Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
core::chemical::ResidueType Member List

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

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
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
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_bond(std::string const &atom_name1, std::string const &atom_name2)core::chemical::ResidueType
add_bond(std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel)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_rotamer(Size const chino, Real const mean, Real const sdev)core::chemical::ResidueType
add_cut_bond(std::string const &atom_name1, std::string const &atom_name2)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_variant_type(VariantType const &variant_type)core::chemical::ResidueTypeinline
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
assign_internal_coordinates()core::chemical::ResidueType
assign_internal_coordinates(std::string const &current_atom)core::chemical::ResidueTypeprivate
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_2_residue_connection_map_core::chemical::ResidueTypeprivate
atom_base(Size const atomno) const core::chemical::ResidueType
atom_base_core::chemical::ResidueTypeprivate
atom_forms_residue_connection(Size const atomid)core::chemical::ResidueTypeinline
atom_index(std::string const &name) const core::chemical::ResidueType
atom_index_core::chemical::ResidueTypeprivate
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 ind) const core::chemical::ResidueTypeinline
atom_is_polar_hydrogen_core::chemical::ResidueTypeprivate
atom_name(Size const index) const core::chemical::ResidueType
atom_type(Size const atomno) const core::chemical::ResidueType
atom_type_set() const core::chemical::ResidueTypeinline
atom_type_set_ptr() const core::chemical::ResidueTypeinline
atom_types_core::chemical::ResidueTypeprivate
atoms_core::chemical::ResidueTypeprivate
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
base_restype_name(std::string const &in)core::chemical::ResidueTypeinline
base_restype_name() const core::chemical::ResidueTypeinline
base_restype_name_core::chemical::ResidueTypeprivate
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::ResidueTypeinline
bonded_neighbor_core::chemical::ResidueTypeprivate
bonded_neighbor_type_core::chemical::ResidueTypeprivate
bonded_neighbor_types(Size const atomno) const core::chemical::ResidueTypeinline
bonded_orbitals(Size const atomno) const core::chemical::ResidueTypeinline
branch_point_atoms_core::chemical::ResidueTypeprivate
calculate_icoor(std::string const &child, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3)core::chemical::ResidueType
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_atoms(Size const chino) const core::chemical::ResidueTypeinline
chi_atoms() const core::chemical::ResidueTypeinline
chi_atoms_core::chemical::ResidueTypeprivate
chi_rotamers(Size const chino) const core::chemical::ResidueTypeinline
chi_rotamers_core::chemical::ResidueTypeprivate
clone() const core::chemical::ResidueType
cut_bond_neighbor(Size const atomno) const core::chemical::ResidueTypeinline
cut_bond_neighbor_core::chemical::ResidueTypeprivate
debug_dump_icoor()core::chemical::ResidueType
defined_adducts() const core::chemical::ResidueTypeinline
defined_adducts_core::chemical::ResidueTypeprivate
delete_atom(std::string const &name)core::chemical::ResidueTypeinline
delete_atoms_core::chemical::ResidueTypeprivate
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
element_set() const core::chemical::ResidueTypeinline
elements_core::chemical::ResidueTypeprivate
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
get_mol_data() 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_RotamerLibraryName() const core::chemical::ResidueType
get_use_ncaa_rotlib() const core::chemical::ResidueTypeinline
Haro_index() const core::chemical::ResidueTypeinline
Haro_index_core::chemical::ResidueTypeprivate
has(std::string const &atom_name) const core::chemical::ResidueTypeinline
has_atom_name(std::string const &name) const core::chemical::ResidueType
has_orbital(std::string const &orbital_name) const core::chemical::ResidueTypeinline
has_property(std::string const &property) const core::chemical::ResidueTypeinline
has_sc_orbitals() const core::chemical::ResidueTypeinline
has_sc_orbitals_core::chemical::ResidueTypeprivate
has_variant_type(VariantType const &variant_type) const core::chemical::ResidueTypeinline
heavyatom_has_polar_hydrogens(Size ind) const core::chemical::ResidueTypeinline
heavyatom_has_polar_hydrogens_core::chemical::ResidueTypeprivate
heavyatom_is_an_acceptor(Size ind) const core::chemical::ResidueTypeinline
heavyatom_is_an_acceptor_core::chemical::ResidueTypeprivate
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
icoor(Size const atm) const core::chemical::ResidueType
is_acetylated_nterminus() const core::chemical::ResidueTypeinline
is_acetylated_nterminus_core::chemical::ResidueTypeprivate
is_adduct() const core::chemical::ResidueTypeinline
is_adduct_core::chemical::ResidueTypeprivate
is_aromatic() const core::chemical::ResidueTypeinline
is_aromatic_core::chemical::ResidueTypeprivate
is_branch_point() const core::chemical::ResidueTypeinline
is_carbohydrate() const core::chemical::ResidueTypeinline
is_carbohydrate_core::chemical::ResidueTypeprivate
is_charged() const core::chemical::ResidueTypeinline
is_charged_core::chemical::ResidueTypeprivate
is_coarse() const core::chemical::ResidueTypeinline
is_coarse_core::chemical::ResidueTypeprivate
is_DNA() const core::chemical::ResidueTypeinline
is_DNA_core::chemical::ResidueTypeprivate
is_ligand() const core::chemical::ResidueTypeinline
is_ligand_core::chemical::ResidueTypeprivate
is_lower_terminus() const core::chemical::ResidueTypeinline
is_lower_terminus_core::chemical::ResidueTypeprivate
is_methylated_cterminus() const core::chemical::ResidueTypeinline
is_methylated_cterminus_core::chemical::ResidueTypeprivate
is_NA() const core::chemical::ResidueTypeinline
is_NA_core::chemical::ResidueTypeprivate
is_phosphonate_core::chemical::ResidueTypeprivate
is_phosphonate_upper_core::chemical::ResidueTypeprivate
is_polar() const core::chemical::ResidueTypeinline
is_polar_core::chemical::ResidueTypeprivate
is_polymer() const core::chemical::ResidueTypeinline
is_polymer_core::chemical::ResidueTypeprivate
is_protein() const core::chemical::ResidueTypeinline
is_protein_core::chemical::ResidueTypeprivate
is_proton_chi(Size const chino) const core::chemical::ResidueTypeinline
is_proton_chi_core::chemical::ResidueTypeprivate
is_RNA() const core::chemical::ResidueTypeinline
is_RNA_core::chemical::ResidueTypeprivate
is_surface() const core::chemical::ResidueTypeinline
is_surface_core::chemical::ResidueTypeprivate
is_terminus() const core::chemical::ResidueTypeinline
is_terminus_core::chemical::ResidueTypeprivate
is_upper_terminus() const core::chemical::ResidueTypeinline
is_upper_terminus_core::chemical::ResidueTypeprivate
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
mm_atom_type(Size const atomno) const core::chemical::ResidueType
mm_atom_types_core::chemical::ResidueTypeprivate
mol_data_core::chemical::ResidueTypeprivate
molar_mass() const core::chemical::ResidueTypeinline
molar_mass_core::chemical::ResidueTypeprivate
molecular_mass() const core::chemical::ResidueTypeinline
molecular_mass_core::chemical::ResidueTypeprivate
n_actcoord_atoms_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_orbitals() const core::chemical::ResidueTypeinline
n_orbitals_core::chemical::ResidueTypeprivate
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
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
natoms_core::chemical::ResidueTypeprivate
nbr_atom(std::string const &atom_name)core::chemical::ResidueTypeinline
nbr_atom() const core::chemical::ResidueTypeinline
nbr_atom_core::chemical::ResidueTypeprivate
nbr_radius(Real const radius)core::chemical::ResidueTypeinline
nbr_radius() const core::chemical::ResidueTypeinline
nbr_radius_core::chemical::ResidueTypeprivate
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
ndihe_core::chemical::ResidueTypeprivate
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
num_bondangles() const core::chemical::ResidueTypeinline
number_bonded_heavyatoms(Size const atomno) const core::chemical::ResidueTypeinline
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_bonded_neighbor_core::chemical::ResidueTypeprivate
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
parents_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
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
reorder_primary_data(AtomIndices const &old2new)core::chemical::ResidueTypeprivate
report_adducts()core::chemical::ResidueType
require_final() const core::chemical::ResidueTypeinline
requires_actcoord() const core::chemical::ResidueTypeinline
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
rna_residuetype_core::chemical::ResidueTypeprivate
RNA_type() const 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::ResidueTypeinline
set_atom_base(std::string const &atom_name1, std::string const &atom_name2)core::chemical::ResidueType
set_atom_type(std::string const &atom_name, std::string const &atom_type_name)core::chemical::ResidueType
set_backbone_heavyatom(std::string const &name)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(Size const &index, 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_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_lower_connect_atom(std::string const &atm_name)core::chemical::ResidueType
set_mainchain_atoms(AtomIndices const &mainchain)core::chemical::ResidueTypeinline
set_mm_atom_type(std::string const &atom_name, std::string const &mm_atom_type_name)core::chemical::ResidueType
set_mol_data(sdf::MolData const &mol_data)core::chemical::ResidueTypeinline
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_proton_chi(Size chino, utility::vector1< Real > dihedral_samples, utility::vector1< Real > extra_samples)core::chemical::ResidueType
set_RotamerLibraryName(std::string const &filename)core::chemical::ResidueType
set_upper_connect_atom(std::string const &atm_name)core::chemical::ResidueType
set_use_ncaa_rotlib(bool flag)core::chemical::ResidueTypeinline
setup_atom_ordering(AtomIndices &old2new)core::chemical::ResidueTypeprivate
show_all_atom_names(std::ostream &out) 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
variant_types() const core::chemical::ResidueTypeinline
variant_types_core::chemical::ResidueTypeprivate
variants_match(ResidueType const &other) const core::chemical::ResidueType
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
Generated on Sat Jun 1 2013 12:26:00 for Rosetta 3.5 by   doxygen 1.8.4