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core::chemical::ResidueTypeBase Member List

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

aa(AA const &type)core::chemical::ResidueTypeBaseinline
aa(std::string const &type)core::chemical::ResidueTypeBaseinline
aa() const core::chemical::ResidueTypeBaseinline
aa_core::chemical::ResidueTypeBaseprivate
add_adduct(Adduct &adduct_in)core::chemical::ResidueTypeBaseinline
add_numeric_property(std::string const &tag, core::Real value)core::chemical::ResidueTypeBase
add_property(std::string const &property)core::chemical::ResidueTypeBase
add_property(core::chemical::ResidueProperty const property)core::chemical::ResidueTypeBase
add_string_property(std::string const &tag, std::string value)core::chemical::ResidueTypeBase
add_variant_type(VariantType const variant_type)core::chemical::ResidueTypeBase
add_variant_type(std::string const &variant_type)core::chemical::ResidueTypeBase
atom_alias(std::string const &name) const core::chemical::ResidueTypeBaseinline
atom_aliases() const core::chemical::ResidueTypeBaseinline
atom_aliases()core::chemical::ResidueTypeBaseinlineprotected
atom_aliases_core::chemical::ResidueTypeBaseprivate
atom_type_set() const core::chemical::ResidueTypeBaseinline
atom_type_set(AtomTypeSetCOP setting)core::chemical::ResidueTypeBaseprotected
atom_type_set_ptr() const core::chemical::ResidueTypeBaseinline
atom_types_core::chemical::ResidueTypeBaseprivate
backbone_aa(std::string const &type)core::chemical::ResidueTypeBaseinline
backbone_aa(core::chemical::AA const type)core::chemical::ResidueTypeBaseinline
backbone_aa() const core::chemical::ResidueTypeBaseinline
backbone_aa_core::chemical::ResidueTypeBaseprivate
backbone_aa_raw() const core::chemical::ResidueTypeBaseinlineprotected
base_analogue(std::string const &type)core::chemical::ResidueTypeBaseinline
base_analogue() const core::chemical::ResidueTypeBaseinline
base_analogue_core::chemical::ResidueTypeBaseprivate
base_analogue_raw() const core::chemical::ResidueTypeBaseinlineprotected
base_name() const core::chemical::ResidueTypeBaseinline
base_name(std::string const &base_name_in)core::chemical::ResidueTypeBaseinline
base_name_core::chemical::ResidueTypeBaseprivate
canonical_atom_alias(std::string const &name) const core::chemical::ResidueTypeBaseinline
canonical_atom_aliases() const core::chemical::ResidueTypeBaseinline
canonical_atom_aliases()core::chemical::ResidueTypeBaseinlineprotected
canonical_atom_aliases_core::chemical::ResidueTypeBaseprivate
custom_variant_types() const core::chemical::ResidueTypeBase
defined_adducts() const core::chemical::ResidueTypeBaseinline
defined_adducts_core::chemical::ResidueTypeBaseprivate
defines_custom_rama_prepro_map(bool const pre_proline_position) const core::chemical::ResidueTypeBase
delete_property(std::string const &property)core::chemical::ResidueTypeBase
delete_property(core::chemical::ResidueProperty const property)core::chemical::ResidueTypeBase
disulfide_atom_name_core::chemical::ResidueTypeBaseprivate
element_set() const core::chemical::ResidueTypeBaseinline
element_set_ptr() const core::chemical::ResidueTypeBaseinline
elements_core::chemical::ResidueTypeBaseprivate
enable_custom_variant_types()core::chemical::ResidueTypeBase
force_nbr_atom_orient() const core::chemical::ResidueTypeBaseinline
force_nbr_atom_orient(bool force_orient)core::chemical::ResidueTypeBaseinline
force_nbr_atom_orient_core::chemical::ResidueTypeBaseprivate
gasteiger_atom_types_core::chemical::ResidueTypeBaseprivate
gasteiger_atom_typeset() const core::chemical::ResidueTypeBase
get_base_type_cop() const =0core::chemical::ResidueTypeBasepure virtual
get_disulfide_atom_name() const core::chemical::ResidueTypeBaseinline
get_metal_binding_atoms() const core::chemical::ResidueTypeBaseinline
get_numeric_property(std::string const &tag) const core::chemical::ResidueTypeBase
get_orbitals()core::chemical::ResidueTypeBaseinlineprotected
get_orbitals_index()core::chemical::ResidueTypeBaseinlineprotected
get_rama_prepro_mainchain_torsion_potential_name(bool const pre_proline_position) const core::chemical::ResidueTypeBase
get_rama_prepro_map_file_name(bool const pre_proline_position) const core::chemical::ResidueTypeBase
get_string_property(std::string const &tag) const core::chemical::ResidueTypeBase
has(std::string const &atom_name) const =0core::chemical::ResidueTypeBasepure virtual
has_orbital(std::string const &orbital_name) const core::chemical::ResidueTypeBaseinline
has_orbital_types() const core::chemical::ResidueTypeBaseinline
has_property(std::string const &property) const core::chemical::ResidueTypeBase
has_property(ResidueProperty const property) const core::chemical::ResidueTypeBase
has_variant_type(VariantType const variant_type) const core::chemical::ResidueTypeBase
has_variant_type(std::string const &variant_type) const core::chemical::ResidueTypeBase
interchangeability_group() const core::chemical::ResidueTypeBaseinline
interchangeability_group(std::string const &setting)core::chemical::ResidueTypeBaseinline
interchangeability_group_core::chemical::ResidueTypeBaseprivate
is_achiral_backbone() const core::chemical::ResidueTypeBaseinline
is_achiral_sidechain() const core::chemical::ResidueTypeBaseinline
is_base_type() const =0core::chemical::ResidueTypeBasepure virtual
is_d_aa() const core::chemical::ResidueTypeBaseinline
is_d_rna() const core::chemical::ResidueTypeBaseinline
is_DNA() const core::chemical::ResidueTypeBaseinline
is_l_aa() const core::chemical::ResidueTypeBaseinline
is_l_rna() const core::chemical::ResidueTypeBaseinline
is_metapatched() const core::chemical::ResidueTypeBaseinline
is_metapatched_core::chemical::ResidueTypeBaseprivate
is_peptoid() const core::chemical::ResidueTypeBaseinline
is_polymer() const core::chemical::ResidueTypeBaseinline
is_protein() const core::chemical::ResidueTypeBaseinline
is_r_peptoid() const core::chemical::ResidueTypeBaseinline
is_RNA() const core::chemical::ResidueTypeBaseinline
is_s_peptoid() const core::chemical::ResidueTypeBaseinline
mainchain_potentials_match(ResidueTypeBase const &other) const core::chemical::ResidueTypeBase
metal_binding_atoms()core::chemical::ResidueTypeBaseinlineprotected
metal_binding_atoms_core::chemical::ResidueTypeBaseprivate
mm_atom_types_core::chemical::ResidueTypeBaseprivate
mm_atom_types_ptr() const core::chemical::ResidueTypeBaseinline
mode() const core::chemical::ResidueTypeBaseinline
mode_core::chemical::ResidueTypeBaseprivate
n_orbitals() const core::chemical::ResidueTypeBase
n_virtual_atoms() const =0core::chemical::ResidueTypeBasepure virtual
na_analogue(std::string const &type)core::chemical::ResidueTypeBaseinline
na_analogue() const core::chemical::ResidueTypeBaseinline
na_analogue_core::chemical::ResidueTypeBaseprivate
na_analogue_raw() const core::chemical::ResidueTypeBaseinlineprotected
name() const core::chemical::ResidueTypeBaseinline
name(std::string const &name_in)core::chemical::ResidueTypeBaseinline
name1() const core::chemical::ResidueTypeBaseinline
name1(char const code)core::chemical::ResidueTypeBaseinline
name1_core::chemical::ResidueTypeBaseprivate
name3() const core::chemical::ResidueTypeBaseinline
name3(std::string const &name_in)core::chemical::ResidueTypeBaseinline
name3_core::chemical::ResidueTypeBaseprivate
name_core::chemical::ResidueTypeBaseprivate
natoms() const =0core::chemical::ResidueTypeBasepure virtual
nbonds() const =0core::chemical::ResidueTypeBasepure virtual
net_formal_charge() const core::chemical::ResidueTypeBaseinline
net_formal_charge(signed long int charge_in)core::chemical::ResidueTypeBaseinline
net_formal_charge_core::chemical::ResidueTypeBaseprivate
nheavyatoms() const =0core::chemical::ResidueTypeBasepure virtual
operator=(ResidueTypeBase const &)=defaultcore::chemical::ResidueTypeBaseprotected
orbital(Size const orbital_index) const core::chemical::ResidueTypeBase
orbital(std::string const &orbital_name) const core::chemical::ResidueTypeBase
orbital_index(std::string const &name) const core::chemical::ResidueTypeBase
orbital_type(Size const orbital_index) const core::chemical::ResidueTypeBase
orbital_types_core::chemical::ResidueTypeBaseprivate
orbital_types_ptr() const core::chemical::ResidueTypeBaseinline
orbitals_core::chemical::ResidueTypeBaseprivate
orbitals_index_core::chemical::ResidueTypeBaseprivate
properties() const core::chemical::ResidueTypeBaseinline
properties_core::chemical::ResidueTypeBaseprivate
rama_prepro_mainchain_torsion_potential_name_core::chemical::ResidueTypeBaseprivate
rama_prepro_mainchain_torsion_potential_name_beforeproline_core::chemical::ResidueTypeBaseprivate
rama_prepro_map_file_name_core::chemical::ResidueTypeBaseprivate
rama_prepro_map_file_name_beforeproline_core::chemical::ResidueTypeBaseprivate
remap_pdb_atom_names(bool rename)core::chemical::ResidueTypeBaseinline
remap_pdb_atom_names() const core::chemical::ResidueTypeBaseinline
remap_pdb_atom_names_core::chemical::ResidueTypeBaseprivate
remove_variant_type(VariantType const variant_type)core::chemical::ResidueTypeBase
remove_variant_type(std::string const &variant_type)core::chemical::ResidueTypeBase
report_adducts() const core::chemical::ResidueTypeBase
reset_mainchain_torsion_potential_names()core::chemical::ResidueTypeBase
ResidueTypeBase()core::chemical::ResidueTypeBaseprotected
ResidueTypeBase(AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types)core::chemical::ResidueTypeBaseprotected
ResidueTypeBase(ResidueTypeBase const &)=defaultcore::chemical::ResidueTypeBaseprotected
rotamer_library_specification(rotamers::RotamerLibrarySpecificationOP)core::chemical::ResidueTypeBase
rotamer_library_specification() const core::chemical::ResidueTypeBase
rotamer_library_specification_core::chemical::ResidueTypeBaseprivate
rotamer_library_specification_nonconst()core::chemical::ResidueTypeBase
set_adduct_flag(bool adduct_in)core::chemical::ResidueTypeBase
set_disulfide_atom_name(std::string const &n)core::chemical::ResidueTypeBaseinline
set_gasteiger_atom_typeset(gasteiger::GasteigerAtomTypeSetCOP setting)core::chemical::ResidueTypeBase
set_metapatched()core::chemical::ResidueTypeBaseinline
set_orbital_typeset(orbitals::OrbitalTypeSetCOP setting)core::chemical::ResidueTypeBaseinline
set_properties(ResiduePropertiesOP properties)core::chemical::ResidueTypeBase
set_rama_prepro_mainchain_torsion_potential_name(std::string const &name_in, bool const pre_proline_position)core::chemical::ResidueTypeBase
set_rama_prepro_map_file_name(std::string const &filename_in, bool const pre_proline_position)core::chemical::ResidueTypeBase
show(std::ostream &output=std::cout, bool output_atomic_details=false) const =0core::chemical::ResidueTypeBasepure virtual
show_all_atom_names(std::ostream &out) const =0core::chemical::ResidueTypeBasepure virtual
strip_rotamer_library_specification()core::chemical::ResidueTypeBase
variant_type_enums() const core::chemical::ResidueTypeBase
variant_types() const core::chemical::ResidueTypeBase
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