Rosetta Core  2014.35
core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > Member List

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

AA typedefcore::pack::dunbrack::SingleResiduePeptoidLibrary
aa() const core::pack::dunbrack::SingleResiduePeptoidLibraryinline
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::RotamericSingleResiduePeptoidLibrary< T >protected
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 core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
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 core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
best_rotamer_energy(conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< 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::SingleResiduePeptoidLibraryinline
bin_rotameric_chi(Real chi, Size which_chi) const core::pack::dunbrack::SingleResiduePeptoidLibraryinline
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::RotamericSingleResiduePeptoidLibrary< 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::RotamericSingleResiduePeptoidLibrary< T >protectedvirtual
CIS_OMG_LOWER_RANGEcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
CIS_OMG_UPPER_RANGEcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
cis_packed_rotno_2_sorted_rotno_core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >private
cis_rotamers_core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >private
CIS_UPPER_TRANS_LOWER_SPLITcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
correct_termini_derivatives(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< 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::RotamericSingleResiduePeptoidLibrary< T >protected
declare_all_existing_rotwells_encountered()core::pack::dunbrack::SingleResiduePeptoidLibraryprotected
dun02() const core::pack::dunbrack::SingleResiduePeptoidLibraryinlineprotected
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::RotamericSingleResiduePeptoidLibrary< T >protected
eval_rotameric_energy_deriv(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< 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::RotamericSingleResiduePeptoidLibrary< T >virtual
find_another_representative_for_unlikely_rotamer(conformation::Residue const &rsd, Size4 &rotwell) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
get_all_rotamer_samples(Real omg, Real phi, Real psi) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
get_omg_from_rsd(conformation::Residue const &rsd, pose::Pose const &pose) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedvirtual
get_omgphipsi_bins(Real omg, Real phi, Real psi, Size &omgbin, Size &phibin, Size &psibin, Size &omgbin_next, Size &phibin_next, Size &psibin_next, Real &omg_alpha, Real &phi_alpha, Real &psi_alpha) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
get_omgphipsi_bins(Real omg, Real phi, Real psi, Size &omgbin, Size &phibin, Size &psibin) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
get_phi_from_rsd(conformation::Residue const &rsd, pose::Pose const &pose) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedvirtual
get_probability_for_rotamer(Real omg, Real phi, Real psi, Size rot_ind) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
get_psi_from_rsd(conformation::Residue const &rsd, pose::Pose const &pose) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedvirtual
get_rotamer(Real omg, Real phi, Real psi, Size rot_ind) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
get_rotamer_from_chi(ChiVector const &chi, RotVector &rot) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
get_rotamer_from_chi_static(ChiVector const &chi, Size4 &rot) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
get_rotamer_from_chi_static(Real4 const &chi, Size4 &rot) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
interpolate_rotamers(conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, Size const packed_rotno, PackedDunbrackRotamer< T, Real > &interpolated_rotamer) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
interpolate_rotamers(typename ObjexxFCL::FArray4D< PackedDunbrackRotamer< T > > const &rotamers, ObjexxFCL::FArray4D< Size > const &packed_rotno_2_sorted_rotno, RotamerLibraryScratchSpace &scratch, Size const packed_rotno, Size const omgbin, Size const phibin, Size const psibin, Size const omgbin_next, Size const phibin_next, Size const psibin_next, Real const omg_alpha, Real const phi_alpha, Real const psi_alpha, PackedDunbrackRotamer< T, Real > &interpolated_rotamer) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
is_cis_omg(Real omg_angle) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >inlineprotected
is_trans_omg(Real omg_angle) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >inlineprotected
mark_rotwell_exists(utility::vector1< Size > const &rotwell)core::pack::dunbrack::SingleResiduePeptoidLibraryprotected
memory_usage_dynamic() const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedvirtual
memory_usage_in_bytes() const core::pack::dunbrack::SingleResiduePeptoidLibraryvirtual
memory_usage_static() const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedvirtual
n_chi_bins() const core::pack::dunbrack::SingleResiduePeptoidLibraryinlineprotected
N_OMG_BINScore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
n_packed_rots() const core::pack::dunbrack::SingleResiduePeptoidLibraryinlineprotected
N_PHI_BINScore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
n_possible_rots() const core::pack::dunbrack::SingleResiduePeptoidLibraryinlineprotected
N_PSI_BINScore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
n_rotamer_bins() const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
n_rotamer_bins_for_aa(chemical::AA const aa, RotVector &rot)core::pack::dunbrack::SingleResiduePeptoidLibrarystatic
n_rotamer_bins_for_aa_02(chemical::AA const aa, RotVector &rot)core::pack::dunbrack::SingleResiduePeptoidLibrarystatic
n_rotameric_bins_for_aa(chemical::AA const aa, RotVector &rot, bool dun02)core::pack::dunbrack::SingleResiduePeptoidLibrarystatic
nchi() const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
NEUTRAL_OMGcore::pack::dunbrack::SingleResiduePeptoidLibrarystatic
NEUTRAL_PHIcore::pack::dunbrack::SingleResiduePeptoidLibrarystatic
NEUTRAL_PSIcore::pack::dunbrack::SingleResiduePeptoidLibrarystatic
OMG_BINRANGEcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
packed_rotamer_2_regular_rotamer(PackedDunbrackRotamer< T, P > const &packedrot) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
packed_rotno_2_rotwell(Size const packed_rotno, utility::vector1< Size > &rotwell) const core::pack::dunbrack::SingleResiduePeptoidLibrary
packed_rotno_2_rotwell(Size const packed_rotno, Size4 &rotwell) const core::pack::dunbrack::SingleResiduePeptoidLibrary
packed_rotno_2_rotwell(Size const packed_rotno) const core::pack::dunbrack::SingleResiduePeptoidLibrary
packed_rotno_2_sorted_rotno(Real omg_angle) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
packed_rotno_2_sorted_rotno(Real omg_angle)core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
parent typedefcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
PHI_BINRANGEcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
prob_to_accumulate(Real, Real)core::pack::dunbrack::SingleResiduePeptoidLibrary
prob_to_accumulate_buried(Real)core::pack::dunbrack::SingleResiduePeptoidLibrary
prob_to_accumulate_nonburied(Real)core::pack::dunbrack::SingleResiduePeptoidLibrary
probability_to_accumulate_while_building_rotamers(bool buried) const core::pack::dunbrack::SingleResiduePeptoidLibrary
PSI_BINRANGEcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
read_from_binary(utility::io::izstream &in)core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
read_from_file(utility::io::izstream &in)core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
read_options()core::pack::dunbrack::SingleResiduePeptoidLibrary
rotamer_energy(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
rotamer_energy_deriv(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
RotamericSingleResiduePeptoidLibrary()core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
rotamers(Real omg_angle) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
rotamers(Real omg_angle)core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protected
rotno_2_packed_rotno(Size const rotno) const core::pack::dunbrack::SingleResiduePeptoidLibrary
rotno_2_rotwell(Size const rotno, utility::vector1< Size > &rotwell) const core::pack::dunbrack::SingleResiduePeptoidLibrary
rotwell_2_packed_rotno(utility::vector1< Size > const &rotwell) const core::pack::dunbrack::SingleResiduePeptoidLibrary
rotwell_2_packed_rotno(Size4 const &rotwell) const core::pack::dunbrack::SingleResiduePeptoidLibrary
rotwell_2_rotno(utility::vector1< Size > const &rotwell) const core::pack::dunbrack::SingleResiduePeptoidLibrary
rotwell_2_rotno(Size4 const &rotwell) const core::pack::dunbrack::SingleResiduePeptoidLibrary
RSD_OMG_INDEXcore::pack::dunbrack::SingleResiduePeptoidLibrarystatic
RSD_PHI_INDEXcore::pack::dunbrack::SingleResiduePeptoidLibrarystatic
RSD_PSI_INDEXcore::pack::dunbrack::SingleResiduePeptoidLibrarystatic
set_n_chi_bins(utility::vector1< Size > const &)core::pack::dunbrack::SingleResiduePeptoidLibrary
SingleResiduePeptoidLibrary classcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >friend
core::pack::dunbrack::SingleResiduePeptoidLibrary::SingleResiduePeptoidLibrary(Size const n_rotameric_chi)core::pack::dunbrack::SingleResiduePeptoidLibrary
TRANS_OMG_LOWER_RANGEcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
TRANS_OMG_UPPER_RANGEcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
trans_packed_rotno_2_sorted_rotno_core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >private
trans_rotamers_core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >private
TRANS_UPPER_CIS_LOWER_SPLITcore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >protectedstatic
verify_omgphipsi_bins(Real omg, Real phi, Real psi, Size const omgbin, Size const phibin, Size const psibin, Size const omgbin_next, Size const phibin_next, Size const psibin_next) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >private
write_to_binary(utility::io::ozstream &out) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
write_to_file(utility::io::ozstream &out) const core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
~RotamericSingleResiduePeptoidLibrary()core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >virtual
~SingleResiduePeptoidLibrary()core::pack::dunbrack::SingleResiduePeptoidLibraryvirtual
~SingleResidueRotamerLibrary()core::pack::dunbrack::SingleResidueRotamerLibraryvirtual