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core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > Member List

This is the complete list of members for core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >, including all inherited members.

AA typedefcore::pack::dunbrack::SingleResidueDunbrackLibrary
aa() const core::pack::dunbrack::SingleResidueDunbrackLibraryinline
assign_chi_for_interpolated_rotamer(PackedDunbrackRotamer< T, Real > const &interpolated_rotamer, conformation::Residue const &rsd, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
assign_random_rotamer(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center, Size &packed_rotno) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
assign_random_rotamer_with_bias(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
best_rotamer_energy(conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
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 core::pack::dunbrack::SingleResidueDunbrackLibraryinline
bin_rotameric_chi(Real chi, Size which_chi) const core::pack::dunbrack::SingleResidueDunbrackLibraryinline
build_rotamers(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, 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, RotamerVector &rotamers, PackedDunbrackRotamer< T, Real > const &interpolated_rotamer) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >private
chisamples_for_rotamer_and_chi(chemical::ResidueType const &rsd_type, pack::task::ResidueLevelTask const &rtask, bool buried, Size const chi_index, RotamericData< T > 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 core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protectedvirtual
correct_termini_derivatives(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
create_rotamers_from_chisets(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< ChiSetOP > const &chi_set_vector, RotamerVector &rotamers) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
declare_all_existing_rotwells_encountered()core::pack::dunbrack::SingleResidueDunbrackLibraryprotected
dun02() const core::pack::dunbrack::SingleResidueDunbrackLibraryinlineprotected
enumerate_chi_sets(chemical::ResidueType const &rsd_type, pack::task::PackerTask const &task, Size const seqpos, bool buried, RotamericData< T > const &rotamer_data, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, utility::vector1< ChiSetOP > &chi_set_vector) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
eval_rotameric_energy_deriv(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
fill_rotamer_vector(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, 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, RotamerVector &rotamers) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
find_another_representative_for_unlikely_rotamer(conformation::Residue const &rsd, Size4 &rotwell) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
get_all_rotamer_samples(Real phi, Real psi) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
get_phi_from_rsd(conformation::Residue const &rsd) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protectedvirtual
get_phipsi_bins(Real phi, Real psi, Size &phibin, Size &psibin, Size &phibin_next, Size &psibin_next, Real &phi_alpha, Real &psi_alpha) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
get_phipsi_bins(Real phi, Real psi, Size &phibin, Size &psibin) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
get_probability_for_rotamer(Real phi, Real psi, Size rot_ind) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
get_psi_from_rsd(conformation::Residue const &rsd) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protectedvirtual
get_rotamer(Real phi, Real psi, Size rot_ind) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
get_rotamer_from_chi(ChiVector const &chi, RotVector &rot) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
get_rotamer_from_chi_static(ChiVector const &chi, Size4 &rot) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
get_rotamer_from_chi_static(Real4 const &chi, Size4 &rot) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
initialize_bicubic_splines()core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
interpolate_rotamers(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, Size const packed_rotno, PackedDunbrackRotamer< T, Real > &interpolated_rotamer) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
interpolate_rotamers(RotamerLibraryScratchSpace &scratch, Size const packed_rotno, Size const phibin, Size const psibin, Size const phibin_next, Size const psibin_next, Real const phi_alpha, Real const psi_alpha, PackedDunbrackRotamer< T, Real > &interpolated_rotamer) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
mark_rotwell_exists(utility::vector1< Size > const &rotwell)core::pack::dunbrack::SingleResidueDunbrackLibraryprotected
memory_usage_dynamic() const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protectedvirtual
memory_usage_in_bytes() const core::pack::dunbrack::SingleResidueDunbrackLibraryvirtual
memory_usage_static() const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protectedvirtual
n_chi_bins() const core::pack::dunbrack::SingleResidueDunbrackLibraryinlineprotected
n_packed_rots() const core::pack::dunbrack::SingleResidueDunbrackLibraryinlineprotected
N_PHIPSI_BINScore::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protectedstatic
n_possible_rots() const core::pack::dunbrack::SingleResidueDunbrackLibraryinlineprotected
n_rotamer_bins() const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
n_rotamer_bins_for_aa(chemical::AA const aa, RotVector &rot)core::pack::dunbrack::SingleResidueDunbrackLibrarystatic
n_rotamer_bins_for_aa_02(chemical::AA const aa, RotVector &rot)core::pack::dunbrack::SingleResidueDunbrackLibrarystatic
n_rotameric_bins_for_aa(chemical::AA const aa, RotVector &rot, bool dun02)core::pack::dunbrack::SingleResidueDunbrackLibrarystatic
nchi() const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
NEUTRAL_PHIcore::pack::dunbrack::SingleResidueDunbrackLibrarystatic
NEUTRAL_PSIcore::pack::dunbrack::SingleResidueDunbrackLibrarystatic
packed_rotamer_2_regular_rotamer(PackedDunbrackRotamer< T, P > const &packedrot) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protected
packed_rotno_2_rotwell(Size const packed_rotno, utility::vector1< Size > &rotwell) const core::pack::dunbrack::SingleResidueDunbrackLibrary
packed_rotno_2_rotwell(Size const packed_rotno, Size4 &rotwell) const core::pack::dunbrack::SingleResidueDunbrackLibrary
packed_rotno_2_rotwell(Size const packed_rotno) const core::pack::dunbrack::SingleResidueDunbrackLibrary
packed_rotno_2_sorted_rotno() const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >inlineprotected
packed_rotno_2_sorted_rotno()core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >inlineprotected
packed_rotno_2_sorted_rotno_core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >private
parent typedefcore::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
PHIPSI_BINRANGEcore::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >protectedstatic
prob_to_accumulate(Real, Real)core::pack::dunbrack::SingleResidueDunbrackLibrary
prob_to_accumulate_buried(Real)core::pack::dunbrack::SingleResidueDunbrackLibrary
prob_to_accumulate_nonburied(Real)core::pack::dunbrack::SingleResidueDunbrackLibrary
probability_to_accumulate_while_building_rotamers(bool buried) const core::pack::dunbrack::SingleResidueDunbrackLibrary
read_from_binary(utility::io::izstream &in)core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
read_from_file(utility::io::izstream &in, bool first_line_three_letter_code_already_read)core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
read_options()core::pack::dunbrack::SingleResidueDunbrackLibrary
rotamer_energy(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
rotamer_energy_deriv(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
RotamericSingleResidueDunbrackLibrary(AA const aa_in, bool dun02)core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
rotamers() const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >inlineprotected
rotamers()core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >inlineprotected
rotamers_core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >private
rotno_2_packed_rotno(Size const rotno) const core::pack::dunbrack::SingleResidueDunbrackLibrary
rotno_2_rotwell(Size const rotno, utility::vector1< Size > &rotwell) const core::pack::dunbrack::SingleResidueDunbrackLibrary
rotwell_2_packed_rotno(utility::vector1< Size > const &rotwell) const core::pack::dunbrack::SingleResidueDunbrackLibrary
rotwell_2_packed_rotno(Size4 const &rotwell) const core::pack::dunbrack::SingleResidueDunbrackLibrary
rotwell_2_rotno(utility::vector1< Size > const &rotwell) const core::pack::dunbrack::SingleResidueDunbrackLibrary
rotwell_2_rotno(Size4 const &rotwell) const core::pack::dunbrack::SingleResidueDunbrackLibrary
set_n_chi_bins(utility::vector1< Size > const &)core::pack::dunbrack::SingleResidueDunbrackLibrary
SingleResidueDunbrackLibrary classcore::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >friend
core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary(AA const aa, Size const n_rotameric_chi, bool dun02)core::pack::dunbrack::SingleResidueDunbrackLibrary
verify_phipsi_bins(Real phi, Real psi, Size const phibin, Size const psibin, Size const phibin_next, Size const psibin_next) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >private
write_to_binary(utility::io::ozstream &out) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
write_to_file(utility::io::ozstream &out) const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
~RotamericSingleResidueDunbrackLibrary()core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >virtual
~SingleResidueDunbrackLibrary()core::pack::dunbrack::SingleResidueDunbrackLibraryvirtual
~SingleResidueRotamerLibrary()core::pack::dunbrack::SingleResidueRotamerLibraryvirtual