Rosetta Core  2014.35
Public Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
core::chemical::ResidueProperties Class Reference

#include <ResidueProperties.hh>

Public Member Functions

 ResidueProperties ()
 Default constructor. More...
 
 ResidueProperties (ResidueProperties const &object_to_copy)
 Copy constructor. More...
 
ResidueProperties & operator= (ResidueProperties const &object_to_copy)
 
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...
 
utility::vector1< VariantType >
const & 		variant_types () const
 get all the variant types for this ResidueType More...
 
bool has_variant_type (VariantType const &variant_type) const
 Get whether or not this ResidueType has the requested VariantType. More...
 
void add_variant_type (VariantType const &variant_type)
 Add a variant type to this ResidueType. 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...
 

Private Member Functions

void init ()
 
void copy_data (ResidueProperties &to, ResidueProperties const &from)
 

Static Private Member Functions

static ResidueProperty const & get_property_from_string (std::string const &property)
 
static std::string const & get_string_from_property (ResidueProperty const property)
 

Private Attributes

utility::vector1< bool > general_property_status_
 
utility::vector1< VariantType > 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 ( )

Default constructor.

References init().

core::chemical::ResidueProperties::ResidueProperties ( ResidueProperties const &  object_to_copy)

Copy constructor.

References copy_data().

core::chemical::ResidueProperties::~ResidueProperties ( )
virtual

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::add_variant_type ( VariantType const &  variant_type)

Add a variant type to this ResidueType.

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

References has_variant_type(), and variant_types_.

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

References general_property_status_, numeric_properties_, string_properties_, and variant_types_.

Referenced by operator=(), and ResidueProperties().

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(), list, and core::chemical::N_RESIDUE_PROPERTIES.

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

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

References core::chemical::_1_ACETYLAMINO_SUGAR, core::chemical::_1_AMINO_SUGAR, core::chemical::_1_DEOXY_SUGAR, core::chemical::_1_PHOSPHATE, core::chemical::_2_ACETYLAMINO_SUGAR, core::chemical::_2_AMINO_SUGAR, core::chemical::_2_DEOXY_SUGAR, core::chemical::_2_KETOALDONIC_ACID, core::chemical::_2_PHOSPHATE, core::chemical::_3_ACETYLAMINO_SUGAR, core::chemical::_3_AMINO_SUGAR, core::chemical::_3_DEOXY_SUGAR, core::chemical::_3_KETOALDONIC_ACID, core::chemical::_3_PHOSPHATE, core::chemical::_4_ACETYLAMINO_SUGAR, core::chemical::_4_AMINO_SUGAR, core::chemical::_4_DEOXY_SUGAR, core::chemical::_4_KETOALDONIC_ACID, core::chemical::_4_PHOSPHATE, core::chemical::_5_ACETYLAMINO_SUGAR, core::chemical::_5_AMINO_SUGAR, core::chemical::_5_DEOXY_SUGAR, core::chemical::_5_KETOALDONIC_ACID, core::chemical::_5_PHOSPHATE, core::chemical::_6_ACETYLAMINO_SUGAR, core::chemical::_6_AMINO_SUGAR, core::chemical::_6_DEOXY_SUGAR, core::chemical::_6_KETOALDONIC_ACID, core::chemical::_6_PHOSPHATE, core::chemical::_7_ACETYLAMINO_SUGAR, core::chemical::_7_AMINO_SUGAR, core::chemical::_7_DEOXY_SUGAR, core::chemical::_7_KETOALDONIC_ACID, core::chemical::_7_PHOSPHATE, core::chemical::_8_ACETYLAMINO_SUGAR, core::chemical::_8_AMINO_SUGAR, core::chemical::_8_DEOXY_SUGAR, core::chemical::_8_KETOALDONIC_ACID, core::chemical::_8_PHOSPHATE, core::chemical::_9_ACETYLAMINO_SUGAR, core::chemical::_9_AMINO_SUGAR, core::chemical::_9_DEOXY_SUGAR, core::chemical::_9_PHOSPHATE, core::chemical::ACETYLATED_NTERMINUS, core::chemical::ADDUCT, core::chemical::ALDONIC_ACID, core::chemical::ALDOSE, core::chemical::ALPHA_AA, core::chemical::ALPHA_SUGAR, core::chemical::AROMATIC, core::chemical::BETA_AA, core::chemical::BETA_SUGAR, core::chemical::BRANCH_LOWER_TERMINUS, core::chemical::BRANCH_POINT, core::chemical::CARBOHYDRATE, core::chemical::CHARGED, core::chemical::COARSE, core::chemical::CYCLIC, core::chemical::D_AA, core::chemical::D_SUGAR, core::chemical::DNA, core::chemical::FURANOSE, core::chemical::KETOSE, core::chemical::L_AA, core::chemical::L_SUGAR, core::chemical::LIGAND, core::chemical::LIPID, core::chemical::LOWER_TERMINUS, core::chemical::LOWERTERM_TRUNC, core::chemical::MEMBRANE, core::chemical::METAL, core::chemical::METALBINDING, core::chemical::METHYLATED_CTERMINUS, core::chemical::NA, core::chemical::OXETOSE, core::chemical::OXIROSE, core::chemical::PEPTOID, core::chemical::PHOSPHONATE, core::chemical::PHOSPHONATE_UPPER, core::chemical::POLAR, core::chemical::POLYMER, core::chemical::PROTEIN, core::chemical::PYRANOSE, core::chemical::RNA, core::chemical::SC_ORBITALS, core::chemical::SEPTANOSE, core::chemical::SIALIC_ACID, core::chemical::SURFACE, core::chemical::TAUTOMER, core::chemical::TERMINUS, core::chemical::UPPER_TERMINUS, core::chemical::UPPERTERM_TRUNC, core::chemical::URONIC_ACID, core::chemical::VIRTUAL_RESIDUE, and core::chemical::WATER.

Referenced by has_property(), and set_property().

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

References core::chemical::_1_ACETYLAMINO_SUGAR, core::chemical::_1_AMINO_SUGAR, core::chemical::_1_DEOXY_SUGAR, core::chemical::_1_PHOSPHATE, core::chemical::_2_ACETYLAMINO_SUGAR, core::chemical::_2_AMINO_SUGAR, core::chemical::_2_DEOXY_SUGAR, core::chemical::_2_KETOALDONIC_ACID, core::chemical::_2_PHOSPHATE, core::chemical::_3_ACETYLAMINO_SUGAR, core::chemical::_3_AMINO_SUGAR, core::chemical::_3_DEOXY_SUGAR, core::chemical::_3_KETOALDONIC_ACID, core::chemical::_3_PHOSPHATE, core::chemical::_4_ACETYLAMINO_SUGAR, core::chemical::_4_AMINO_SUGAR, core::chemical::_4_DEOXY_SUGAR, core::chemical::_4_KETOALDONIC_ACID, core::chemical::_4_PHOSPHATE, core::chemical::_5_ACETYLAMINO_SUGAR, core::chemical::_5_AMINO_SUGAR, core::chemical::_5_DEOXY_SUGAR, core::chemical::_5_KETOALDONIC_ACID, core::chemical::_5_PHOSPHATE, core::chemical::_6_ACETYLAMINO_SUGAR, core::chemical::_6_AMINO_SUGAR, core::chemical::_6_DEOXY_SUGAR, core::chemical::_6_KETOALDONIC_ACID, core::chemical::_6_PHOSPHATE, core::chemical::_7_ACETYLAMINO_SUGAR, core::chemical::_7_AMINO_SUGAR, core::chemical::_7_DEOXY_SUGAR, core::chemical::_7_KETOALDONIC_ACID, core::chemical::_7_PHOSPHATE, core::chemical::_8_ACETYLAMINO_SUGAR, core::chemical::_8_AMINO_SUGAR, core::chemical::_8_DEOXY_SUGAR, core::chemical::_8_KETOALDONIC_ACID, core::chemical::_8_PHOSPHATE, core::chemical::_9_ACETYLAMINO_SUGAR, core::chemical::_9_AMINO_SUGAR, core::chemical::_9_DEOXY_SUGAR, core::chemical::_9_PHOSPHATE, core::chemical::ACETYLATED_NTERMINUS, core::chemical::ADDUCT, core::chemical::ALDONIC_ACID, core::chemical::ALDOSE, core::chemical::ALPHA_AA, core::chemical::ALPHA_SUGAR, core::chemical::AROMATIC, core::chemical::BETA_AA, core::chemical::BETA_SUGAR, core::chemical::BRANCH_LOWER_TERMINUS, core::chemical::BRANCH_POINT, core::chemical::CARBOHYDRATE, core::chemical::CHARGED, core::chemical::COARSE, core::chemical::CYCLIC, core::chemical::D_AA, core::chemical::D_SUGAR, core::chemical::DNA, core::chemical::FURANOSE, core::chemical::KETOSE, core::chemical::L_AA, core::chemical::L_SUGAR, core::chemical::LIGAND, core::chemical::LIPID, core::chemical::LOWER_TERMINUS, core::chemical::LOWERTERM_TRUNC, core::chemical::MEMBRANE, core::chemical::METAL, core::chemical::METALBINDING, core::chemical::METHYLATED_CTERMINUS, core::chemical::N_RESIDUE_PROPERTIES, core::chemical::NA, core::chemical::OXETOSE, core::chemical::OXIROSE, core::chemical::PEPTOID, core::chemical::PHOSPHONATE, core::chemical::PHOSPHONATE_UPPER, core::chemical::POLAR, core::chemical::POLYMER, core::chemical::PROTEIN, core::chemical::PYRANOSE, core::chemical::RNA, core::chemical::SC_ORBITALS, core::chemical::SEPTANOSE, core::chemical::SIALIC_ACID, core::chemical::SURFACE, core::chemical::TAUTOMER, core::chemical::TERMINUS, core::chemical::UPPER_TERMINUS, core::chemical::UPPERTERM_TRUNC, core::chemical::URONIC_ACID, core::chemical::VIRTUAL_RESIDUE, and core::chemical::WATER.

Referenced by get_list_of_properties().

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_, and get_property_from_string().

bool core::chemical::ResidueProperties::has_variant_type ( VariantType const &  variant_type) const

Get whether or not this ResidueType has the requested VariantType.

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

References variant_types_.

Referenced by add_variant_type().

void core::chemical::ResidueProperties::init ( )
private

References general_property_status_, and core::chemical::N_RESIDUE_PROPERTIES.

Referenced by ResidueProperties().

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)

References copy_data().

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::show ( std::ostream &  output = std::cout) const
virtual

Generate string representation of ResidueProperties for debugging purposes.

References get_list_of_properties().

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

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

References string_properties_.

utility::vector1< VariantType > const& core::chemical::ResidueProperties::variant_types ( ) const
inline

get all the variant types for this ResidueType

References variant_types_.

Member Data Documentation

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

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

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

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

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

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

utility::vector1< VariantType > core::chemical::ResidueProperties::variant_types_
private

Referenced by add_variant_type(), copy_data(), has_variant_type(), and variant_types().

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