Rosetta Core  2014.35
core::scoring::rna::RNA_LowResolutionPotential Member List

This is the complete list of members for core::scoring::rna::RNA_LowResolutionPotential, including all inherited members.

atom_numbers_for_backbone_score_calculations_core::scoring::rna::RNA_LowResolutionPotentialprivate
axis_bin_width_core::scoring::rna::RNA_LowResolutionPotentialprivate
axis_num_bins_core::scoring::rna::RNA_LowResolutionPotentialprivate
backbone_backbone_bin_width_core::scoring::rna::RNA_LowResolutionPotentialprivate
backbone_backbone_distance_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
backbone_backbone_num_bins_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_atom_dist_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_bin_width_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_check_atom_neighbor_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_distance_cutoff() const core::scoring::rna::RNA_LowResolutionPotentialinline
base_backbone_distance_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_num_bins_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_rho_cutoff() const core::scoring::rna::RNA_LowResolutionPotentialinline
base_backbone_rho_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_rho_fade_zone_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_table_size_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_z_cutoff() const core::scoring::rna::RNA_LowResolutionPotentialinline
base_backbone_z_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_backbone_z_fade_zone_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_stack_max_height_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_stack_min_height_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_stack_radius2_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_stack_radius_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_stack_rho_fade_zone_core::scoring::rna::RNA_LowResolutionPotentialprivate
base_stack_z_fade_zone_core::scoring::rna::RNA_LowResolutionPotentialprivate
basepair_xy_bin_width_core::scoring::rna::RNA_LowResolutionPotentialprivate
basepair_xy_num_bins_core::scoring::rna::RNA_LowResolutionPotentialprivate
basepair_xy_table_size_core::scoring::rna::RNA_LowResolutionPotentialprivate
basepair_xy_z_fade_zone_core::scoring::rna::RNA_LowResolutionPotentialprivate
check_atom_numbers_for_backbone_oxygens(core::chemical::ResidueTypeSetCAP &rsd_set, core::chemical::AA const &aa) const core::scoring::rna::RNA_LowResolutionPotentialprivate
check_clear_for_stacking(pose::Pose &pose, Size const &i, int const &sign) const core::scoring::rna::RNA_LowResolutionPotential
check_for_base_neighbor(conformation::Residue const &rsd1, Vector const &heavy_atom_j, Real &atom_cutoff_weight) const core::scoring::rna::RNA_LowResolutionPotential
check_forming_base_pair(pose::Pose &pose, Size const &i, Size const &j) const core::scoring::rna::RNA_LowResolutionPotential
dummy_derivcore::scoring::rna::RNA_LowResolutionPotentialstatic
eval_atom_derivative_base_base(id::AtomID const &atom_id, pose::Pose const &pose, scoring::EnergyMap const &weights, Vector &F1, Vector &F2) const core::scoring::rna::RNA_LowResolutionPotential
eval_atom_derivative_rna_backbone_backbone(id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const core::scoring::rna::RNA_LowResolutionPotential
eval_atom_derivative_rna_base_backbone(id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const core::scoring::rna::RNA_LowResolutionPotential
eval_atom_derivative_rna_repulsive(id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const core::scoring::rna::RNA_LowResolutionPotential
eval_rna_base_pair_energy(rna::RNA_RawBaseBaseInfo &rna_raw_base_base_info, conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, Vector const &centroid1, Vector const &centroid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const core::scoring::rna::RNA_LowResolutionPotential
eval_rna_base_pair_energy_one_way(rna::RNA_RawBaseBaseInfo &rna_raw_base_base_info, conformation::Residue const &res_i, conformation::Residue const &res_j, pose::Pose const &pose, Vector const &centroid1, Vector const &centroid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const core::scoring::rna::RNA_LowResolutionPotentialprivate
fade_core::scoring::rna::RNA_LowResolutionPotentialprivate
fill_atom_numbers_for_backbone_oxygens(core::chemical::ResidueTypeSetCAP &rsd_set, core::chemical::AA const &aa)core::scoring::rna::RNA_LowResolutionPotentialprivate
finalize(pose::Pose &pose) const core::scoring::rna::RNA_LowResolutionPotential
find_backbone_oxygen_atom(ObjexxFCL::FArray2D< Size > const &atom_number_for_backbone_score_calculations, Size const &i, Size const &atom_num_i) const core::scoring::rna::RNA_LowResolutionPotentialprivate
find_backbone_oxygen_atom(Size const &atom_num_i) const core::scoring::rna::RNA_LowResolutionPotentialprivate
get_rna_axis_score(Real const cos_theta, Real &deriv=dummy_deriv) const core::scoring::rna::RNA_LowResolutionPotentialprivate
get_rna_backbone_backbone_score(Distance const &r, Size const &atom_num_j_bin, Real &deriv=dummy_deriv) const core::scoring::rna::RNA_LowResolutionPotentialprivate
get_rna_backbone_backbone_xy(Distance const x, Distance const y, conformation::Residue const &res_i, Size const &atom_num_j_bin) const core::scoring::rna::RNA_LowResolutionPotentialprivate
get_rna_base_backbone_xy(Distance const x, Distance const y, Distance const z, conformation::Residue const &res_i, Size const &atom_num_j_bin, bool const deriv_check=false, Real &deriv_x=dummy_deriv, Real &deriv_y=dummy_deriv, Real &deriv_z=dummy_deriv) const core::scoring::rna::RNA_LowResolutionPotentialprivate
get_rna_basepair_xy(Distance const x, Distance const y, Distance const z, Real const cos_theta, conformation::Residue const &res_i, conformation::Residue const &res_j, bool const deriv_check=true, Real &deriv_x=dummy_deriv, Real &deriv_y=dummy_deriv, Real &deriv_z=dummy_deriv) const core::scoring::rna::RNA_LowResolutionPotentialprivate
get_rna_repulsive_score(Distance const &r, Size const &atom_num_j_bin, Real &deriv=dummy_deriv) const core::scoring::rna::RNA_LowResolutionPotentialprivate
get_rna_stack_score(Distance const x, Distance const y, Distance const z, Real &deriv_x=dummy_deriv, Real &deriv_y=dummy_deriv, Real &deriv_z=dummy_deriv) const core::scoring::rna::RNA_LowResolutionPotential
get_rna_stagger_score(Distance const height, Real &deriv=dummy_deriv) const core::scoring::rna::RNA_LowResolutionPotentialprivate
get_zeta_cutoff(conformation::Residue const &res_i, Real &zeta_hoogsteen_cutoff, Real &zeta_sugar_cutoff) const core::scoring::rna::RNA_LowResolutionPotential
initialize_atom_numbers_for_backbone_score_calculations()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_more_precise_base_pair_cutoffs()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_rna_axis()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_rna_backbone_backbone()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_rna_backbone_backbone_weights()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_RNA_backbone_oxygen_atoms()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_rna_base_backbone_xy()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_rna_basepair_xy()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_rna_repulsive_weights()core::scoring::rna::RNA_LowResolutionPotentialprivate
initialize_rna_stagger()core::scoring::rna::RNA_LowResolutionPotentialprivate
interpolate_core::scoring::rna::RNA_LowResolutionPotentialprivate
more_precise_base_pair_classification(bool const &value)core::scoring::rna::RNA_LowResolutionPotentialinline
more_precise_base_pair_classification_core::scoring::rna::RNA_LowResolutionPotentialprivate
num_RNA_backbone_oxygen_atoms_core::scoring::rna::RNA_LowResolutionPotentialprivate
num_RNA_base_pair_orientations_core::scoring::rna::RNA_LowResolutionPotentialprivate
num_RNA_res_types_core::scoring::rna::RNA_LowResolutionPotentialprivate
o2p_index_within_special_backbone_atoms_core::scoring::rna::RNA_LowResolutionPotentialprivate
o2prime_index_within_special_backbone_atoms_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_axis_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_backbone_backbone_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const core::scoring::rna::RNA_LowResolutionPotential
rna_backbone_backbone_pair_energy_one_way(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_backbone_backbone_potential_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_backbone_backbone_weight_core::scoring::rna::RNA_LowResolutionPotentialprivate
RNA_backbone_oxygen_atoms_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_base_backbone_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &centroid1, Vector const &centroid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const core::scoring::rna::RNA_LowResolutionPotential
rna_base_backbone_pair_energy_one_way(conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &centroid1, core::kinematics::Stub const &stub1) const core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_base_backbone_xy_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_basepair_radius_cutoff2_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_basepair_radius_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_basepair_stagger_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_basepair_xy_core::scoring::rna::RNA_LowResolutionPotentialprivate
RNA_LowResolutionPotential()core::scoring::rna::RNA_LowResolutionPotential
rna_repulse_all_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_repulsive_distance_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_repulsive_max_penalty_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_repulsive_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const core::scoring::rna::RNA_LowResolutionPotential
rna_repulsive_pair_energy_one_way(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_repulsive_screen_scale_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_repulsive_weight_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_stagger_core::scoring::rna::RNA_LowResolutionPotentialprivate
rna_verbose_core::scoring::rna::RNA_LowResolutionPotentialprivate
setup_precise_zeta_cutoffs(chemical::AA const &na_rad, std::string const &hoogsteen_cutoff_atom, std::string const &sugar_cutoff_atom)core::scoring::rna::RNA_LowResolutionPotentialprivate
stagger_bin_width_core::scoring::rna::RNA_LowResolutionPotentialprivate
stagger_distance_cutoff_core::scoring::rna::RNA_LowResolutionPotentialprivate
stagger_num_bins_core::scoring::rna::RNA_LowResolutionPotentialprivate
update_rna_base_base_interactions(pose::Pose &pose) const core::scoring::rna::RNA_LowResolutionPotential
update_rna_base_pair_list(pose::Pose &pose) const core::scoring::rna::RNA_LowResolutionPotential
update_rna_centroid_info(pose::Pose &pose) const core::scoring::rna::RNA_LowResolutionPotential
zeta_hoogsteen_cutoff_precise_core::scoring::rna::RNA_LowResolutionPotentialprivate
zeta_sugar_cutoff_precise_core::scoring::rna::RNA_LowResolutionPotentialprivate