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core::conformation::Residue Member List

This is the complete list of members for core::conformation::Residue, including all inherited members.

aa() const core::conformation::Residueinline
abase2(Size const atomno) const core::conformation::Residueinline
accpt_pos() const core::conformation::Residueinline
accpt_pos_sc() const core::conformation::Residueinline
actcoord() const core::conformation::Residueinline
actcoord()core::conformation::Residueinline
actcoord_core::conformation::Residueprivate
actcoord_atoms() const core::conformation::Residueinline
actual_residue_connection(Size resconnid) const core::conformation::Residueinline
all_bb_atoms() const core::conformation::Residueinline
annotated_name(bool const show_all_variants=true) const core::conformation::Residue
apply_transform_downstream(core::Size const atomno, core::Size const upstream_atomno, numeric::xyzMatrix< Real > const &R, Vector const &v)core::conformation::Residueprivate
apply_transform_Rx_plus_v(numeric::xyzMatrix< Real > R, Vector v)core::conformation::Residue
assign_orbitals()core::conformation::Residueprivate
atom(Size const atm_index) const core::conformation::Residueinline
atom(Size const atm_index)core::conformation::Residueinline
atom(std::string const &atm_name) const core::conformation::Residueinline
atom(std::string const &atm_name)core::conformation::Residueinline
atom_base(Size const atomno) const core::conformation::Residueinline
atom_begin()core::conformation::Residueinline
atom_begin() const core::conformation::Residueinline
atom_depends_on_lower(core::Size const atom_index) const core::conformation::Residue
atom_depends_on_upper(core::Size const atom_index) const core::conformation::Residue
atom_end()core::conformation::Residueinline
atom_end() const core::conformation::Residueinline
atom_index(std::string const &atm) const core::conformation::Residueinline
atom_is_backbone(Size const atomno) const core::conformation::Residueinline
atom_is_hydrogen(Size const atomno) const core::conformation::Residueinline
atom_is_polar_hydrogen(Size ind) const core::conformation::Residueinline
atom_name(Size const atm) const core::conformation::Residueinline
atom_type(Size const atomno) const core::conformation::Residueinline
atom_type_index(Size const atomno) const core::conformation::Residueinline
atom_type_set() const core::conformation::Residueinline
atomic_charge(Size const atomno) const core::conformation::Residueinline
AtomIndices typedefcore::conformation::Residue
atoms() const core::conformation::Residueinline
atoms()core::conformation::Residueinline
atoms_core::conformation::Residueprivate
atoms_with_orb_index() const core::conformation::Residueinline
AtomType typedefcore::conformation::Residue
attached_H_begin(Size const atom) const core::conformation::Residueinline
attached_H_begin() const core::conformation::Residueinline
attached_H_end(Size const atom) const core::conformation::Residueinline
attached_H_end() const core::conformation::Residueinline
backbone_aa() const core::conformation::Residueinline
bonded_neighbor(Size const atm) const core::conformation::Residueinline
bonded_orbitals(Size const atm) const core::conformation::Residueinline
build_atom_ideal(int const atomno, Conformation const &conformation) const core::conformation::Residueinline
build_orbital_xyz(Size const orbital_index) const core::conformation::Residueinline
carbohydrate_info() const core::conformation::Residue
chain() const core::conformation::Residueinline
chain(core::Size const setting)core::conformation::Residueinline
chain_core::conformation::Residueprivate
chi() const core::conformation::Residueinline
chi()core::conformation::Residueinline
chi(utility::vector1< Real > const &chis)core::conformation::Residueinline
chi(Size const chino) const core::conformation::Residueinline
chi_core::conformation::Residueprivate
chi_atoms() const core::conformation::Residueinline
chi_atoms(Size const chino) const core::conformation::Residueinline
chi_rotamers(Size const chino) const core::conformation::Residueinline
clear_residue_connections()core::conformation::Residue
clone() const core::conformation::Residue
clone_flipping_chirality(core::chemical::ResidueTypeSet const &residue_type_set) const core::conformation::Residue
connect_atom(Residue const &other) const core::conformation::Residue
connect_map(Size resconn_index) const core::conformation::Residueinline
connect_map_core::conformation::Residueprivate
connect_map_size() const core::conformation::Residueinline
connected_residue_at_lower() const core::conformation::Residue
connected_residue_at_resconn(Size const resconn_index) const core::conformation::Residueinline
connected_residue_at_upper() const core::conformation::Residue
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::Residueinline
connections_to_residue(Size const other_resid) const core::conformation::Residueinline
connections_to_residues_core::conformation::Residueprivate
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::Residueinline
create_rotamer() const core::conformation::Residueinline
cut_bond_neighbor(Size const atm) const core::conformation::Residueinline
data() const core::conformation::Residueinline
data_cache_core::conformation::Residueprivate
data_ptr() const core::conformation::Residueinline
determine_nonstandard_polymer_status()core::conformation::Residueprivate
fill_missing_atoms(utility::vector1< bool > &missing, Conformation const &conformation, bool fail=true)core::conformation::Residue
first_adjacent_heavy_atom(uint const atom_index) const core::conformation::Residue
first_sidechain_atom() const core::conformation::Residueinline
first_sidechain_hydrogen() const core::conformation::Residueinline
get_adjacent_heavy_atoms(uint const atom_index) const core::conformation::Residue
get_atoms_exocyclic_to_ring_atom(uint const atom_index) const core::conformation::Residue
get_hydrogens_bonded_to_ring_atom(uint const atom_index) const core::conformation::Residue
get_metal_binding_atoms(AtomIndices &metal_binding_indices) const core::conformation::Residueinline
get_pseudobonds_to_residue(Size resid) const core::conformation::Residue
get_self_ptr() const core::conformation::Residueinline
get_self_ptr()core::conformation::Residueinline
get_self_weak_ptr() const core::conformation::Residueinline
get_self_weak_ptr()core::conformation::Residueinline
get_substituents_to_ring_atom(uint const atom_index) const core::conformation::Residue
Haro_index() const core::conformation::Residueinline
has(std::string const &atm) const core::conformation::Residueinline
has_incomplete_connection() const core::conformation::Residue
has_incomplete_connection(core::Size const atomno) const core::conformation::Residue
has_lower_connect() const core::conformation::Residueinline
has_property(std::string const &property) const core::conformation::Residueinline
has_sc_orbitals() const core::conformation::Residueinline
has_shadow_atoms() const core::conformation::Residueinline
has_upper_connect() const core::conformation::Residueinline
has_variant_type(chemical::VariantType const variant_type) const core::conformation::Residueinline
heavyatom_has_polar_hydrogens(Size ind) const core::conformation::Residueinline
heavyatom_is_an_acceptor(Size ind) const core::conformation::Residueinline
heavyAtoms_end() const core::conformation::Residueinline
Hpol_index() const core::conformation::Residueinline
Hpos_apolar() const core::conformation::Residueinline
Hpos_polar() const core::conformation::Residueinline
Hpos_polar_sc() const core::conformation::Residueinline
icoor(Size const atm) const core::conformation::Residueinline
init_residue_from_other(Residue const &src)core::conformation::Residueprivate
inter_residue_connection_partner(int connid, Conformation const &conformation) const core::conformation::Residue
is_apolar() const core::conformation::Residueinline
is_aramid() const core::conformation::Residueinline
is_aromatic() const core::conformation::Residueinline
is_bonded(Residue const &other) const core::conformation::Residueinline
is_bonded(Size const other_residue_index) const core::conformation::Residueinline
is_branch_point() const core::conformation::Residueinline
is_carbohydrate() const core::conformation::Residueinline
is_charged() const core::conformation::Residueinline
is_coarse() const core::conformation::Residueinline
is_d_rna() const core::conformation::Residueinline
is_DNA() const core::conformation::Residueinline
is_l_rna() const core::conformation::Residueinline
is_ligand() const core::conformation::Residueinline
is_lower_terminus() const core::conformation::Residueinline
is_meta_aramid() const core::conformation::Residueinline
is_metal() const core::conformation::Residueinline
is_metalbinding() const core::conformation::Residueinline
is_NA() const core::conformation::Residueinline
is_ortho_aramid() const core::conformation::Residueinline
is_para_aramid() const core::conformation::Residueinline
is_peptoid() const core::conformation::Residueinline
is_polar() const core::conformation::Residueinline
is_polymer() const core::conformation::Residueinline
is_polymer_bonded(Residue const &other) const core::conformation::Residueinline
is_polymer_bonded(Size const other_index) const core::conformation::Residueinline
is_post_methylene_meta_aramid() const core::conformation::Residueinline
is_post_methylene_ortho_aramid() const core::conformation::Residueinline
is_post_methylene_para_aramid() const core::conformation::Residueinline
is_pre_methylene_meta_aramid() const core::conformation::Residueinline
is_pre_methylene_ortho_aramid() const core::conformation::Residueinline
is_pre_methylene_para_aramid() const core::conformation::Residueinline
is_pre_methylene_post_methylene_meta_aramid() const core::conformation::Residueinline
is_pre_methylene_post_methylene_ortho_aramid() const core::conformation::Residueinline
is_pre_methylene_post_methylene_para_aramid() const core::conformation::Residueinline
is_protein() const core::conformation::Residueinline
is_pseudo_bonded(Residue const &other) const core::conformation::Residueinline
is_pseudo_bonded(Size const other_index) const core::conformation::Residueinline
is_purine() const core::conformation::Residueinline
is_pyrimidine() const core::conformation::Residueinline
is_repulsive(Size const atomno) const core::conformation::Residueinline
is_RNA() const core::conformation::Residueinline
is_similar_aa(Residue const &other) const core::conformation::Residueinline
is_similar_rotamer(Residue const &other) const core::conformation::Residue
is_sri() const core::conformation::Residueinline
is_surface() const core::conformation::Residueinline
is_terminus() const core::conformation::Residueinline
is_TNA() const core::conformation::Residueinline
is_triazolemer() const core::conformation::Residueinline
is_upper_terminus() const core::conformation::Residueinline
is_virtual(Size const atomno) const core::conformation::Residueinline
is_virtual_residue() const core::conformation::Residueinline
is_water() const core::conformation::Residueinline
last_backbone_atom() const core::conformation::Residueinline
lower_connect() const core::conformation::Residueinline
lower_connect_atom() const core::conformation::Residueinline
mainchain_atom(Size const i) const core::conformation::Residueinline
mainchain_atoms() const core::conformation::Residueinline
mainchain_torsion(Size const torsion) const core::conformation::Residueinline
mainchain_torsions() const core::conformation::Residueinline
mainchain_torsions()core::conformation::Residueinline
mainchain_torsions(utility::vector1< Real > const &torsions)core::conformation::Residueinline
mainchain_torsions_core::conformation::Residueprivate
mark_connect_incomplete(Size resconn_index)core::conformation::Residue
mirrored_relative_to_type() const core::conformation::Residueinline
mirrored_relative_to_type_core::conformation::Residueprivate
misplaced() const core::conformation::Residueinline
misplaced_core::conformation::Residueprivate
mm_atom_name(Size const atom) const core::conformation::Residueinline
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::Residueinline
n_hbond_donors() const core::conformation::Residueinline
n_mainchain_atoms() const core::conformation::Residueinline
n_non_polymeric_residue_connections() const core::conformation::Residueinline
n_nus() const core::conformation::Residueinline
n_orbitals() const core::conformation::Residueinline
n_polymeric_residue_connections() const core::conformation::Residueinline
n_possible_residue_connections() const core::conformation::Residueinline
n_virtual_atoms() const core::conformation::Residueinline
na_analogue() const core::conformation::Residueinline
name() const core::conformation::Residueinline
name1() const core::conformation::Residueinline
name3() const core::conformation::Residueinline
natoms() const core::conformation::Residueinline
nbr_atom() const core::conformation::Residueinline
nbr_atom_xyz() const core::conformation::Residueinline
nbr_radius() const core::conformation::Residueinline
nbrs(Size const atm) const core::conformation::Residueinline
nchi() const core::conformation::Residueinline
nheavyatoms() const core::conformation::Residueinline
nonconst_data()core::conformation::Residueinline
nonconst_data_ptr()core::conformation::Residueinline
nonstandard_polymer_core::conformation::Residueprivate
nu(core::uint const index) const core::conformation::Residueinline
nu_atoms() const core::conformation::Residueinline
nu_atoms(core::uint const index) const core::conformation::Residueinline
nus() const core::conformation::Residueinline
nus()core::conformation::Residueinline
nus_core::conformation::Residueprivate
operator=(Residue const &rhs)core::conformation::Residueprivate
orbital_name(Size const orbital_index) const core::conformation::Residueinline
orbital_type(Size const orbital_index) const core::conformation::Residueinline
orbital_type_index(Size const orbital_index) const core::conformation::Residueinline
orbital_xyz(Size const orbital_index) const core::conformation::Residueinline
orbitals_core::conformation::Residueprivate
orient_onto_location(Size center, Size nbr1, Size nbr2, Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton)core::conformation::Residue
orient_onto_location(Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton)core::conformation::Residue
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::Residueprivate
orient_onto_residue_peptoid(Residue const &src, Conformation const &conformation)core::conformation::Residue
path_distance(Size atom) const core::conformation::Residueinline
path_distance(Size at1, Size at2) const core::conformation::Residueinline
path_distances() const core::conformation::Residueinline
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::Residueinline
polymeric_sequence_distance(Residue const &other) const core::conformation::Residueinline
pseudobonds() const core::conformation::Residueinline
pseudobonds_core::conformation::Residueprivate
requires_actcoord() const core::conformation::Residueinline
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 &current_rsd, Conformation const &conformation, bool preserve_c_beta=false, bool allow_alternate_backbone_matching=false)core::conformation::Residue
Residue(Residue const &src)core::conformation::Residue
Residue(Residue const &src, core::chemical::ResidueTypeCOP new_restype, bool flip_chirality)core::conformation::Residueprivate
residue_connect_atom_index(Size const resconn_id) const core::conformation::Residueinline
residue_connection(Size const resconn_index) const core::conformation::Residueinline
residue_connection_conn_id(Size const resconn_index) const core::conformation::Residueinline
residue_connection_partner(Size const resconn_index) const core::conformation::Residueinline
residue_connection_partner(Size const resconn_index, Size const otherres, Size const other_connid)core::conformation::Residue
ResidueType typedefcore::conformation::Residue
ResidueTypeCOP typedefcore::conformation::Residue
ring_conformer(core::uint const ring_num, core::Real limit=90.0) const core::conformation::Residue
RNA_info() const core::conformation::Residueinline
rsd_type_core::conformation::Residueprivate
rsd_type_ptr_core::conformation::Residueprivate
select_orient_atoms(Size &center, Size &nbr1, Size &nbr2) const core::conformation::Residue
seqpos() const core::conformation::Residueinline
seqpos(Size const setting)core::conformation::Residueinline
seqpos_core::conformation::Residueprivate
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_mirrored_relative_to_type(bool const setting)core::conformation::Residueinline
set_orbital_xyz(core::Size const orbital_index, Vector const &xyz_in)core::conformation::Residueinline
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::Residueinline
type() const core::conformation::Residueinline
type_ptr() const core::conformation::Residueinline
update_actcoord()core::conformation::Residue
update_connections_to_other_residue(Residue const &other_rsd)core::conformation::Residue
update_connections_to_residues()core::conformation::Residueprivate
update_nus()core::conformation::Residue
update_orbital_coords()core::conformation::Residueinline
update_sequence_numbering(utility::vector1< Size > const &old2new)core::conformation::Residue
upper_connect() const core::conformation::Residueinline
upper_connect_atom() const core::conformation::Residueinline
xyz(Size const atm_index) const core::conformation::Residueinline
xyz(std::string const &atm_name) const core::conformation::Residueinline
~Residue() overridecore::conformation::Residue