Rosetta Core  2014.35
core::chemical::ResidueType Member List

This is the complete list of members for core::chemical::ResidueType, including all inherited members.

aa(AA const &type)core::chemical::ResidueTypeinline
aa(std::string const &type)core::chemical::ResidueTypeinline
aa() const core::chemical::ResidueTypeinline
aa_core::chemical::ResidueTypeprivate
abase2(Size const atomno) const core::chemical::ResidueType
abase2_core::chemical::ResidueTypeprivate
abase2_indices_core::chemical::ResidueTypeprivate
acceptor_atoms()core::chemical::ResidueType
accpt_pos() const core::chemical::ResidueTypeinline
accpt_pos_core::chemical::ResidueTypeprivate
accpt_pos_sc() const core::chemical::ResidueTypeinline
accpt_pos_sc_core::chemical::ResidueTypeprivate
actcoord_atoms() const core::chemical::ResidueTypeinline
actcoord_atoms_core::chemical::ResidueTypeprivate
actcoord_atoms_indices_core::chemical::ResidueTypeprivate
add_actcoord_atom(std::string const &atom)core::chemical::ResidueType
add_adduct(Adduct &adduct_in)core::chemical::ResidueTypeinline
add_atom(std::string const &atom_name, std::string const &atom_type_name, std::string const &mm_atom_type_name, Real const charge)core::chemical::ResidueType
add_atom(std::string const &atom_name="")core::chemical::ResidueType
add_atom_alias(std::string const &rosetta_atom, std::string const &alias)core::chemical::ResidueType
add_bond(std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel=SingleBond)core::chemical::ResidueType
add_bond(VD atom1, VD atom2, BondName bondLabel=SingleBond)core::chemical::ResidueType
add_chi(Size const chino, VD atom1, VD atom2, VD atom3, VD atom4)core::chemical::ResidueType
add_chi(VD atom1, VD atom2, VD atom3, VD atom4)core::chemical::ResidueType
add_chi(Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)core::chemical::ResidueType
add_chi(std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)core::chemical::ResidueType
add_chi_rotamer(Size const chino, Real const mean, Real const sdev)core::chemical::ResidueType
add_chi_rotamer_to_last_chi(core::Angle const mean, core::Angle const sdev)core::chemical::ResidueType
add_cut_bond(std::string const &atom_name1, std::string const &atom_name2)core::chemical::ResidueType
add_metalbinding_atom(std::string const atom_name)core::chemical::ResidueType
add_nu(core::uint const nu_index, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)core::chemical::ResidueType
add_numeric_property(std::string const &tag, core::Real value)core::chemical::ResidueType
add_orbital(std::string &orbital_name, std::string &orbital_type_name)core::chemical::ResidueType
add_orbital_bond(std::string const &atom_name1, std::string const &orbital_name)core::chemical::ResidueType
add_property(std::string const &property)core::chemical::ResidueType
add_residue_connection(std::string const &atom_name)core::chemical::ResidueType
add_string_property(std::string const &tag, std::string value)core::chemical::ResidueType
add_variant_type(VariantType const &variant_type)core::chemical::ResidueType
all_bb_atoms() const core::chemical::ResidueTypeinline
all_bb_atoms_core::chemical::ResidueTypeprivate
all_sc_atoms() const core::chemical::ResidueTypeinline
all_sc_atoms_core::chemical::ResidueTypeprivate
apolar_hydrogens()core::chemical::ResidueType
aromatic_atoms()core::chemical::ResidueType
assign_internal_coordinates()core::chemical::ResidueType
assign_internal_coordinates(core::chemical::VD new_root)core::chemical::ResidueType
assign_neighbor_atom()core::chemical::ResidueType
atom(Size const atom_index)core::chemical::ResidueType
atom(Size const atom_index) const core::chemical::ResidueType
atom(std::string const &atom_name)core::chemical::ResidueType
atom(std::string const &atom_name) const core::chemical::ResidueType
atom(VD const atom_vd)core::chemical::ResidueType
atom(VD const atom_vd) const core::chemical::ResidueType
atom_2_residue_connection_map_core::chemical::ResidueTypeprivate
atom_aliases_core::chemical::ResidueTypeprivate
atom_base(Size const atomno) const core::chemical::ResidueType
atom_base(VD const atomno) const core::chemical::ResidueType
atom_base_core::chemical::ResidueTypeprivate
atom_base_indices_core::chemical::ResidueTypeprivate
atom_being_shadowed(Size atom_shadowing) const core::chemical::ResidueTypeinline
atom_forms_residue_connection(Size const atomid)core::chemical::ResidueTypeinline
atom_index(std::string const &name) const core::chemical::ResidueType
atom_index(VD const &vd) const core::chemical::ResidueType
atom_is_backbone(Size const atomno) const core::chemical::ResidueTypeinline
atom_is_hydrogen(Size const atomno) const core::chemical::ResidueTypeinline
atom_is_polar_hydrogen(Size atomno) const core::chemical::ResidueTypeinline
atom_iterators() const core::chemical::ResidueTypeinline
atom_name(Size const index) const core::chemical::ResidueType
atom_name(VD const vd) const core::chemical::ResidueType
atom_name_to_vd_core::chemical::ResidueTypeprivate
atom_shadowed_core::chemical::ResidueTypeprivate
atom_shadowed_indices_core::chemical::ResidueTypeprivate
atom_type(Size const atomno) const core::chemical::ResidueType
atom_type(VD const vd) const core::chemical::ResidueType
atom_type_set() const core::chemical::ResidueTypeinline
atom_type_set_ptr() const core::chemical::ResidueTypeinline
atom_types_core::chemical::ResidueTypeprivate
atom_vertex(std::string const &name) const core::chemical::ResidueType
atom_vertex(Size const &atomno) const core::chemical::ResidueType
atoms_are_bonded(core::Size const atomindex1, core::Size const atomindex2) const core::chemical::ResidueType
atoms_last_controlled_by_chi() const core::chemical::ResidueTypeinline
atoms_last_controlled_by_chi(Size chi) const core::chemical::ResidueTypeinline
atoms_last_controlled_by_chi_core::chemical::ResidueTypeprivate
atoms_with_orb_index() const core::chemical::ResidueTypeinline
atoms_with_orb_index_core::chemical::ResidueTypeprivate
atoms_within_one_bond_of_a_residue_connection(Size resconn) const core::chemical::ResidueTypeinline
atoms_within_one_bond_of_a_residue_connection_core::chemical::ResidueTypeprivate
atoms_within_two_bonds_of_a_residue_connection(Size resconn) const core::chemical::ResidueTypeinline
atoms_within_two_bonds_of_a_residue_connection_core::chemical::ResidueTypeprivate
attached_H_begin(Size const atom) const core::chemical::ResidueTypeinline
attached_H_begin() const core::chemical::ResidueTypeinline
attached_H_begin_core::chemical::ResidueTypeprivate
attached_H_end(Size const atom) const core::chemical::ResidueTypeinline
attached_H_end() const core::chemical::ResidueTypeinline
attached_H_end_core::chemical::ResidueTypeprivate
autodetermine_chi_bonds(core::Size max_proton_chi_samples=500)core::chemical::ResidueType
backbone_aa(std::string const &type)core::chemical::ResidueTypeinline
backbone_aa() const core::chemical::ResidueTypeinline
backbone_aa_core::chemical::ResidueTypeprivate
base_restype_name(std::string const &in)core::chemical::ResidueTypeinline
base_restype_name() const core::chemical::ResidueTypeinline
base_restype_name_core::chemical::ResidueTypeprivate
bond(ED const ed)core::chemical::ResidueType
bond(ED const ed) const core::chemical::ResidueType
bond(std::string const &atom1, std::string const &atom2)core::chemical::ResidueType
bond(std::string const &atom1, std::string const &atom2) const core::chemical::ResidueType
bond_iterators() const core::chemical::ResidueTypeinline
bond_iterators(VD const &atom) const core::chemical::ResidueTypeinline
bondangle(Size const bondang) const core::chemical::ResidueTypeinline
bondangle_atom_sets_core::chemical::ResidueTypeprivate
bondangles_for_atom(Size atomno) const core::chemical::ResidueTypeinline
bondangles_for_atom_core::chemical::ResidueTypeprivate
bonded_neighbor(Size const atomno) const core::chemical::ResidueType
bonded_neighbor_core::chemical::ResidueTypeprivate
bonded_neighbor_iterators(VD const &atom) const core::chemical::ResidueType
bonded_neighbor_type_core::chemical::ResidueTypeprivate
bonded_neighbor_types(Size const atomno) const core::chemical::ResidueType
bonded_orbitals(Size const atomno) const core::chemical::ResidueTypeinline
carbohydrate_info() const core::chemical::ResidueType
carbohydrate_info_core::chemical::ResidueTypeprivate
chi_2_proton_chi(Size chi_index) const core::chemical::ResidueTypeinline
chi_2_proton_chi_core::chemical::ResidueTypeprivate
chi_atom_vds(Size const chino) const core::chemical::ResidueTypeinline
chi_atoms(Size const chino) const core::chemical::ResidueTypeinline
chi_atoms() const core::chemical::ResidueTypeinline
chi_atoms_core::chemical::ResidueTypeprivate
chi_atoms_indices_core::chemical::ResidueTypeprivate
chi_rotamers(Size const chino) const core::chemical::ResidueTypeinline
chi_rotamers_core::chemical::ResidueTypeprivate
clone() const core::chemical::ResidueType
conformer_set_core::chemical::ResidueTypeprivate
cut_bond_neighbor(Size const atomno) const core::chemical::ResidueTypeinline
cut_bond_neighbor_core::chemical::ResidueTypeprivate
cut_bond_neighbor_indices_core::chemical::ResidueTypeprivate
debug_dump_icoor() const core::chemical::ResidueType
defined_adducts() const core::chemical::ResidueTypeinline
defined_adducts_core::chemical::ResidueTypeprivate
delete_atom(std::string const &name)core::chemical::ResidueType
delete_atom(Size const index)core::chemical::ResidueType
delete_atom_alias(std::string const &alias)core::chemical::ResidueType
delete_property(std::string const &property)core::chemical::ResidueType
dihedral(Size const dihe) const core::chemical::ResidueTypeinline
dihedral_atom_sets_core::chemical::ResidueTypeprivate
dihedrals_for_atom(Size atomno) const core::chemical::ResidueTypeinline
dihedrals_for_atom_core::chemical::ResidueTypeprivate
dump_vd_info() const core::chemical::ResidueType
element_set() const core::chemical::ResidueTypeinline
elements_core::chemical::ResidueTypeprivate
fill_ideal_xyz_from_icoor()core::chemical::ResidueType
finalize()core::chemical::ResidueType
finalized_core::chemical::ResidueTypeprivate
first_sidechain_atom() const core::chemical::ResidueTypeinline
first_sidechain_hydrogen() const core::chemical::ResidueTypeinline
first_sidechain_hydrogen_core::chemical::ResidueTypeprivate
force_bb_core::chemical::ResidueTypeprivate
force_nbr_atom_orient(bool force_orient)core::chemical::ResidueTypeinline
force_nbr_atom_orient() const core::chemical::ResidueTypeinline
force_nbr_atom_orient_core::chemical::ResidueTypeprivate
gasteiger_atom_type(Size const atomno) const core::chemical::ResidueType
gasteiger_atom_types_core::chemical::ResidueTypeprivate
generate_atom_indices()core::chemical::ResidueTypeprivate
get_metal_binding_atoms(AtomIndices &metal_binding_indices) const core::chemical::ResidueTypeinline
get_ncaa_rotlib_n_bin_per_rot(Size n_rot)core::chemical::ResidueTypeinline
get_ncaa_rotlib_n_bin_per_rot() const core::chemical::ResidueTypeinline
get_ncaa_rotlib_path() const core::chemical::ResidueTypeinline
get_numeric_property(std::string const &tag) const core::chemical::ResidueType
get_peptoid_rotlib_n_bin_per_rot(Size n_rot)core::chemical::ResidueTypeinline
get_peptoid_rotlib_n_bin_per_rot() const core::chemical::ResidueTypeinline
get_peptoid_rotlib_path() const core::chemical::ResidueTypeinline
get_RotamerLibraryName() const core::chemical::ResidueType
get_string_property(std::string const &tag) const core::chemical::ResidueType
get_use_ncaa_rotlib() const core::chemical::ResidueTypeinline
get_use_peptoid_rotlib() const core::chemical::ResidueTypeinline
graph() const core::chemical::ResidueTypeinline
graph_core::chemical::ResidueTypeprivate
Haro_index() const core::chemical::ResidueTypeinline
Haro_index_core::chemical::ResidueTypeprivate
has(std::string const &atom_name) const core::chemical::ResidueTypeinline
has(VD const vd) const core::chemical::ResidueTypeinline
has_orbital(std::string const &orbital_name) const core::chemical::ResidueTypeinline
has_property(std::string const &property) const core::chemical::ResidueType
has_sc_orbitals() const core::chemical::ResidueType
has_variant_type(VariantType const &variant_type) const core::chemical::ResidueType
heavy_atom_with_hydrogens()core::chemical::ResidueType
heavy_atom_with_polar_hydrogens()core::chemical::ResidueType
heavy_atoms()core::chemical::ResidueType
heavyatom_has_polar_hydrogens(Size atomno) const core::chemical::ResidueTypeinline
heavyatom_is_an_acceptor(Size atomno) const core::chemical::ResidueTypeinline
Hpol_index() const core::chemical::ResidueTypeinline
Hpol_index_core::chemical::ResidueTypeprivate
Hpos_apolar() const core::chemical::ResidueTypeinline
Hpos_apolar_core::chemical::ResidueTypeprivate
Hpos_polar() const core::chemical::ResidueTypeinline
Hpos_polar_core::chemical::ResidueTypeprivate
Hpos_polar_sc() const core::chemical::ResidueTypeinline
Hpos_polar_sc_core::chemical::ResidueTypeprivate
hydrogens()core::chemical::ResidueType
icoor(Size const atm) const core::chemical::ResidueType
icoor(VD const atm) const core::chemical::ResidueType
icoor_core::chemical::ResidueTypeprivate
improper_dihedral(Size const dihe) const core::chemical::ResidueTypeinline
improper_dihedral_atom_sets_core::chemical::ResidueTypeprivate
improper_dihedrals_for_atom(Size atomno) const core::chemical::ResidueTypeinline
improper_dihedrals_for_atom_core::chemical::ResidueTypeprivate
interchangeability_group() const core::chemical::ResidueTypeinline
interchangeability_group(std::string setting)core::chemical::ResidueTypeinline
interchangeability_group_core::chemical::ResidueTypeprivate
is_acetylated_nterminus() const core::chemical::ResidueType
is_adduct() const core::chemical::ResidueType
is_alpha_aa() const core::chemical::ResidueType
is_aromatic() const core::chemical::ResidueType
is_beta_aa() const core::chemical::ResidueType
is_branch_lower_terminus() const core::chemical::ResidueType
is_carbohydrate() const core::chemical::ResidueType
is_charged() const core::chemical::ResidueType
is_coarse() const core::chemical::ResidueType
is_cyclic() const core::chemical::ResidueType
is_d_aa() const core::chemical::ResidueType
is_DNA() const core::chemical::ResidueType
is_l_aa() const core::chemical::ResidueType
is_ligand() const core::chemical::ResidueType
is_lipid() const core::chemical::ResidueType
is_lower_terminus() const core::chemical::ResidueType
is_membrane() const core::chemical::ResidueType
is_metal() const core::chemical::ResidueType
is_metalbinding() const core::chemical::ResidueType
is_methylated_cterminus() const core::chemical::ResidueType
is_NA() const core::chemical::ResidueType
is_peptoid() const core::chemical::ResidueType
is_polar() const core::chemical::ResidueType
is_polymer() const core::chemical::ResidueType
is_protein() const core::chemical::ResidueType
is_proton_chi(Size const chino) const core::chemical::ResidueTypeinline
is_proton_chi_core::chemical::ResidueTypeprivate
is_RNA() const core::chemical::ResidueType
is_surface() const core::chemical::ResidueType
is_terminus() const core::chemical::ResidueType
is_upper_terminus() const core::chemical::ResidueType
is_virtual(Size const &atomno) const core::chemical::ResidueType
is_virtual_residue() const core::chemical::ResidueType
last_backbone_atom() const core::chemical::ResidueTypeinline
last_controlling_chi() const core::chemical::ResidueTypeinline
last_controlling_chi(Size atomno) const core::chemical::ResidueTypeinline
last_controlling_chi_core::chemical::ResidueTypeprivate
lower_connect() const core::chemical::ResidueType
lower_connect_atom() const core::chemical::ResidueType
lower_connect_id() const core::chemical::ResidueTypeinline
lower_connect_id_core::chemical::ResidueTypeprivate
mainchain_atom(Size const atm) const core::chemical::ResidueTypeinline
mainchain_atoms() const core::chemical::ResidueTypeinline
mainchain_atoms_core::chemical::ResidueTypeprivate
mainchain_atoms_indices_core::chemical::ResidueTypeprivate
mass() const core::chemical::ResidueTypeinline
mass_core::chemical::ResidueTypeprivate
metal_binding_atoms_core::chemical::ResidueTypeprivate
mm_atom_type(Size const atomno) const core::chemical::ResidueType
mm_atom_types_core::chemical::ResidueTypeprivate
n_backbone_heavyatoms_core::chemical::ResidueTypeprivate
n_hbond_acceptors() const core::chemical::ResidueTypeinline
n_hbond_acceptors_core::chemical::ResidueTypeprivate
n_hbond_donors() const core::chemical::ResidueTypeinline
n_hbond_donors_core::chemical::ResidueTypeprivate
n_non_polymeric_residue_connections() const core::chemical::ResidueTypeinline
n_non_polymeric_residue_connections_core::chemical::ResidueTypeprivate
n_nus() const core::chemical::ResidueTypeinline
n_orbitals() const core::chemical::ResidueType
n_polymeric_residue_connections() const core::chemical::ResidueTypeinline
n_polymeric_residue_connections_core::chemical::ResidueTypeprivate
n_proton_chi() const core::chemical::ResidueTypeinline
n_residue_connections() const core::chemical::ResidueType
n_residue_connections_for_atom(Size const atomid) const core::chemical::ResidueTypeinline
n_virtual_atoms() const core::chemical::ResidueType
name() const core::chemical::ResidueTypeinline
name(std::string const &name_in)core::chemical::ResidueTypeinline
name1() const core::chemical::ResidueTypeinline
name1(char const code)core::chemical::ResidueTypeinline
name1_core::chemical::ResidueTypeprivate
name3() const core::chemical::ResidueTypeinline
name3(std::string const &name_in)core::chemical::ResidueTypeinline
name3_core::chemical::ResidueTypeprivate
name_core::chemical::ResidueTypeprivate
natoms() const core::chemical::ResidueTypeinline
nbonds() const core::chemical::ResidueTypeinline
nbonds(Size atom) const core::chemical::ResidueTypeinline
nbonds(VD atom) const core::chemical::ResidueTypeinline
nbr_atom(std::string const &atom_name)core::chemical::ResidueTypeinline
nbr_atom(VD vertex)core::chemical::ResidueTypeinline
nbr_atom() const core::chemical::ResidueTypeinline
nbr_atom_core::chemical::ResidueTypeprivate
nbr_atom_indices_core::chemical::ResidueTypeprivate
nbr_radius(Real const radius)core::chemical::ResidueTypeinline
nbr_radius() const core::chemical::ResidueTypeinline
nbr_radius_core::chemical::ResidueTypeprivate
nbr_vertex() const core::chemical::ResidueTypeinline
nbrs(Size const atomno) const core::chemical::ResidueTypeinline
ncaa_rotlib_n_bins_per_rot_core::chemical::ResidueTypeprivate
ncaa_rotlib_n_rots_core::chemical::ResidueTypeprivate
ncaa_rotlib_path_core::chemical::ResidueTypeprivate
nchi() const core::chemical::ResidueTypeinline
ndihe() const core::chemical::ResidueTypeinline
new_orbital_icoor_data(Size const orbital_index) const core::chemical::ResidueType
nheavyatoms() const core::chemical::ResidueTypeinline
nheavyatoms_core::chemical::ResidueTypeprivate
nonadduct_variants_match(ResidueType const &other) const core::chemical::ResidueType
nondefault(bool in)core::chemical::ResidueTypeinline
nondefault_core::chemical::ResidueTypeprivate
note_chi_controls_atom(Size chi, Size atomno)core::chemical::ResidueTypeprivate
nu_atoms(core::uint const nu_index) const core::chemical::ResidueTypeinline
nu_atoms() const core::chemical::ResidueTypeinline
nu_atoms_core::chemical::ResidueTypeprivate
nu_atoms_indices_core::chemical::ResidueTypeprivate
null_vertexcore::chemical::ResidueTypestatic
num_bondangles() const core::chemical::ResidueTypeinline
number_bonded_heavyatoms(Size const atomno) const core::chemical::ResidueType
number_bonded_hydrogens(Size const atomno) const core::chemical::ResidueTypeinline
orbital(Size const orbital_index) const core::chemical::ResidueType
orbital(std::string const &orbital_name) const core::chemical::ResidueType
orbital_icoor_data(Size const orbital_index) const core::chemical::ResidueType
orbital_index(std::string const &name) const core::chemical::ResidueType
orbital_type(int const orbital_index) const core::chemical::ResidueType
orbital_types_core::chemical::ResidueTypeprivate
orbitals_core::chemical::ResidueTypeprivate
orbitals_index_core::chemical::ResidueTypeprivate
order_atoms()core::chemical::ResidueTypeprivate
ordered_atoms_core::chemical::ResidueTypeprivate
path_distance(Size at1, Size at2) const core::chemical::ResidueTypeinline
path_distance(Size atom) const core::chemical::ResidueTypeinline
path_distance_core::chemical::ResidueTypeprivate
path_distances() const core::chemical::ResidueTypeinline
peptoid_rotlib_n_bins_per_rot_core::chemical::ResidueTypeprivate
peptoid_rotlib_n_rots_core::chemical::ResidueTypeprivate
peptoid_rotlib_path_core::chemical::ResidueTypeprivate
perform_checks()core::chemical::ResidueTypeprivate
polar_hydrogens()core::chemical::ResidueType
print_bondangles() const core::chemical::ResidueType
print_dihedrals() const core::chemical::ResidueType
print_pretty_path_distances() const core::chemical::ResidueType
properties() const core::chemical::ResidueType
properties_core::chemical::ResidueTypeprivate
proton_chi_2_chi(Size proton_chi_id) const core::chemical::ResidueTypeinline
proton_chi_extra_samples(Size proton_chi) const core::chemical::ResidueTypeinline
proton_chi_extra_samples_core::chemical::ResidueTypeprivate
proton_chi_samples(Size proton_chi) const core::chemical::ResidueTypeinline
proton_chi_samples_core::chemical::ResidueTypeprivate
proton_chis_core::chemical::ResidueTypeprivate
redefine_chi(Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)core::chemical::ResidueType
remap_pdb_atom_names(bool rename)core::chemical::ResidueTypeinline
remap_pdb_atom_names() const core::chemical::ResidueTypeinline
remap_pdb_atom_names_core::chemical::ResidueTypeprivate
report_adducts()core::chemical::ResidueType
require_final() const core::chemical::ResidueTypeinline
requires_actcoord() const core::chemical::ResidueType
residue_connect_atom_index(Size const resconn_id) const core::chemical::ResidueType
residue_connection(Size const i) const core::chemical::ResidueType
residue_connection(Size const i)core::chemical::ResidueType
residue_connection_id_for_atom(Size const atomid) const core::chemical::ResidueTypeinline
residue_connection_is_polymeric(Size const resconn_id) const core::chemical::ResidueTypeinline
residue_connections_core::chemical::ResidueTypeprivate
residue_connections_for_atom(Size const atomid) const core::chemical::ResidueTypeinline
residue_type_set() const core::chemical::ResidueType
residue_type_set(ResidueTypeSetCAP set_in)core::chemical::ResidueType
residue_type_set_core::chemical::ResidueTypeprivate
ResidueType(AtomTypeSetCAP atom_types, ElementSetCAP element_types, MMAtomTypeSetCAP mm_atom_types, orbitals::OrbitalTypeSetCAP orbital_types)core::chemical::ResidueType
ResidueType(ResidueType const &residue_type)core::chemical::ResidueType
ring_conformer_set() const core::chemical::ResidueType
rings()core::chemical::ResidueTypeinline
rings_and_their_edges_core::chemical::ResidueTypeprivate
rna_residue_type_core::chemical::ResidueTypeprivate
RNA_type() const core::chemical::ResidueType
root_atom() const core::chemical::ResidueTypeinline
root_atom_core::chemical::ResidueTypeprivate
rotamer_aa(AA const &type)core::chemical::ResidueTypeinline
rotamer_aa(std::string const &type)core::chemical::ResidueTypeinline
rotamer_aa() const core::chemical::ResidueTypeinline
rotamer_aa_core::chemical::ResidueTypeprivate
rotamer_library_name_core::chemical::ResidueTypeprivate
select_orient_atoms(Size &center, Size &nbr1, Size &nbr2) const core::chemical::ResidueType
serialized_core::chemical::ResidueTypemutable
set_adduct_flag(bool adduct_in)core::chemical::ResidueType
set_atom_base(std::string const &atom_name1, std::string const &atom_name2)core::chemical::ResidueType
set_atom_base(VD const &atom1, VD const &atom2)core::chemical::ResidueType
set_atom_type(std::string const &atom_name, std::string const &atom_type_name)core::chemical::ResidueTypeinline
set_atom_type(VD atom, std::string const &atom_type_name)core::chemical::ResidueType
set_backbone_heavyatom(std::string const &name)core::chemical::ResidueType
set_gasteiger_atom_type(std::string const &atom_name, std::string const &gasteiger_atom_type_name)core::chemical::ResidueType
set_gasteiger_typeset(gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types)core::chemical::ResidueType
set_icoor(std::string const &atm, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3, bool const update_xyz=false)core::chemical::ResidueType
set_icoor(VD const &atm, Real const phi, Real const theta, Real const d, VD const &stub_atom1, VD const &stub_atom2, VD const &stub_atom3, bool const update_xyz=false)core::chemical::ResidueType
set_ideal_xyz(std::string const &atm, Vector const &xyz_in)core::chemical::ResidueType
set_ideal_xyz(Size index, Vector const &xyz_in)core::chemical::ResidueType
set_ideal_xyz(VD atm, Vector const &xyz_in)core::chemical::ResidueType
set_lower_connect_atom(std::string const &atm_name)core::chemical::ResidueType
set_mainchain_atoms(AtomIndices const &mainchain)core::chemical::ResidueType
set_mm_atom_type(std::string const &atom_name, std::string const &mm_atom_type_name)core::chemical::ResidueType
set_ncaa_rotlib_n_bin_per_rot(utility::vector1< Size > n_bins_per_rot)core::chemical::ResidueType
set_ncaa_rotlib_n_rotameric_bins(Size n_rots)core::chemical::ResidueTypeinline
set_ncaa_rotlib_n_rotameric_bins() const core::chemical::ResidueTypeinline
set_ncaa_rotlib_path(std::string const &path)core::chemical::ResidueTypeinline
set_orbital_icoor_id(std::string const &orbital, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3)core::chemical::ResidueType
set_peptoid_rotlib_n_bin_per_rot(utility::vector1< Size > n_bins_per_rot)core::chemical::ResidueType
set_peptoid_rotlib_n_rotameric_bins(Size n_rots)core::chemical::ResidueTypeinline
set_peptoid_rotlib_n_rotameric_bins() const core::chemical::ResidueTypeinline
set_peptoid_rotlib_path(std::string const &path)core::chemical::ResidueTypeinline
set_proton_chi(Size chino, utility::vector1< Real > const &dihedral_samples, utility::vector1< Real > const &extra_samples)core::chemical::ResidueType
set_RotamerLibraryName(std::string const &filename)core::chemical::ResidueType
set_shadowing_atom(std::string const &atom, std::string const &atom_being_shadowed)core::chemical::ResidueType
set_upper_connect_atom(std::string const &atm_name)core::chemical::ResidueType
set_use_ncaa_rotlib(bool flag)core::chemical::ResidueTypeinline
set_use_peptoid_rotlib(bool flag)core::chemical::ResidueTypeinline
setup_atom_ordering()core::chemical::ResidueTypeprivate
show(std::ostream &output=std::cout, bool output_atomic_details=false) const core::chemical::ResidueType
show_all_atom_names(std::ostream &out) const core::chemical::ResidueType
smallest_ring_size(VD const &atom, core::Size const &max_size=999999) const core::chemical::ResidueType
update_actcoord(conformation::Residue &rot) const core::chemical::ResidueType
update_derived_data()core::chemical::ResidueTypeprivate
update_last_controlling_chi()core::chemical::ResidueTypeprivate
update_residue_connection_mapping()core::chemical::ResidueTypeprivate
upper_connect() const core::chemical::ResidueType
upper_connect_atom() const core::chemical::ResidueType
upper_connect_id() const core::chemical::ResidueTypeinline
upper_connect_id_core::chemical::ResidueTypeprivate
use_ncaa_rotlib_core::chemical::ResidueTypeprivate
use_peptoid_rotlib_core::chemical::ResidueTypeprivate
variant_types() const core::chemical::ResidueType
variants_match(ResidueType const &other) const core::chemical::ResidueType
vd_to_index_core::chemical::ResidueTypeprivate
within1bonds_sets_for_atom(Size atomid) const core::chemical::ResidueTypeinline
within1bonds_sets_for_atom_core::chemical::ResidueTypeprivate
within2bonds_sets_for_atom(Size atomid) const core::chemical::ResidueTypeinline
within2bonds_sets_for_atom_core::chemical::ResidueTypeprivate
~ResidueType()core::chemical::ResidueTypevirtual