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core::chemical::ResidueProperties Class Reference

#include <ResidueProperties.hh>

Inheritance diagram for core::chemical::ResidueProperties:
Inheritance graph
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Public Member Functions

 ResidueProperties (ResidueType const *residue_type)
 Constructor with owning ResidueType. More...
 
 ResidueProperties (ResidueProperties const &object_to_copy, ResidueType const *new_owner)
 Copy constructor. More...
 
virtual ~ResidueProperties ()
 
virtual void show (std::ostream &output=std::cout) const
 Generate string representation of ResidueProperties for debugging purposes. More...
 
bool has_property (ResidueProperty const property) const
 Get whether or not this ResidueType has the requested property. More...
 
bool has_property (std::string const &property) const
 Get whether or not this ResidueType has the requested property by string. More...
 
void set_property (ResidueProperty const property, bool const setting)
 Set the status of the given property for this ResidueType. More...
 
void set_property (std::string const &property, bool const setting)
 Set the status of the given property for this ResidueType by string. More...
 
bool is_variant_type (VariantType const variant_type) const
 Get whether or not this ResidueType is of the requested VariantType. More...
 
bool is_variant_type (std::string const &variant_type) const
 Get whether or not this ResidueType is of the requested VariantType by string. More...
 
void set_variant_type (VariantType const variant_type, bool const setting)
 Set the status of a given VariantType for this ResidueType. More...
 
void set_variant_type (std::string const &variant_type, bool const setting)
 Set the status of a given VariantType for this ResidueType by string. More...
 
bool has_custom_variant_types () const
 Does this ResidueType contain additional VariantTypes than the standard list? More...
 
void enable_custom_variant_types ()
 Turn on the ability to create VariantTypes "on-the-fly". More...
 
void add_numeric_property (std::string const &tag, core::Real const value)
 Add a numeric property. More...
 
void add_string_property (std::string const &tag, std::string const &value)
 Add a string property. More...
 
std::map< std::string,
core::Real > const & 		numeric_properties () const
 
std::map< std::string,
std::string > const & 		string_properties () const
 
utility::vector1< std::string > get_list_of_properties () const
 Generate and return a list of strings representing the properties of this ResidueType. More...
 
utility::vector1< VariantType > get_list_of_variant_enums () const
 Return a list of VariantType enums for this ResidueType. More...
 
utility::vector1< std::string >
const & 		get_list_of_custom_variants_by_reference () const
 Get a const-access reference to the list of custom VariantType strings for this ResidueType. More...
 
utility::vector1< std::string > get_list_of_variants () const
 Generate and return a list of strings representing the VariantTypes of this ResidueType. More...
 
utility::vector1< std::string > get_list_of_custom_variants () const
 Return a list of custom VariantTypes only for this ResidueType. More...
 

Static Public Member Functions

static ResidueProperty const & get_property_from_string (std::string const &property)
 Static constant data access. More...
 
static std::string const & get_string_from_property (ResidueProperty const property)
 Get a string from the corresponding ResidueProperty enum value. More...
 
static VariantType const & get_variant_from_string (std::string const &variant)
 
static std::string const & get_string_from_variant (VariantType const variant)
 

Private Member Functions

 ResidueProperties ()
 
 ResidueProperties (ResidueProperties const &object_to_copy)
 
ResidueProperties & operator= (ResidueProperties const &object_to_copy)
 
void init (ResidueType const *residue_type)
 
void copy_data (ResidueProperties &to, ResidueProperties const &from)
 

Private Attributes

ResidueType const * residue_type_
 
utility::vector1< bool > general_property_status_
 
utility::vector1< bool > variant_type_status_
 
bool has_custom_variant_types_
 
utility::vector1< std::string > custom_variant_types_
 
std::map< std::string, core::Real > numeric_properties_
 
std::map< std::string,
std::string > 		string_properties_
 

Detailed Description

This is a container class for the large assortment of properties associated with ResidueTypes. It prevents ResidueType from becoming cluttered with an over-abundance of properties and related methods.

Remarks
This is the first step in a major refactor of how properties are handled in Rosetta. For now, I have just gathered all the properties related code into one place, so that changes to the system can be more readily made. Previous behavior has been maintained. In the future, I have several ideas for further improvements. ~Labonte

Constructor & Destructor Documentation

core::chemical::ResidueProperties::ResidueProperties ( ResidueType const *  residue_type)

Constructor with owning ResidueType.

References init().

core::chemical::ResidueProperties::ResidueProperties ( ResidueProperties const &  object_to_copy,
ResidueType const *  new_owner 
)

Copy constructor.

References copy_data(), and residue_type_.

core::chemical::ResidueProperties::~ResidueProperties ( )
virtual
core::chemical::ResidueProperties::ResidueProperties ( )
private
core::chemical::ResidueProperties::ResidueProperties ( ResidueProperties const &  object_to_copy)
private

Member Function Documentation

void core::chemical::ResidueProperties::add_numeric_property ( std::string const &  tag,
core::Real const  value 
)

Add a numeric property.

Note
This function was copied from its old location in ResidueType.

References numeric_properties_.

void core::chemical::ResidueProperties::add_string_property ( std::string const &  tag,
std::string const &  value 
)

Add a string property.

Note
This function was copied from its old location in ResidueType.

References string_properties_.

void core::chemical::ResidueProperties::copy_data ( ResidueProperties &  to,
ResidueProperties const &  from 
)
private

References custom_variant_types_, general_property_status_, has_custom_variant_types_, numeric_properties_, string_properties_, and variant_type_status_.

Referenced by ResidueProperties().

void core::chemical::ResidueProperties::enable_custom_variant_types ( )
inline

Turn on the ability to create VariantTypes "on-the-fly".

Custom" VariantTypes as strings are permitted for the enzdes and metalloproteins cases. Do not enable unless you have a good reason to, as string look-ups are less efficient and more error-prone.

References has_custom_variant_types_.

utility::vector1< std::string > core::chemical::ResidueProperties::get_list_of_custom_variants ( ) const
inline

Return a list of custom VariantTypes only for this ResidueType.

References custom_variant_types_.

Referenced by core::chemical::variants_match_with_exceptions().

utility::vector1< std::string > const & core::chemical::ResidueProperties::get_list_of_custom_variants_by_reference ( ) const

Get a const-access reference to the list of custom VariantType strings for this ResidueType.

This will not include enum-based standard variants.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References custom_variant_types_.

utility::vector1< std::string > core::chemical::ResidueProperties::get_list_of_properties ( ) const

Generate and return a list of strings representing the properties of this ResidueType.

References core::chemical::FIRST_PROPERTY, general_property_status_, get_string_from_property(), and core::chemical::N_PROPERTIES.

Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_properties(), show(), and core::chemical::write_topology_file().

utility::vector1< VariantType > core::chemical::ResidueProperties::get_list_of_variant_enums ( ) const

Return a list of VariantType enums for this ResidueType.

This will not include custom, string-based variant types generated on the fly.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::FIRST_VARIANT, core::chemical::N_VARIANTS, and variant_type_status_.

utility::vector1< std::string > core::chemical::ResidueProperties::get_list_of_variants ( ) const

Generate and return a list of strings representing the VariantTypes of this ResidueType.

This will include both custom, string-based variants made on-the-fly AND the standard variants that are enumerated.

References custom_variant_types_, core::chemical::FIRST_VARIANT, get_string_from_variant(), has_custom_variant_types_, core::chemical::N_VARIANTS, and variant_type_status_.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::conformation::form_disulfide_helper(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::environment::ProtectedConformation::match_variants(), core::chemical::ResidueTypeSelector::match_variants(), core::pose::MiniPose::MiniPose(), core::chemical::Selector_MATCH_VARIANTS::operator[](), core::chemical::Selector_NO_VARIANTS::operator[](), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose(), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), and show().

ResidueProperty const & core::chemical::ResidueProperties::get_property_from_string ( std::string const &  property)
static

Static constant data access.

Get the ResidueProperty enum value from the corresponding string. This private static class method is defined in ResidueProperty_mappings.cc, which is auto-generated by the add_ResidueType_enum_files.py script. Note – made public because it's a handy function for other code to use (VKM, 22 July 2015).

References core::chemical::ACETYL_SUGAR, core::chemical::ACETYLAMINO_SUGAR, core::chemical::ACETYLATED_NTERMINUS, core::chemical::ACHIRAL_BACKBONE, core::chemical::ADDUCT, core::chemical::ALDONIC_ACID, core::chemical::ALDOSE, core::chemical::ALIPHATIC, core::chemical::ALPHA_AA, core::chemical::ALPHA_SUGAR, core::chemical::AMINO_SUGAR, core::chemical::AROMATIC, core::chemical::BETA_AA, core::chemical::BETA_SUGAR, core::chemical::BRANCH_LOWER_TERMINUS, core::chemical::BRANCH_POINT, core::chemical::C1_MODIFIED, core::chemical::C2_MODIFIED, core::chemical::C3_MODIFIED, core::chemical::C4_MODIFIED, core::chemical::C5_MODIFIED, core::chemical::C6_MODIFIED, core::chemical::C7_MODIFIED, core::chemical::C8_MODIFIED, core::chemical::C9_MODIFIED, core::chemical::C_METHYLATED_SUGAR, core::chemical::CANONICAL_AA, core::chemical::CANONICAL_NUCLEIC, core::chemical::CARBOHYDRATE, core::chemical::CHARGED, core::chemical::COARSE, core::chemical::CYCLIC, core::chemical::D_AA, core::chemical::D_SUGAR, core::chemical::DEOXY_SUGAR, core::chemical::DISULFIDE_BONDED, core::chemical::DNA, core::chemical::ELECTROPHILE, core::chemical::FRAGMENT, core::chemical::FURANOSE, core::chemical::GAMMA_AA, core::chemical::GLYCOSIDE, core::chemical::HEPTOSE, core::chemical::HEXOSE, core::chemical::HYDROPHOBIC, core::chemical::INVERTED_VIRTUAL_RESIDUE, core::chemical::KETOSE, core::chemical::L_AA, core::chemical::L_SUGAR, core::chemical::LIGAND, core::chemical::LIPID, core::chemical::LOWER_TERMINUS, core::chemical::LOWERTERM_CAP, core::chemical::LOWERTERM_TRUNC, core::chemical::MEMBRANE, core::chemical::METAL, core::chemical::METALBINDING, core::chemical::METHYLATED_CTERMINUS, core::chemical::NEGATIVE_CHARGE, core::chemical::NONOSE, core::chemical::OCTOSE, core::chemical::OXETOSE, core::chemical::OXIROSE, core::chemical::PENTOSE, core::chemical::PEPTOID, core::chemical::PHOSPHATE, core::chemical::PHOSPHONATE, core::chemical::PHOSPHONATE_UPPER, core::chemical::PNA, core::chemical::POLAR, core::chemical::POLYMER, core::chemical::POSITIVE_CHARGE, core::chemical::PROTEIN, core::chemical::PYRANOSE, core::chemical::R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::RNA, core::chemical::SC_ORBITALS, core::chemical::SEPTANOSE, core::chemical::SIALIC_ACID, core::chemical::SIDECHAIN_AMINE, core::chemical::SIDECHAIN_THIOL, core::chemical::SOLVENT, core::chemical::SRI, core::chemical::SULFATED_SUGAR, core::chemical::SULFOAMINO_SUGAR, core::chemical::SURFACE, core::chemical::TAUTOMER, core::chemical::TERMINUS, core::chemical::TETROSE, core::chemical::TRIAZOLE_LINKER, core::chemical::TRIOSE, core::chemical::UPPER_TERMINUS, core::chemical::UPPERTERM_CAP, core::chemical::UPPERTERM_TRUNC, core::chemical::URONIC_ACID, core::chemical::VIRTUAL_RESIDUE, and core::chemical::WATER.

Referenced by has_property(), core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_property(), and set_property().

std::string const & core::chemical::ResidueProperties::get_string_from_property ( ResidueProperty const  property)
static

Get a string from the corresponding ResidueProperty enum value.

This private static class method is defined in ResidueProperty_mappings.cc, which is auto-generated by the add_ResidueType_enum_files.py script. Note – made public because it's a handy function for other code to use (VKM, 22 July 2015).

References core::chemical::ACETYL_SUGAR, core::chemical::ACETYLAMINO_SUGAR, core::chemical::ACETYLATED_NTERMINUS, core::chemical::ACHIRAL_BACKBONE, core::chemical::ADDUCT, core::chemical::ALDONIC_ACID, core::chemical::ALDOSE, core::chemical::ALIPHATIC, core::chemical::ALPHA_AA, core::chemical::ALPHA_SUGAR, core::chemical::AMINO_SUGAR, core::chemical::AROMATIC, core::chemical::BETA_AA, core::chemical::BETA_SUGAR, core::chemical::BRANCH_LOWER_TERMINUS, core::chemical::BRANCH_POINT, core::chemical::C1_MODIFIED, core::chemical::C2_MODIFIED, core::chemical::C3_MODIFIED, core::chemical::C4_MODIFIED, core::chemical::C5_MODIFIED, core::chemical::C6_MODIFIED, core::chemical::C7_MODIFIED, core::chemical::C8_MODIFIED, core::chemical::C9_MODIFIED, core::chemical::C_METHYLATED_SUGAR, core::chemical::CANONICAL_AA, core::chemical::CANONICAL_NUCLEIC, core::chemical::CARBOHYDRATE, core::chemical::CHARGED, core::chemical::COARSE, core::chemical::CYCLIC, core::chemical::D_AA, core::chemical::D_SUGAR, core::chemical::DEOXY_SUGAR, core::chemical::DISULFIDE_BONDED, core::chemical::DNA, core::chemical::ELECTROPHILE, core::chemical::FRAGMENT, core::chemical::FURANOSE, core::chemical::GAMMA_AA, core::chemical::GLYCOSIDE, core::chemical::HEPTOSE, core::chemical::HEXOSE, core::chemical::HYDROPHOBIC, core::chemical::INVERTED_VIRTUAL_RESIDUE, core::chemical::KETOSE, core::chemical::L_AA, core::chemical::L_SUGAR, core::chemical::LIGAND, core::chemical::LIPID, core::chemical::LOWER_TERMINUS, core::chemical::LOWERTERM_CAP, core::chemical::LOWERTERM_TRUNC, core::chemical::MEMBRANE, core::chemical::METAL, core::chemical::METALBINDING, core::chemical::METHYLATED_CTERMINUS, core::chemical::N_PROPERTIES, core::chemical::NEGATIVE_CHARGE, core::chemical::NONOSE, core::chemical::OCTOSE, core::chemical::OXETOSE, core::chemical::OXIROSE, core::chemical::PENTOSE, core::chemical::PEPTOID, core::chemical::PHOSPHATE, core::chemical::PHOSPHONATE, core::chemical::PHOSPHONATE_UPPER, core::chemical::PNA, core::chemical::POLAR, core::chemical::POLYMER, core::chemical::POSITIVE_CHARGE, core::chemical::PROTEIN, core::chemical::PYRANOSE, core::chemical::R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::RNA, core::chemical::SC_ORBITALS, core::chemical::SEPTANOSE, core::chemical::SIALIC_ACID, core::chemical::SIDECHAIN_AMINE, core::chemical::SIDECHAIN_THIOL, core::chemical::SOLVENT, core::chemical::SRI, core::chemical::SULFATED_SUGAR, core::chemical::SULFOAMINO_SUGAR, core::chemical::SURFACE, core::chemical::TAUTOMER, core::chemical::TERMINUS, core::chemical::TETROSE, core::chemical::TRIAZOLE_LINKER, core::chemical::TRIOSE, core::chemical::UPPER_TERMINUS, core::chemical::UPPERTERM_CAP, core::chemical::UPPERTERM_TRUNC, core::chemical::URONIC_ACID, core::chemical::VIRTUAL_RESIDUE, and core::chemical::WATER.

Referenced by get_list_of_properties(), and core::scoring::aa_composition_energy::AACompositionPropertiesSet::one_line_report().

std::string const & core::chemical::ResidueProperties::get_string_from_variant ( VariantType const  variant)
static

References core::chemical::A3B_HBS_POST, core::chemical::A3B_HBS_PRE, core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::chemical::ACETYLATION, core::chemical::ADDUCT_VARIANT, core::chemical::ALDONIC_ACID_VARIANT, core::chemical::ALTERNATIVE_PROTONATION, core::chemical::BLOCK_STACK_ABOVE, core::chemical::BLOCK_STACK_BELOW, core::chemical::BRANCH_LOWER_TERMINUS_VARIANT, core::chemical::BULGE, core::chemical::C1_ACETYLAMINO_SUGAR, core::chemical::C1_AMINO_SUGAR, core::chemical::C1_BRANCH_POINT, core::chemical::C1_DEOXY_SUGAR, core::chemical::C1_METHYLATED_SUGAR, core::chemical::C1_PHOSPHATE, core::chemical::C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C1_SULFATED_SUGAR, core::chemical::C1_SULFOAMINO_SUGAR, core::chemical::C2_ACETYLAMINO_SUGAR, core::chemical::C2_AMINO_SUGAR, core::chemical::C2_BRANCH_POINT, core::chemical::C2_DEOXY_SUGAR, core::chemical::C2_KETOALDONIC_ACID, core::chemical::C2_METHYLATED_SUGAR, core::chemical::C2_PHOSPHATE, core::chemical::C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C2_SULFATED_SUGAR, core::chemical::C2_SULFOAMINO_SUGAR, core::chemical::C3_ACETYLAMINO_SUGAR, core::chemical::C3_AMINO_SUGAR, core::chemical::C3_BRANCH_POINT, core::chemical::C3_DEOXY_SUGAR, core::chemical::C3_KETOALDONIC_ACID, core::chemical::C3_METHYLATED_SUGAR, core::chemical::C3_PHOSPHATE, core::chemical::C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C3_SULFATED_SUGAR, core::chemical::C3_SULFOAMINO_SUGAR, core::chemical::C4_ACETYLAMINO_SUGAR, core::chemical::C4_AMINO_SUGAR, core::chemical::C4_BRANCH_POINT, core::chemical::C4_DEOXY_SUGAR, core::chemical::C4_KETOALDONIC_ACID, core::chemical::C4_METHYLATED_SUGAR, core::chemical::C4_PHOSPHATE, core::chemical::C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C4_SULFATED_SUGAR, core::chemical::C4_SULFOAMINO_SUGAR, core::chemical::C5_ACETYLAMINO_SUGAR, core::chemical::C5_AMINO_SUGAR, core::chemical::C5_BRANCH_POINT, core::chemical::C5_DEOXY_SUGAR, core::chemical::C5_KETOALDONIC_ACID, core::chemical::C5_METHYLATED_SUGAR, core::chemical::C5_PHOSPHATE, core::chemical::C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C5_SULFATED_SUGAR, core::chemical::C5_SULFOAMINO_SUGAR, core::chemical::C6_ACETYLAMINO_SUGAR, core::chemical::C6_AMINO_SUGAR, core::chemical::C6_BRANCH_POINT, core::chemical::C6_DEOXY_SUGAR, core::chemical::C6_KETOALDONIC_ACID, core::chemical::C6_METHYLATED_SUGAR, core::chemical::C6_PHOSPHATE, core::chemical::C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C6_SULFATED_SUGAR, core::chemical::C6_SULFOAMINO_SUGAR, core::chemical::C7_ACETYLAMINO_SUGAR, core::chemical::C7_AMINO_SUGAR, core::chemical::C7_BRANCH_POINT, core::chemical::C7_DEOXY_SUGAR, core::chemical::C7_KETOALDONIC_ACID, core::chemical::C7_METHYLATED_SUGAR, core::chemical::C7_PHOSPHATE, core::chemical::C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C7_SULFATED_SUGAR, core::chemical::C7_SULFOAMINO_SUGAR, core::chemical::C8_ACETYLAMINO_SUGAR, core::chemical::C8_AMINO_SUGAR, core::chemical::C8_BRANCH_POINT, core::chemical::C8_DEOXY_SUGAR, core::chemical::C8_KETOALDONIC_ACID, core::chemical::C8_METHYLATED_SUGAR, core::chemical::C8_PHOSPHATE, core::chemical::C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C8_SULFATED_SUGAR, core::chemical::C8_SULFOAMINO_SUGAR, core::chemical::C9_ACETYLAMINO_SUGAR, core::chemical::C9_AMINO_SUGAR, core::chemical::C9_BRANCH_POINT, core::chemical::C9_DEOXY_SUGAR, core::chemical::C9_METHYLATED_SUGAR, core::chemical::C9_PHOSPHATE, core::chemical::C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C9_SULFATED_SUGAR, core::chemical::C9_SULFOAMINO_SUGAR, core::chemical::C_METHYLAMIDATION, core::chemical::CARBOXYLATION, core::chemical::CENTROID_WITH_HA, core::chemical::CTERM_CONNECT, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::DEPROTONATED, core::chemical::DIIODINATION, core::chemical::DIMETHYLATION, core::chemical::DISULFIDE, core::chemical::FIVE_PRIME_END_OH, core::chemical::FIVE_PRIME_END_PHOSPHATE, core::chemical::FIVE_PRIME_PACKABLE_PHOSPHATE, core::chemical::FIVE_PRIME_PHOSPHATE, core::chemical::HBS_POST, core::chemical::HBS_PRE, core::chemical::HYDROXYLATION, core::chemical::HYDROXYLATION1, core::chemical::HYDROXYLATION2, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::LOWERTERM_TRUNC_VARIANT, core::chemical::METHYL_GLYCOSIDE, core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::METHYLATED_NTERM_VARIANT, core::chemical::METHYLATION, core::chemical::N_ACETYLATION, core::chemical::N_VARIANTS, core::chemical::NE2_CONNECT, core::chemical::NTERM_CONNECT, core::chemical::OOP_POST, core::chemical::OOP_PRE, core::chemical::PHOSPHONATE_UPPER_VARIANT, core::chemical::PHOSPHORYLATION, core::chemical::PROTONATED, core::chemical::PROTONATED_H1_ADENOSINE, core::chemical::REPLONLY, core::chemical::REPLS_BB, core::chemical::SC_BRANCH_POINT, core::chemical::SC_FRAGMENT, core::chemical::SG_CONNECT, core::chemical::SHOVE_BB, core::chemical::SIDECHAIN_CONJUGATION, core::chemical::SPECIAL_ROT, core::chemical::SULFATION, core::chemical::THREE_PRIME_END_OH, core::chemical::THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, core::chemical::THREE_PRIME_PACKABLE_PHOSPHATE, core::chemical::THREE_PRIME_PHOSPHATE, core::chemical::TRIAZOLAMERC, core::chemical::TRIAZOLAMERN, core::chemical::TRIMETHYLATION, core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::UPPERTERM_TRUNC_VARIANT, core::chemical::URONIC_ACID_VARIANT, core::chemical::VIRTUAL_BACKBONE_EXCEPT_C1PRIME, core::chemical::VIRTUAL_BASE, core::chemical::VIRTUAL_BASE_HEAVY_ATOM, core::chemical::VIRTUAL_BB, core::chemical::VIRTUAL_DNA_PHOSPHATE, core::chemical::VIRTUAL_NTERM, core::chemical::VIRTUAL_O2PRIME_HYDROGEN, core::chemical::VIRTUAL_PHOSPHATE, core::chemical::VIRTUAL_RESIDUE_VARIANT, core::chemical::VIRTUAL_RIBOSE, core::chemical::VIRTUAL_RNA_RESIDUE, core::chemical::VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE, core::chemical::VIRTUAL_SIDE_CHAIN, and core::chemical::ZN_CONNECT.

Referenced by get_list_of_variants(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), and core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed().

VariantType const & core::chemical::ResidueProperties::get_variant_from_string ( std::string const &  variant)
static

References core::chemical::A3B_HBS_POST, core::chemical::A3B_HBS_PRE, core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::chemical::ACETYLATION, core::chemical::ADDUCT_VARIANT, core::chemical::ALDONIC_ACID_VARIANT, core::chemical::ALTERNATIVE_PROTONATION, core::chemical::BLOCK_STACK_ABOVE, core::chemical::BLOCK_STACK_BELOW, core::chemical::BRANCH_LOWER_TERMINUS_VARIANT, core::chemical::BULGE, core::chemical::C1_ACETYLAMINO_SUGAR, core::chemical::C1_AMINO_SUGAR, core::chemical::C1_BRANCH_POINT, core::chemical::C1_DEOXY_SUGAR, core::chemical::C1_METHYLATED_SUGAR, core::chemical::C1_PHOSPHATE, core::chemical::C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C1_SULFATED_SUGAR, core::chemical::C1_SULFOAMINO_SUGAR, core::chemical::C2_ACETYLAMINO_SUGAR, core::chemical::C2_AMINO_SUGAR, core::chemical::C2_BRANCH_POINT, core::chemical::C2_DEOXY_SUGAR, core::chemical::C2_KETOALDONIC_ACID, core::chemical::C2_METHYLATED_SUGAR, core::chemical::C2_PHOSPHATE, core::chemical::C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C2_SULFATED_SUGAR, core::chemical::C2_SULFOAMINO_SUGAR, core::chemical::C3_ACETYLAMINO_SUGAR, core::chemical::C3_AMINO_SUGAR, core::chemical::C3_BRANCH_POINT, core::chemical::C3_DEOXY_SUGAR, core::chemical::C3_KETOALDONIC_ACID, core::chemical::C3_METHYLATED_SUGAR, core::chemical::C3_PHOSPHATE, core::chemical::C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C3_SULFATED_SUGAR, core::chemical::C3_SULFOAMINO_SUGAR, core::chemical::C4_ACETYLAMINO_SUGAR, core::chemical::C4_AMINO_SUGAR, core::chemical::C4_BRANCH_POINT, core::chemical::C4_DEOXY_SUGAR, core::chemical::C4_KETOALDONIC_ACID, core::chemical::C4_METHYLATED_SUGAR, core::chemical::C4_PHOSPHATE, core::chemical::C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C4_SULFATED_SUGAR, core::chemical::C4_SULFOAMINO_SUGAR, core::chemical::C5_ACETYLAMINO_SUGAR, core::chemical::C5_AMINO_SUGAR, core::chemical::C5_BRANCH_POINT, core::chemical::C5_DEOXY_SUGAR, core::chemical::C5_KETOALDONIC_ACID, core::chemical::C5_METHYLATED_SUGAR, core::chemical::C5_PHOSPHATE, core::chemical::C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C5_SULFATED_SUGAR, core::chemical::C5_SULFOAMINO_SUGAR, core::chemical::C6_ACETYLAMINO_SUGAR, core::chemical::C6_AMINO_SUGAR, core::chemical::C6_BRANCH_POINT, core::chemical::C6_DEOXY_SUGAR, core::chemical::C6_KETOALDONIC_ACID, core::chemical::C6_METHYLATED_SUGAR, core::chemical::C6_PHOSPHATE, core::chemical::C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C6_SULFATED_SUGAR, core::chemical::C6_SULFOAMINO_SUGAR, core::chemical::C7_ACETYLAMINO_SUGAR, core::chemical::C7_AMINO_SUGAR, core::chemical::C7_BRANCH_POINT, core::chemical::C7_DEOXY_SUGAR, core::chemical::C7_KETOALDONIC_ACID, core::chemical::C7_METHYLATED_SUGAR, core::chemical::C7_PHOSPHATE, core::chemical::C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C7_SULFATED_SUGAR, core::chemical::C7_SULFOAMINO_SUGAR, core::chemical::C8_ACETYLAMINO_SUGAR, core::chemical::C8_AMINO_SUGAR, core::chemical::C8_BRANCH_POINT, core::chemical::C8_DEOXY_SUGAR, core::chemical::C8_KETOALDONIC_ACID, core::chemical::C8_METHYLATED_SUGAR, core::chemical::C8_PHOSPHATE, core::chemical::C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C8_SULFATED_SUGAR, core::chemical::C8_SULFOAMINO_SUGAR, core::chemical::C9_ACETYLAMINO_SUGAR, core::chemical::C9_AMINO_SUGAR, core::chemical::C9_BRANCH_POINT, core::chemical::C9_DEOXY_SUGAR, core::chemical::C9_METHYLATED_SUGAR, core::chemical::C9_PHOSPHATE, core::chemical::C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, core::chemical::C9_SULFATED_SUGAR, core::chemical::C9_SULFOAMINO_SUGAR, core::chemical::C_METHYLAMIDATION, core::chemical::CARBOXYLATION, core::chemical::CENTROID_WITH_HA, core::chemical::CTERM_CONNECT, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::DEPROTONATED, core::chemical::DIIODINATION, core::chemical::DIMETHYLATION, core::chemical::DISULFIDE, core::chemical::FIVE_PRIME_END_OH, core::chemical::FIVE_PRIME_END_PHOSPHATE, core::chemical::FIVE_PRIME_PACKABLE_PHOSPHATE, core::chemical::FIVE_PRIME_PHOSPHATE, core::chemical::HBS_POST, core::chemical::HBS_PRE, core::chemical::HYDROXYLATION, core::chemical::HYDROXYLATION1, core::chemical::HYDROXYLATION2, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::LOWERTERM_TRUNC_VARIANT, core::chemical::METHYL_GLYCOSIDE, core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::METHYLATED_NTERM_VARIANT, core::chemical::METHYLATION, core::chemical::N_ACETYLATION, core::chemical::NE2_CONNECT, core::chemical::NO_VARIANT, core::chemical::NTERM_CONNECT, core::chemical::OOP_POST, core::chemical::OOP_PRE, core::chemical::PHOSPHONATE_UPPER_VARIANT, core::chemical::PHOSPHORYLATION, core::chemical::PROTONATED, core::chemical::PROTONATED_H1_ADENOSINE, core::chemical::REPLONLY, core::chemical::REPLS_BB, core::chemical::SC_BRANCH_POINT, core::chemical::SC_FRAGMENT, core::chemical::SG_CONNECT, core::chemical::SHOVE_BB, core::chemical::SIDECHAIN_CONJUGATION, core::chemical::SPECIAL_ROT, core::chemical::SULFATION, core::chemical::THREE_PRIME_END_OH, core::chemical::THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, core::chemical::THREE_PRIME_PACKABLE_PHOSPHATE, core::chemical::THREE_PRIME_PHOSPHATE, core::chemical::TRIAZOLAMERC, core::chemical::TRIAZOLAMERN, core::chemical::TRIMETHYLATION, core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::UPPERTERM_TRUNC_VARIANT, core::chemical::URONIC_ACID_VARIANT, core::chemical::VIRTUAL_BACKBONE_EXCEPT_C1PRIME, core::chemical::VIRTUAL_BASE, core::chemical::VIRTUAL_BASE_HEAVY_ATOM, core::chemical::VIRTUAL_BB, core::chemical::VIRTUAL_DNA_PHOSPHATE, core::chemical::VIRTUAL_NTERM, core::chemical::VIRTUAL_O2PRIME_HYDROGEN, core::chemical::VIRTUAL_PHOSPHATE, core::chemical::VIRTUAL_RESIDUE_VARIANT, core::chemical::VIRTUAL_RIBOSE, core::chemical::VIRTUAL_RNA_RESIDUE, core::chemical::VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE, core::chemical::VIRTUAL_SIDE_CHAIN, and core::chemical::ZN_CONNECT.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), core::chemical::ResidueTypeFinder::adds_any_variant(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), core::chemical::ResidueTypeFinder::apply_metapatches_recursively(), core::chemical::ResidueTypeFinder::apply_patches_recursively(), core::chemical::ResidueTypeFinder::check_variant_sets_have_all_candidate_variants(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::chemical::ResidueTypeFinder::deletes_any_variant(), core::chemical::ResidueTypeFinder::has_disallowed_variant(), is_variant_type(), protocols::environment::ProtectedConformation::match_variants(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose(), set_variant_type(), core::chemical::ResidueTypeFinder::variant_exceptions(), and core::chemical::ResidueTypeFinder::variants().

bool core::chemical::ResidueProperties::has_custom_variant_types ( ) const
inline

Does this ResidueType contain additional VariantTypes than the standard list?

References has_custom_variant_types_.

Referenced by core::chemical::variants_match_with_exceptions().

bool core::chemical::ResidueProperties::has_property ( ResidueProperty const  property) const
inline

Get whether or not this ResidueType has the requested property.

References general_property_status_.

bool core::chemical::ResidueProperties::has_property ( std::string const &  property) const

Get whether or not this ResidueType has the requested property by string.

References general_property_status_, get_property_from_string(), and core::chemical::TR().

void core::chemical::ResidueProperties::init ( ResidueType const *  residue_type)
private

References general_property_status_, has_custom_variant_types_, core::chemical::N_PROPERTIES, core::chemical::N_VARIANTS, residue_type_, and variant_type_status_.

Referenced by ResidueProperties().

bool core::chemical::ResidueProperties::is_variant_type ( VariantType const  variant_type) const
inline

Get whether or not this ResidueType is of the requested VariantType.

References core::chemical::NO_VARIANT, and variant_type_status_.

Referenced by core::chemical::variants_match_with_exceptions().

bool core::chemical::ResidueProperties::is_variant_type ( std::string const &  variant_type) const

Get whether or not this ResidueType is of the requested VariantType by string.

References custom_variant_types_, get_variant_from_string(), has_custom_variant_types_, core::chemical::NO_VARIANT, core::chemical::TR(), and variant_type_status_.

std::map< std::string, core::Real > const& core::chemical::ResidueProperties::numeric_properties ( ) const
inline

References numeric_properties_.

ResidueProperties& core::chemical::ResidueProperties::operator= ( ResidueProperties const &  object_to_copy)
private
void core::chemical::ResidueProperties::set_property ( ResidueProperty const  property,
bool const  setting 
)
inline

Set the status of the given property for this ResidueType.

References general_property_status_.

void core::chemical::ResidueProperties::set_property ( std::string const &  property,
bool const  setting 
)

Set the status of the given property for this ResidueType by string.

References general_property_status_, and get_property_from_string().

void core::chemical::ResidueProperties::set_variant_type ( VariantType const  variant_type,
bool const  setting 
)
inline

Set the status of a given VariantType for this ResidueType.

References variant_type_status_.

void core::chemical::ResidueProperties::set_variant_type ( std::string const &  variant_type,
bool const  setting 
)

Set the status of a given VariantType for this ResidueType by string.

References custom_variant_types_, get_variant_from_string(), has_custom_variant_types_, core::chemical::ResidueType::name(), core::chemical::NO_VARIANT, residue_type_, core::chemical::TR(), and variant_type_status_.

void core::chemical::ResidueProperties::show ( std::ostream &  output = std::cout) const
virtual

Generate string representation of ResidueProperties for debugging purposes.

References get_list_of_properties(), get_list_of_variants(), update_ResidueType_enum_files::properties, and update_ResidueType_enum_files::variants.

Referenced by core::chemical::operator<<().

std::map< std::string, std::string > const& core::chemical::ResidueProperties::string_properties ( ) const
inline

References string_properties_.

Member Data Documentation

utility::vector1< std::string > core::chemical::ResidueProperties::custom_variant_types_
private

Referenced by copy_data(), get_list_of_custom_variants(), get_list_of_custom_variants_by_reference(), get_list_of_variants(), is_variant_type(), and set_variant_type().

utility::vector1< bool > core::chemical::ResidueProperties::general_property_status_
private

Referenced by copy_data(), get_list_of_properties(), has_property(), init(), and set_property().

bool core::chemical::ResidueProperties::has_custom_variant_types_
private

Referenced by copy_data(), enable_custom_variant_types(), get_list_of_variants(), has_custom_variant_types(), init(), is_variant_type(), and set_variant_type().

std::map<std::string,core::Real> core::chemical::ResidueProperties::numeric_properties_
private

Referenced by add_numeric_property(), copy_data(), and numeric_properties().

ResidueType const* core::chemical::ResidueProperties::residue_type_
private

Referenced by init(), ResidueProperties(), and set_variant_type().

std::map<std::string,std::string> core::chemical::ResidueProperties::string_properties_
private

Referenced by add_string_property(), copy_data(), and string_properties().

utility::vector1< bool > core::chemical::ResidueProperties::variant_type_status_
private

Referenced by copy_data(), get_list_of_variant_enums(), get_list_of_variants(), init(), is_variant_type(), and set_variant_type().

The documentation for this class was generated from the following files:
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