aa() const | core::conformation::Residue | inline |
abase2(int const atomno) const | core::conformation::Residue | inline |
accpt_pos() const | core::conformation::Residue | inline |
accpt_pos_sc() const | core::conformation::Residue | inline |
actcoord() const | core::conformation::Residue | inline |
actcoord() | core::conformation::Residue | inline |
actcoord_ | core::conformation::Residue | private |
actcoord_atoms() const | core::conformation::Residue | inline |
actual_residue_connection(Size resconnid) const | core::conformation::Residue | inline |
all_bb_atoms() const | core::conformation::Residue | inline |
apply_transform_downstream(int const atomno, numeric::xyzMatrix< Real > const &R, Vector const &v) | core::conformation::Residue | private |
apply_transform_Rx_plus_v(numeric::xyzMatrix< Real > R, Vector v) | core::conformation::Residue | |
assign_nus() | core::conformation::Residue | private |
assign_orbitals() | core::conformation::Residue | private |
atom(Size const atm_index) const | core::conformation::Residue | inline |
atom(Size const atm_index) | core::conformation::Residue | inline |
atom(std::string const &atm_name) const | core::conformation::Residue | inline |
atom(std::string const &atm_name) | core::conformation::Residue | inline |
atom_base(int const atomno) const | core::conformation::Residue | inline |
atom_begin() | core::conformation::Residue | inline |
atom_begin() const | core::conformation::Residue | inline |
atom_end() | core::conformation::Residue | inline |
atom_end() const | core::conformation::Residue | inline |
atom_index(std::string const &atm) const | core::conformation::Residue | inline |
atom_is_backbone(int const atomno) const | core::conformation::Residue | inline |
atom_is_hydrogen(Size const atomno) const | core::conformation::Residue | inline |
atom_is_polar_hydrogen(Size ind) const | core::conformation::Residue | inline |
atom_name(int const atm) const | core::conformation::Residue | inline |
atom_type(int const atomno) const | core::conformation::Residue | inline |
atom_type_index(Size const atomno) const | core::conformation::Residue | |
atom_type_set() const | core::conformation::Residue | inline |
atomic_charge(int const atomno) const | core::conformation::Residue | |
AtomIndices typedef | core::conformation::Residue | |
atoms() const | core::conformation::Residue | inline |
atoms() | core::conformation::Residue | inline |
atoms_ | core::conformation::Residue | private |
atoms_with_orb_index() const | core::conformation::Residue | inline |
AtomType typedef | core::conformation::Residue | |
attached_H_begin(int const atom) const | core::conformation::Residue | inline |
attached_H_begin() const | core::conformation::Residue | inline |
attached_H_end(int const atom) const | core::conformation::Residue | inline |
attached_H_end() const | core::conformation::Residue | inline |
backbone_aa() const | core::conformation::Residue | inline |
bonded_neighbor(int const atm) const | core::conformation::Residue | inline |
bonded_orbitals(int const atm) const | core::conformation::Residue | inline |
build_atom_ideal(int const atomno, Conformation const &conformation) const | core::conformation::Residue | inline |
build_orbital_xyz(Size const orbital_index) const | core::conformation::Residue | inline |
carbohydrate_info() const | core::conformation::Residue | |
chain() const | core::conformation::Residue | inline |
chain(int const setting) | core::conformation::Residue | inline |
chain_ | core::conformation::Residue | private |
chi() const | core::conformation::Residue | inline |
chi() | core::conformation::Residue | inline |
chi(utility::vector1< Real > const &chis) | core::conformation::Residue | inline |
chi(Size const chino) const | core::conformation::Residue | inline |
chi_ | core::conformation::Residue | private |
chi_atoms() const | core::conformation::Residue | inline |
chi_atoms(int const chino) const | core::conformation::Residue | inline |
chi_rotamers(Size const chino) const | core::conformation::Residue | inline |
clear_residue_connections() | core::conformation::Residue | |
clone() const | core::conformation::Residue | |
clone_flipping_chirality() const | core::conformation::Residue | |
connect_atom(Residue const &other) const | core::conformation::Residue | |
connect_map(Size resconn_index) const | core::conformation::Residue | inline |
connect_map_ | core::conformation::Residue | private |
connect_map_size() const | core::conformation::Residue | inline |
connected_residue_at_resconn(Size const resconn_index) const | core::conformation::Residue | inline |
connection_distance(conformation::Conformation const &conf, Size const resconn_index, Vector const &matchpoint) const | core::conformation::Residue | |
connection_incomplete(Size resconnid) const | core::conformation::Residue | |
connections_match(Residue const &other) const | core::conformation::Residue | |
connections_to_residue(Residue const &other) const | core::conformation::Residue | inline |
connections_to_residue(Size const other_resid) const | core::conformation::Residue | inline |
connections_to_residues_ | core::conformation::Residue | private |
copy_residue_connections(Residue const &src_rsd) | core::conformation::Residue | |
copy_residue_connections_from(Residue const &src) | core::conformation::Residue | |
create_residue() const | core::conformation::Residue | inline |
create_rotamer() const | core::conformation::Residue | inline |
cut_bond_neighbor(int const atm) const | core::conformation::Residue | inline |
data_cache_ | core::conformation::Residue | private |
data_ptr() const | core::conformation::Residue | |
determine_nonstandard_polymer_status() | core::conformation::Residue | private |
fill_missing_atoms(utility::vector1< bool > missing, Conformation const &conformation) | core::conformation::Residue | |
first_adjacent_heavy_atom(uint const atom_index) const | core::conformation::Residue | |
first_sidechain_atom() const | core::conformation::Residue | inline |
first_sidechain_hydrogen() const | core::conformation::Residue | inline |
get_adjacent_heavy_atoms(uint const atom_index) const | core::conformation::Residue | |
get_metal_binding_atoms(AtomIndices &metal_binding_indices) const | core::conformation::Residue | inline |
get_pseudobonds_to_residue(Size resid) const | core::conformation::Residue | |
get_self_ptr() const | core::conformation::Residue | inline |
get_self_ptr() | core::conformation::Residue | inline |
get_self_weak_ptr() const | core::conformation::Residue | inline |
get_self_weak_ptr() | core::conformation::Residue | inline |
Haro_index() const | core::conformation::Residue | inline |
has(std::string const &atm) const | core::conformation::Residue | inline |
has_incomplete_connection() const | core::conformation::Residue | |
has_incomplete_connection(core::Size const atomno) const | core::conformation::Residue | |
has_lower_connect() const | core::conformation::Residue | inline |
has_property(std::string const &property) const | core::conformation::Residue | inline |
has_sc_orbitals() const | core::conformation::Residue | inline |
has_shadow_atoms() const | core::conformation::Residue | inline |
has_upper_connect() const | core::conformation::Residue | inline |
has_variant_type(chemical::VariantType const variant_type) const | core::conformation::Residue | inline |
heavyatom_has_polar_hydrogens(Size ind) const | core::conformation::Residue | inline |
heavyatom_is_an_acceptor(Size ind) const | core::conformation::Residue | inline |
heavyAtoms_end() const | core::conformation::Residue | inline |
Hpol_index() const | core::conformation::Residue | inline |
Hpos_apolar() const | core::conformation::Residue | inline |
Hpos_polar() const | core::conformation::Residue | inline |
Hpos_polar_sc() const | core::conformation::Residue | inline |
icoor(int const atm) const | core::conformation::Residue | inline |
init_residue_from_other(Residue const &src) | core::conformation::Residue | private |
is_apolar() const | core::conformation::Residue | inline |
is_aromatic() const | core::conformation::Residue | inline |
is_bonded(Residue const &other) const | core::conformation::Residue | |
is_bonded(Size const other_index) const | core::conformation::Residue | |
is_branch_lower_terminus() const | core::conformation::Residue | inline |
is_branch_point() const | core::conformation::Residue | inline |
is_carbohydrate() const | core::conformation::Residue | inline |
is_charged() const | core::conformation::Residue | inline |
is_coarse() const | core::conformation::Residue | inline |
is_DNA() const | core::conformation::Residue | inline |
is_ligand() const | core::conformation::Residue | inline |
is_lower_terminus() const | core::conformation::Residue | inline |
is_metal() const | core::conformation::Residue | inline |
is_metalbinding() const | core::conformation::Residue | inline |
is_NA() const | core::conformation::Residue | inline |
is_peptoid() const | core::conformation::Residue | inline |
is_polar() const | core::conformation::Residue | inline |
is_polymer() const | core::conformation::Residue | inline |
is_polymer_bonded(Residue const &other) const | core::conformation::Residue | |
is_polymer_bonded(Size const other_index) const | core::conformation::Residue | |
is_protein() const | core::conformation::Residue | inline |
is_pseudo_bonded(Residue const &other) const | core::conformation::Residue | inline |
is_pseudo_bonded(Size const other_index) const | core::conformation::Residue | inline |
is_repulsive(Size const &atomno) const | core::conformation::Residue | |
is_RNA() const | core::conformation::Residue | inline |
is_similar_aa(Residue const &other) const | core::conformation::Residue | inline |
is_similar_rotamer(Residue const &other) const | core::conformation::Residue | |
is_sri() const | core::conformation::Residue | inline |
is_surface() const | core::conformation::Residue | inline |
is_terminus() const | core::conformation::Residue | inline |
is_triazolemer() const | core::conformation::Residue | inline |
is_upper_terminus() const | core::conformation::Residue | inline |
is_virtual(Size const &atomno) const | core::conformation::Residue | |
is_virtual_residue() const | core::conformation::Residue | inline |
last_backbone_atom() const | core::conformation::Residue | inline |
lower_connect() const | core::conformation::Residue | inline |
lower_connect_atom() const | core::conformation::Residue | inline |
mainchain_atom(Size const i) const | core::conformation::Residue | inline |
mainchain_atoms() const | core::conformation::Residue | inline |
mainchain_torsion(Size const torsion) const | core::conformation::Residue | inline |
mainchain_torsions() const | core::conformation::Residue | inline |
mainchain_torsions() | core::conformation::Residue | inline |
mainchain_torsions(utility::vector1< Real > const &torsions) | core::conformation::Residue | inline |
mainchain_torsions_ | core::conformation::Residue | private |
mm_atom_name(int const atom) const | core::conformation::Residue | inline |
n_bonded_neighbor_all_res(core::Size const atomno, bool virt=false) const | core::conformation::Residue | |
n_current_residue_connections() const | core::conformation::Residue | |
n_hbond_acceptors() const | core::conformation::Residue | inline |
n_hbond_donors() const | core::conformation::Residue | inline |
n_mainchain_atoms() const | core::conformation::Residue | inline |
n_non_polymeric_residue_connections() const | core::conformation::Residue | inline |
n_nus() const | core::conformation::Residue | inline |
n_orbitals() const | core::conformation::Residue | inline |
n_polymeric_residue_connections() const | core::conformation::Residue | inline |
n_possible_residue_connections() const | core::conformation::Residue | inline |
n_virtual_atoms() const | core::conformation::Residue | inline |
name() const | core::conformation::Residue | inline |
name1() const | core::conformation::Residue | inline |
name3() const | core::conformation::Residue | inline |
natoms() const | core::conformation::Residue | inline |
nbr_atom() const | core::conformation::Residue | inline |
nbr_atom_xyz() const | core::conformation::Residue | inline |
nbr_radius() const | core::conformation::Residue | inline |
nbrs(int const atm) const | core::conformation::Residue | inline |
nchi() const | core::conformation::Residue | inline |
nheavyatoms() const | core::conformation::Residue | inline |
nonconst_data_ptr() | core::conformation::Residue | |
nonstandard_polymer_ | core::conformation::Residue | private |
nu(core::uint const index) const | core::conformation::Residue | inline |
nu_atoms() const | core::conformation::Residue | inline |
nu_atoms(core::uint const index) const | core::conformation::Residue | inline |
nus() const | core::conformation::Residue | inline |
nus() | core::conformation::Residue | inline |
nus_ | core::conformation::Residue | private |
operator=(Residue const &rhs) | core::conformation::Residue | private |
orbital_name(int const orbital_index) const | core::conformation::Residue | inline |
orbital_type(int const orbital_index) const | core::conformation::Residue | inline |
orbital_type_index(Size const orbital_index) const | core::conformation::Residue | inline |
orbital_xyz(Size const orbital_index) const | core::conformation::Residue | inline |
orbitals_ | core::conformation::Residue | private |
orient_onto_residue(Residue const &src) | core::conformation::Residue | |
orient_onto_residue(Residue const &src, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) | core::conformation::Residue | |
orient_onto_residue(Residue const &src, Size center, Size nbr1, Size nbr2, Size src_center, Size src_nbr1, Size src_nbr2) | core::conformation::Residue | private |
orient_onto_residue_peptoid(Residue const &src, Conformation const &conformation) | core::conformation::Residue | |
path_distance(int atom) const | core::conformation::Residue | inline |
path_distance(int at1, int at2) const | core::conformation::Residue | inline |
path_distances() const | core::conformation::Residue | inline |
place(Residue const &src, Conformation const &conformation, bool preserve_c_beta=false) | core::conformation::Residue | |
polymeric_oriented_sequence_distance(Residue const &other) const | core::conformation::Residue | inline |
polymeric_sequence_distance(Residue const &other) const | core::conformation::Residue | inline |
pseudobonds() const | core::conformation::Residue | inline |
pseudobonds_ | core::conformation::Residue | private |
requires_actcoord() const | core::conformation::Residue | inline |
Residue(ResidueTypeCOP rsd_type_in, bool const dummy_arg) | core::conformation::Residue | |
Residue(ResidueType const &rsd_type_in, bool const dummy_arg) | core::conformation::Residue | |
Residue(ResidueType const &rsd_type_in, Residue const ¤t_rsd, Conformation const &conformation, bool preserve_c_beta=false) | core::conformation::Residue | |
Residue(Residue const &src) | core::conformation::Residue | |
Residue(Residue const &src, bool const flip_chirality) | core::conformation::Residue | |
residue_connect_atom_index(Size const resconn_id) const | core::conformation::Residue | inline |
residue_connection(int const resconn_index) const | core::conformation::Residue | inline |
residue_connection_conn_id(Size const resconn_index) const | core::conformation::Residue | inline |
residue_connection_partner(Size const resconn_index) const | core::conformation::Residue | inline |
residue_connection_partner(Size const resconn_index, Size const otherres, Size const other_connid) | core::conformation::Residue | |
residue_type_set() const | core::conformation::Residue | inline |
ResidueType typedef | core::conformation::Residue | |
ResidueTypeCOP typedef | core::conformation::Residue | |
ring_conformer(core::uint const ring_num) const | core::conformation::Residue | |
RNA_type() const | core::conformation::Residue | inline |
rsd_type_ | core::conformation::Residue | private |
rsd_type_ptr_ | core::conformation::Residue | private |
select_orient_atoms(Size ¢er, Size &nbr1, Size &nbr2) const | core::conformation::Residue | |
seqpos() const | core::conformation::Residue | inline |
seqpos(Size const setting) | core::conformation::Residue | inline |
seqpos_ | core::conformation::Residue | private |
set_all_chi(utility::vector1< Real > const &chis) | core::conformation::Residue | |
set_all_nu(utility::vector1< Real > const &nus, utility::vector1< Real > const &taus) | core::conformation::Residue | |
set_all_ring_nu(Size start, Size end, utility::vector1< Real > const &nus, utility::vector1< Real > const &taus) | core::conformation::Residue | |
set_chi(int const chino, Real const setting) | core::conformation::Residue | |
set_d(int const chino, Real const setting) | core::conformation::Residue | |
set_orbital_xyz(core::Size const orbital_index, Vector const &xyz_in) | core::conformation::Residue | inline |
set_pseudobonds_to_residue(Size resid, PseudoBondCollectionCOP pbs) | core::conformation::Residue | |
set_tau(Size const nuno, Real const setting) | core::conformation::Residue | |
set_theta(int const chino, Real const setting) | core::conformation::Residue | |
set_xyz(core::Size const atm_index, Vector const &xyz_in) | core::conformation::Residue | |
set_xyz(std::string const &atm_name, Vector const &xyz_in) | core::conformation::Residue | |
show(std::ostream &output=std::cout, bool output_atomic_details=false) const | core::conformation::Residue | |
sidechainAtoms_begin() const | core::conformation::Residue | inline |
type() const | core::conformation::Residue | inline |
update_actcoord() | core::conformation::Residue | |
update_connections_to_other_residue(Residue const &other_rsd) | core::conformation::Residue | |
update_connections_to_residues() | core::conformation::Residue | private |
update_orbital_coords() | core::conformation::Residue | inline |
update_sequence_numbering(utility::vector1< Size > const &old2new) | core::conformation::Residue | |
upper_connect() const | core::conformation::Residue | inline |
upper_connect_atom() const | core::conformation::Residue | inline |
xyz(Size const atm_index) const | core::conformation::Residue | |
xyz(std::string const &atm_name) const | core::conformation::Residue | |
~Residue() | core::conformation::Residue | |