ChiVector new_chi_angles,
bool  perturb_from_rotamer_center 
) const
overridevirtual

Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center is true, then push the rotamer off from the center; for chi angles with a normal distribution, the perturbation is taken from a Gaussian random number with a standard deviation matching the chi angle's standard deviation. For chi angles that are not normally distributed, the behavior is open to the derived classe's interpretation.

Implements core::pack::rotamers::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >.

template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
bool  curr_rotamer_only,
RotamerLibraryScratchSpace scratch 
) const
overridevirtual

Returns the energy of the lowest-energy rotamer accessible to the given residue (based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue's current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

Implements core::pack::rotamers::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >.

References core::conformation::Residue::chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), core::pack::dunbrack::interpolate_rotamers(), core::chemical::element::N, core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >::rotamer_probability(), and core::pack::dunbrack::RotamerLibraryScratchSpace::rotwell().

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::build_rotamers ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scorefxn,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
chemical::ResidueTypeCOP  concrete_residue,
conformation::Residue const &  existing_residue,
utility::vector1< utility::vector1< Real > > const &  extra_chi_steps,
bool  buried,
rotamers::RotamerVector rotamers,
PackedDunbrackRotamer< T, N, Real > const &  interpolated_rotamer 
) const
private

After an interpolated rotamer has been created, this method appends new rotamers to the vector of rotamers, taking extra samples at designated chi intervals if instructed to do so in the extra_chi_steps argument.

Load interpolated rotamer data into a RotamericData object on the stack so that it can be handed into the enumerate_chi_sets method, which itself relies on the "template method" chisamples_for_rotamer_and_chi. Enumerate the chi samples, and build rotamers from these chi samples.

"template method" is a design pattern where a base class calls a polymorphic method that can be overloaded by a derived class, usually in the middle of a function that does a lot of work. See "Design Patterns," Gamma et al.

References core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >::rotamer_probability(), and core::conformation::Residue::seqpos().

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi ( chemical::ResidueType const &  rsd_type,
pack::task::ResidueLevelTask const &  rtask,
bool  buried,
Size const  chi_index,
RotamericData< T, N > const &  rotamer_data,
utility::vector1< Real > const &  extra_steps,
utility::vector1< Real > &  total_chi,
utility::vector1< int > &  total_rot,
utility::vector1< Real > &  total_ex_steps,
utility::vector1< Real > &  chisample_prob 
) const
protectedvirtual
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives ( conformation::Residue const &  rsd,
RotamerLibraryScratchSpace scratch 
) const
protected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::create_rotamers_from_chisets ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scorefxn,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
chemical::ResidueTypeCOP  concrete_residue,
conformation::Residue const &  existing_residue,
utility::vector1< ChiSetOP > const &  chi_set_vector,
rotamers::RotamerVector rotamers 
) const
protected

Once all the chi have been enumerated, building the rotamers is a trivial task. This function is protected so that derived classes may simply enumerate their chi and then invoke this function. This arguably should be moved into the SingleResidueRotamerLibrary base class.

once a list of chi samples has been enumerated, this function instantiates Residue objectes and give them the correct geometry.

References core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pack::task::ResidueLevelTask::preserve_c_beta(), protocols::hotspot_hashing::reject, core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::rotamer_operations(), and core::conformation::Residue::seqpos().

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::enumerate_chi_sets ( chemical::ResidueType const &  rsd_type,
pack::task::PackerTask const &  task,
Size const  seqpos,
bool  buried,
RotamericData< T, N > const &  rotamer_data,
utility::vector1< utility::vector1< Real > > const &  extra_chi_steps,
utility::vector1< ChiSetOP > &  chi_set_vector 
) const
protected

This member function constructs a list of all combinations of chi angles for a rotamer sample. It relies on a virtual function chisamples_for_rotamer_chi that may be overridden by derived classes. With a list of samples for each chi, this function then enumerates all combinations.

References core::chemical::ResidueType::nchi(), core::pack::task::PackerTask::residue_task(), core::pack::dunbrack::RotamericData< T, N >::rotamer(), and core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >::rotamer_probability().

template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
RotamerLibraryScratchSpace scratch,
bool  eval_deriv 
) const
protected

Evaluates the score and chi-deviation penalty for the rotameric chi (in this class, that means all the chi) and stores the answers in the scratch object. If eval_deriv is true, then at the end of this function, scratch contains up-to-date dchidevpen_dbb, dchidevpen_dchi, chimean, chisd, chidev, chidevpen, dchimean_d(phi/psi), dchisd_d(phi/psi) rotwell and rotprob data.

References protocols::cluster::calibur::aa, core::conformation::Residue::chi(), core::pack::dunbrack::RotamerLibraryScratchSpace::chidev(), core::pack::dunbrack::RotamerLibraryScratchSpace::chidevpen(), core::pack::dunbrack::RotamerLibraryScratchSpace::chimean(), core::pack::dunbrack::RotamerLibraryScratchSpace::chisd(), core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dbb(), core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dchi(), core::pack::dunbrack::RotamerLibraryScratchSpace::dchimean_dbb(), core::pack::dunbrack::RotamerLibraryScratchSpace::dchisd_dbb(), core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev_perchi(), core::pack::dunbrack::RotamerLibraryScratchSpace::dneglnrotprob_dbb(), core::pack::dunbrack::RotamerLibraryScratchSpace::drotprob_dbb(), core::sequence::end, core::pack::dunbrack::RotamerLibraryScratchSpace::entropy(), core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_dev(), core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_rot(), core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_semi(), core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_tot(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), core::pack::dunbrack::interpolate_rotamers(), core::chemical::ResidueType::is_mirrored_type(), core::chemical::element::N, core::pack::dunbrack::RotamerLibraryScratchSpace::negln_rotprob(), core::pack::dunbrack::RotamerLibraryScratchSpace::rotprob(), core::pack::dunbrack::RotamerLibraryScratchSpace::rotwell(), protocols::hybridization::score, core::pack::dunbrack::subtract_chi_angles(), and core::conformation::Residue::type().

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scorefxn,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
chemical::ResidueTypeCOP  concrete_residue,
conformation::Residue const &  existing_residue,
utility::vector1< utility::vector1< Real > > const &  extra_chi_steps,
bool  buried,
rotamers::RotamerVector rotamers 
) const
overridevirtual
template<Size T, Size N>
Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::find_another_representative_for_unlikely_rotamer ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
Size4 rotwell 
) const

The new rotamer library represents only 75 of 81 possible arginine rotamers, and 75 of 81 lysine rotamers. In the unlikely event that a rotamer is encountered that's not represented in the library, find another rotamer to represent it. Ideally, this stand-in rotamer would be closest to the input rotamer in physical geometry. (sidechain atom rms, e.g.) The following code instead first looks through all possible rotamers with a Hamming distance of one from input rotamer trying to find one that works, looking first for rotamers from the furthest chi toward the closest chi. If no such rotamer may be found, it gives up and returns the most-probable rotamer for a phi-psi bin.

This function modifies the "rotwell" assigned to this rotamer so that later code that relies on the consistency of the rotwell and packed_rotno information will behave correctly.

Referenced by protocols::features::RotamerInitializer< T, N >::initialize_rotamer().

template<Size T, Size N>
utility::vector1< DunbrackRotamerSampleData > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples ( Real5  bbs) const
overridevirtual

Return all of the rotamer sample data given a particular backbone bin. For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >.

References core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >::chi_mean(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >::chi_sd(), core::pack::dunbrack::interpolate_rotamers(), core::chemical::element::N, core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >::packed_rotno(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >::rotamer_probability(), core::pack::dunbrack::DunbrackRotamerSampleData::set_chi_mean(), core::pack::dunbrack::DunbrackRotamerSampleData::set_chi_sd(), core::pack::dunbrack::DunbrackRotamerSampleData::set_nchi(), core::pack::dunbrack::DunbrackRotamerSampleData::set_prob(), and core::pack::dunbrack::DunbrackRotamerSampleData::set_rotwell().

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_bb_bins ( utility::fixedsizearray1< Real, N > const &  bbs,
utility::fixedsizearray1< Size, N > &  bb_bin,
utility::fixedsizearray1< Size, N > &  bb_bin_next,
utility::fixedsizearray1< Real, N > &  bb_alpha 
) const

The Dunbrack library's phi/psi data for a grid point (x,y) collects data in the neighborhood of (x,y). As an interpolation point p moves toward a grid point (x,y), the (x,y) share in the interpolated value goes to 1. This is distinct from having interpolation wells where an interpolation in the center of a well produces the maximum contribution from that well. Most of the basic::interpolation code is designed for the second interpretation of interpolation, and so CTSA's Dunbrack library code did funky thinks like shift by 5 degrees so that the basic::interpolation code could shift it back by 5 degrees again. The code below makes no such shift.

The alpha fraction is the distance along each axis that the interpolation point has progressed from the lower grid point toward the upper grid point; it ranges from 0 to 1.

References core::chemical::element::N.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library().

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_bb_bins ( utility::fixedsizearray1< Real, N > const &  bbs,
utility::fixedsizearray1< Size, N > &  bb_bin 
) const
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_bb_bins ( utility::vector1< core::Real > const &  bbs,
utility::vector1< core::Size > &  bb_bin 
) const

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::chemical::element::N.

template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_IV_from_rsd ( core::Size  bbn,
conformation::Residue const &  rsd,
pose::Pose const &  pose 
) const
protected

Handle lower-term residues by returning a "neutral" phi value

template<Size T, Size N>
utility::fixedsizearray1< Real, N > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_IVs_from_rsd ( conformation::Residue const &  rsd,
pose::Pose const &  pose 
) const
protected

Handle upper-term residues by returning a "neutral" psi value

References core::chemical::element::N.

template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd ( conformation::Residue const &  rsd) const
overrideprotectedvirtual
template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_probability_for_rotamer ( utility::fixedsizearray1< Real, N >  bbs,
Size  rot_ind 
) const
virtual
template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_probability_for_rotamer ( Real  phi,
Real  psi,
Size  rot_ind 
) const
overridevirtual

Return the probability for a particular rotamer where rotamers are indexed in order of decreasing probability (or something very close to decreasing probability).

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd ( conformation::Residue const &  rsd) const
overrideprotectedvirtual
template<Size T, Size N>
DunbrackRotamerSampleData core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer ( utility::fixedsizearray1< Real, N >  bbs,
Size  rot_ind 
) const
virtual
template<Size T, Size N>
DunbrackRotamerSampleData core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer ( Real  phi,
Real  psi,
Size  rot_ind 
) const
overridevirtual
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi ( ChiVector const &  chi,
RotVector rot 
) const
overridevirtual

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells. Derived class should be consistent, but may be arbitrary in how wells divide angle space.

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >.

Referenced by protocols::features::RotamerInitializer< T, N >::initialize_rotamer().

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static ( ChiVector const &  chi,
Size4 rot 
) const
protected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static ( Real4 const &  chi,
Size4 rot 
) const
protected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static_voronoi ( ChiVector const &  chi,
core::Size rot,
core::conformation::Residue const &  rsd,
core::pose::Pose const &  pose 
) const
protected

Given chi values and a pose residue, return indices specifying the nearest rotamer well centre.

This version uses a Voronoi-inspired algorithm: the nearest rotamer well to the input chi values, in wraparound angle space, is returned. This is compatible with non-canonicals. Might be slightly slower.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >::chi_mean(), core::chemical::ResidueType::is_mirrored_type(), core::chemical::element::N, core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >::packed_rotno(), and core::conformation::Residue::type().

template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::increment_tensor_index_recursively ( utility::fixedsizearray1< Size,(N+1) > &  bb_bin,
utility::fixedsizearray1< Size,(N+1) > const &  bb_bin_maxes,
core::Size const  recursion_level 
) const
protected

Given a RotamericSingleResidueDunbrackLibrary of type T (probably core::Real) and with N backbone dihedrals, a vector of coordinates in the backbone bins tensor, and a vector of sizes for the dimensions of the backbone bins tensor, increment the coordinate in a manner that ensures that all bins can be iterated over.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::initialize_bicubic_splines ( )
protected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
RotamerLibraryScratchSpace scratch,
Size  packed_rotno,
PackedDunbrackRotamer< T, N, Real > &  interpolated_rotamer 
) const
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers ( RotamerLibraryScratchSpace scratch,
Size  packed_rotno,
utility::fixedsizearray1< Size, N > const &  bb_bin,
utility::fixedsizearray1< Size, N > const &  bb_bin_next,
utility::fixedsizearray1< Real, N > const &  bb_alpha,
PackedDunbrackRotamer< T, N, Real > &  interpolated_rotamer,
ChiVector const &  chi = ChiVector(T, 0.0),
bool const  use_chi = false 
) const
protected
template<Size T, Size N>
Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::make_conditional_packed_rotno_index ( Size const  original_bb_index,
Size const  bb_index,
Size const  packed_rotno,
ChiVector const &  chi,
bool const  use_chi 
) const
protected

Given the index of a rotamer in the current backbone bin, find the closest rotamer index in another backbone bin.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >::chi_mean(), and core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >::packed_rotno().

template<Size T, Size N>
Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::memory_usage_dynamic ( ) const
overrideprotectedvirtual

Measures the amount of dynamically allocated data in this class. Must recurse to parent to count parent's dynamically allocated data.

Reimplemented from core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >.

References protocols::analysis::total.

template<Size T, Size N>
Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::memory_usage_static ( ) const
overrideprotectedvirtual

Worker functions.

called only if the library is actually an RSRDL<T> object. Derived classes should not call this function or recurse. Accounts for the statically allocated data that's part of this class.

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >.

template<Size T, Size N>
Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::n_rotamer_bins ( ) const
overridevirtual
template<Size T, Size N>
Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::nbb ( ) const
overridevirtual

the number of backbone dihedrals represented by the library

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >.

References core::chemical::element::N.

template<Size T, Size N>
Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::nchi ( ) const
overridevirtual
template<Size T, Size N>
bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator== ( SingleResidueRotamerLibrary const &  rhs) const
overridevirtual
template<Size T, Size N>
template<class P >
DunbrackRotamer< T, N, P > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::packed_rotamer_2_regular_rotamer ( PackedDunbrackRotamer< T, N, P > const &  packedrot) const
protected
template<Size T, Size N>
ObjexxFCL::FArray2D< Size > const& core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::packed_rotno_2_sorted_rotno ( ) const
inlineprotected
template<Size T, Size N>
ObjexxFCL::FArray2D< Size >& core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::packed_rotno_2_sorted_rotno ( )
inlineprotected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_binary ( utility::io::izstream &  in)
overridevirtual
template<Size T, Size N>
std::string core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_file ( utility::io::izstream &  infile,
bool  first_line_three_letter_code_already_read 
)

Read from input stream; stream may contain data for other amino acids. Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it's already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Author
Rewritten on 8 January 2018 by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References protocols::cluster::calibur::aa, core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(), core::pack::dunbrack::DUNBRACK_FILE_DEFAULT_SCTOR, core::chemical::element::N, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file().

Referenced by core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib().

template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
RotamerLibraryScratchSpace scratch 
) const
overridevirtual

Virtual functions required by the base classes.

Implements core::pack::rotamers::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >.

template<Size T, Size N>
Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
RotamerLibraryScratchSpace scratch 
) const
overridevirtual
template<Size T, Size N>
ObjexxFCL::FArray2D< PackedDunbrackRotamer< T, N > > const& core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamers ( ) const
inlineprotected
template<Size T, Size N>
ObjexxFCL::FArray2D< PackedDunbrackRotamer< T, N > >& core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamers ( )
inlineprotected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::setup_entropy_correction ( )
protected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::setup_entropy_correction ( ) const
protected
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::verify_bb_bins ( utility::fixedsizearray1< Real, N > const &  bbs,
utility::fixedsizearray1< Size, N > const &  bb_bin,
utility::fixedsizearray1< Size, N > const &  bb_bin_next 
) const
private
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::verify_phipsi_bins ( Real  phi,
Real  psi,
Size const  phibin,
Size const  psibin,
Size const  phibin_next,
Size const  psibin_next 
) const
private
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::write_to_binary ( utility::io::ozstream &  out) const
overridevirtual
template<Size T, Size N>
void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::write_to_file ( utility::io::ozstream &  out) const
overridevirtual

Friends And Related Function Documentation

template<Size T, Size N>
friend class RotamericSingleResidueDunbrackLibraryParser
friend
template<Size T, Size N>
friend class SingleResidueDunbrackLibrary
friend

Member Data Documentation

template<Size T, Size N>
utility::fixedsizearray1< Real, N > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::BB_BINRANGE
template<Size T, Size N>
utility::fixedsizearray1< utility::vector1< core::Size >, N> core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::BIN_EQUIVALENTS
template<Size T, Size N>
bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::canonical_aa_
private

Is this a canonical amino acid?

template<Size T, Size N>
bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::canonicals_use_voronoi_
private

Should canonicals use Voronoi-based detection of nearest rotamer well (true), or hard-coded definitions (false)?

Read from options system in constructor. Defaults to false (old behaviour preserved), though if we switch this to true at some point in the future, we could deprecate a lot of hard-coded well definitions.

template<Size T, Size N>
bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_rotamer_well_order_on_read_
private

If true, the order of rotamer wells is auto-corrected from the input rotamer file. False by default – shouldn't be necessary any more, with voronoi-based rotamer interpolation.

template<Size T, Size N>
utility::fixedsizearray1< std::function< Real( conformation::Residue const & rsd, pose::Pose const & pose ) >, N > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::IVs
template<Size T, Size N>
utility::fixedsizearray1< Size, N > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::N_BB_BINS
template<Size T, Size N>
bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::noncanonicals_use_voronoi_
private

Should noncanonicals use Voronoi-based detection of nearest rotamer well (true), or hard-coded definitions (false)?

Read from options system in constructor. Defaults to false (old behaviour preserved), though if we switch this to true at some point in the future, we could deprecate a lot of hard-coded well definitions.

template<Size T, Size N>
ObjexxFCL::FArray2D< Size > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::packed_rotno_2_sorted_rotno_
private

Quick lookup that lists the sorted position for the packed rotamer number given a phi/psi. Indexed by (bb_bin_index, packed_rotno ).

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator==(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::packed_rotno_2_sorted_rotno().

template<Size T, Size N>
bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::peptoid_ = false
private

AMW: one peptoid flag needed.

template<Size T, Size N>
bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::peptoid_is_achiral_ = true
private

VKM: no, two, dammit!

True if the petoid is entirely achiral (i.e. the sidechain is achiral, since the backbone always is). False for peptoids with chiral sidechains.

template<Size T, Size N>
ObjexxFCL::FArray2D< PackedDunbrackRotamer< T, N > > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamers_
private

The (chi_mean, chi_sd, packed_rotno, and prob) data for the chi dihedrals The FArray3D is indexed into by (bb_bin_index, sorted_index ), where sorted index simply means the order for a particular packed_rotno in the list of rotamers sorted by probability and the bb_bin_index is a composite of what you would get from essentially expressing the backbone torsions as a number in base N_BB_BINS (often 36).

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator==(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamers().

template<Size T, Size N>
utility::fixedsizearray1< ObjexxFCL::FArray1D< Real >, ( 1 << N ) > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::ShannonEntropy_n_derivs_
private

The documentation for this class was generated from the following files: