#include <CarbohydrateInfo.hh>

Public Member Functions
	CarbohydrateInfo (core::chemical::ResidueTypeCAP residue_type)
	Standard constructor. More...

	CarbohydrateInfo (CarbohydrateInfo const &object_to_copy)
	Copy constructor. More...

CarbohydrateInfo &	operator= (CarbohydrateInfo const &object_to_copy)

	~CarbohydrateInfo ()

virtual void	show (std::ostream &output=std::cout) const
	Generate string representation of CarbohydrateInfo for debugging purposes. More...

std::string	full_name () const
	Return the full IUPAC name of the monosaccharide. More...

std::string	short_name () const
	Return the abbreviated IUPAC name of the monosaccharide (for use in polysaccharide sequences). More...

std::string	base_name () const
	Return the standard/common, non-residue, short name of the monosaccharide. More...

bool	is_aldose () const
	Return true if the monosaccharide is an aldose. More...

bool	is_ketose () const
	Return true if the monosaccharide is a ketose. More...

bool	is_ketose (core::uint const n) const
	Return true if the monosaccharide is an n-ketose. More...

bool	is_ulose () const
	Return true if the monosaccharide is a 2-ketose. More...

core::uint	anomeric_carbon () const
	Return the anomeric carbon number. More...

std::string	anomeric_carbon_name () const
	Return the atom name of the anomeric carbon. More...

core::uint	anomeric_carbon_index () const
	Return the atom index of the anomeric carbon in this ResidueType. More...

core::uint	cyclic_oxygen () const
	Return the cyclic oxygen number or 0, if linear. More...

std::string	cyclic_oxygen_name () const
	Return the atom name of the cyclic oxygen. More...

core::uint	cyclic_oxygen_index () const
	Return the atom index of the cyclic oxygen in this ResidueType or 0, if linear. More...

core::uint	virtual_cyclic_oxygen_index () const
	Return the atom index of the virtual atom that superimposes with the cyclic oxygen in this ResidueType or 0, if linear. More...

core::Size	n_carbons () const
	Get the number of carbons in the monosaccharide. More...

bool	is_triose () const
	Return true if the monosaccharide is a triose. More...

bool	is_tetrose () const
	Return true if the monosaccharide is a tetrose. More...

bool	is_pentose () const
	Return true if the monosaccharide is a pentose. More...

bool	is_hexose () const
	Return true if the monosaccharide is a hexose. More...

bool	is_heptose () const
	Return true if the monosaccharide is a heptose. More...

bool	is_octose () const
	Return true if the monosaccharide is an octose. More...

bool	is_nonose () const
	Return true if the monosaccharide is a nonose. More...

char	stereochem () const
	Get the stereochemical designation for the monosaccharide. More...

bool	is_L_sugar () const
	Return true if the monosaccharide is an L-sugar. More...

bool	is_D_sugar () const
	Return true if the monosaccharide is a D-sugar. More...

core::Size	ring_size () const
	Get the size of the carbohydrate ring. More...

bool	is_acyclic () const
	Return true if the monosaccharide is linear. More...

bool	is_cyclic () const
	Return true if the monosaccharide is a ring. More...

bool	is_furanose () const
	Return true if the monosaccharide is a furanose. More...

bool	is_pyranose () const
	Return true if the monosaccharide is a pyranose. More...

bool	is_septanose () const
	Return true if the monosaccharide is a septanose. More...

std::string	anomer () const
	Get the anomeric form for the monosaccharide. More...

bool	is_alpha_sugar () const
	Return true if the cyclic monosaccharide is an alpha sugar. More...

bool	is_beta_sugar () const
	Return true if the cyclic monosaccharide is a beta sugar. More...

bool	is_glycoside () const
	Return true if the monosaccharide is attached to something at the anomeric carbon. More...

core::uint	mainchain_glycosidic_bond_acceptor () const
	Return the attachment point of the downstream saccharide residue of the main chain. More...

core::Size	n_branches () const
	Return the number of branches off of this residue. More...

core::uint	branch_point (core::uint i) const
	Return the attachment point of the downstream saccharide residue attached to ith branch off of this residue. More...

bool	has_exocyclic_linkage () const
	Return true if the attachment point of the downstream saccharide is on an exocyclic carbon. More...

bool	is_N_acetylated () const
	Return true if any hydroxyl group has been modified to an acetylated amino group. More...

bool	is_O_acetylated () const
	Return true if any hydroxyl group has been modified by acetylation. More...

bool	is_acetylated () const
	Return true if the sugar has been acetylated at any position. More...

bool	is_amino_sugar () const
	Return true if any hydroxyl group has been modified to an amino group or an acetylated amino group. More...

bool	is_uronic_acid () const
	Return true if the primary hydroxyl group is oxidized to the acid. More...

Static Public Member Functions
static utility::vector1 < std::string > const &	sugar_properties ()
	A list of allowed properties in carbohydrate .params and patch files. More...

static std::map< std::string, std::string > const &	code_to_root_map ()
	A list of Rosetta PDB 3-letter codes for saccharide residues mapped to the corresponding root. More...

Private Member Functions
	CarbohydrateInfo ()

void	init (core::chemical::ResidueTypeCAP residue_type)

void	copy_data (CarbohydrateInfo object_to_copy_to, CarbohydrateInfo object_to_copy_from)

core::Size	get_n_carbons () const

void	read_and_set_properties ()

void	determine_polymer_connections ()

void	determine_IUPAC_names ()

std::string	root_from_code (std::string code) const

Private Attributes
core::chemical::ResidueTypeCAP	residue_type_

std::string	full_name_

std::string	short_name_

core::uint	anomeric_carbon_

std::string	anomeric_carbon_name_

core::uint	anomeric_carbon_index_

core::uint	cyclic_oxygen_

std::string	cyclic_oxygen_name_

core::uint	cyclic_oxygen_index_

core::uint	virtual_cyclic_oxygen_index_

core::Size	n_carbons_

char	stereochem_

core::Size	ring_size_

std::string	anomer_

bool	is_glycoside_

utility::vector1< std::string >	modifications_

core::uint	mainchain_glycosidic_bond_acceptor_

utility::vector1< core::uint >	branch_points_

bool	has_exocyclic_linkage_

Static Private Attributes
static core::Size const	MAX_C_SIZE_LIMIT = 9

static core::Size const	MIN_C_SIZE_LIMIT = 3

Constructor & Destructor Documentation

core::chemical::carbohydrates::CarbohydrateInfo::CarbohydrateInfo ( core::chemical::ResidueTypeCAP residue_type )

Standard constructor.

Parameters

<residue_type> the ResidueType object containing this CarbohydrateInfo

References init().

core::chemical::carbohydrates::CarbohydrateInfo::CarbohydrateInfo ( CarbohydrateInfo const & object_to_copy )

Copy constructor.

References copy_data().

core::chemical::carbohydrates::CarbohydrateInfo::~CarbohydrateInfo ( )

core::chemical::carbohydrates::CarbohydrateInfo::CarbohydrateInfo ( )

private

References init().

Member Function Documentation

std::string core::chemical::carbohydrates::CarbohydrateInfo::anomer ( ) const

inline

Get the anomeric form for the monosaccharide.

Returns: "alpha", "beta", or ""

"alpha" and "beta" designate the stereochemistry at the anomeric carbon of a cyclic sugar.

References anomer_.

core::uint core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon ( ) const

inline

Return the anomeric carbon number.

For linear monosaccharides, this number corresponds to the carbon that is oxidized to the aldehyde or ketone.
See also:
CarbohydrateInfo.anomeric_carbon_name()
CarbohydrateInfo.anomeric_carbon_index()
CarbohydrateInfo.is_aldose()
CarbohydrateInfo.is_ketose()
CarbohydrateInfo.is_ulose()

References anomeric_carbon_.

core::uint core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon_index ( ) const

inline

Return the atom index of the anomeric carbon in this ResidueType.

References anomeric_carbon_index_.

std::string core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon_name ( ) const

inline

Return the atom name of the anomeric carbon.

References anomeric_carbon_name_.

std::string core::chemical::carbohydrates::CarbohydrateInfo::base_name ( ) const

Return the standard/common, non-residue, short name of the monosaccharide.

References is_amino_sugar(), is_uronic_acid(), residue_type_, and root_from_code().

Referenced by show().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::branch_point ( core::uint i ) const

Return the attachment point of the downstream saccharide residue attached to ith branch off of this residue.

Parameters

<i>	the branch point index

Returns: an integer n of (1->n) of polysaccharide nomenclature, where n specifies the attachment point of the downstream monosaccharide residue; e.g., 4 specifies O4

A monosaccharide with a group linked to it at one position is a distinct residue type from the same monosaccharide with the same group linked to it at another position. For example, Rosetta treats (1->4)-beta- D-glucopyranose as an entirely distinct residue type from (1->3)-beta-D-glucopyranose, with separate .params files for each.

See also:
CarbohydrateInfo.mainchain_glycosidic_bond_acceptor()
CarbohydrateInfo.n_branches()

References branch_points_, n_branches(), and PyAssert.

std::map< std::string, std::string > const & core::chemical::carbohydrates::CarbohydrateInfo::code_to_root_map ( )

static

A list of Rosetta PDB 3-letter codes for saccharide residues mapped to the corresponding root.

References basic::options::OptionKeys::in::path::database, basic::options::option, and core::chemical::carbohydrates::read_codes_and_roots_from_database_file().

Referenced by root_from_code().

void core::chemical::carbohydrates::CarbohydrateInfo::copy_data	(	CarbohydrateInfo	object_to_copy_to,
		CarbohydrateInfo	object_to_copy_from
	)

private

core::uint core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen ( ) const

inline

Return the cyclic oxygen number or 0, if linear.

This atom is used as a reference atom for certain torsion angles.
See also:
CarbohydrateInfo.anomeric_carbon()
CarbohydrateInfo.cyclic_oxygen_name()
CarbohydrateInfo.cyclic_oxygen_index()

References cyclic_oxygen_.

core::uint core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen_index ( ) const

inline

Return the atom index of the cyclic oxygen in this ResidueType or 0, if linear.

This atom is used as a reference atom for certain torsion angles.
See also:
CarbohydrateInfo.cyclic_oxygen()
CarbohydrateInfo.cyclic_oxygen_name()
CarbohydrateInfo.anomeric_carbon_index()

References cyclic_oxygen_index_.

std::string core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen_name ( ) const

inline

Return the atom name of the cyclic oxygen.

This atom is used as a reference atom for certain torsion angles.
See also:
CarbohydrateInfo.cyclic_oxygen()
CarbohydrateInfo.anomeric_carbon_name()
CarbohydrateInfo.cyclic_oxygen_index()

References cyclic_oxygen_name_.

void core::chemical::carbohydrates::CarbohydrateInfo::determine_IUPAC_names ( )

private

References anomer_, full_name_, is_acetylated(), is_amino_sugar(), is_glycoside_, is_uronic_acid(), mainchain_glycosidic_bond_acceptor_, modifications_, n_carbons_, residue_type_, ring_size_, root_from_code(), short_name_, and stereochem_.

Referenced by init().

void core::chemical::carbohydrates::CarbohydrateInfo::determine_polymer_connections ( )

private

References anomeric_carbon_, branch_points_, has_exocyclic_linkage_, mainchain_glycosidic_bond_acceptor_, residue_type_, and ring_size_.

Referenced by init().

std::string core::chemical::carbohydrates::CarbohydrateInfo::full_name ( ) const

inline

Return the full IUPAC name of the monosaccharide.

References full_name_.

core::Size core::chemical::carbohydrates::CarbohydrateInfo::get_n_carbons ( ) const

private

References MAX_C_SIZE_LIMIT, MIN_C_SIZE_LIMIT, residue_type_, and utility_exit_with_message.

Referenced by init().

bool core::chemical::carbohydrates::CarbohydrateInfo::has_exocyclic_linkage ( ) const

inline

Return true if the attachment point of the downstream saccharide is on an exocyclic carbon.

References has_exocyclic_linkage_.

void core::chemical::carbohydrates::CarbohydrateInfo::init ( core::chemical::ResidueTypeCAP residue_type )

private

References anomer_, anomeric_carbon_, anomeric_carbon_name_, cyclic_oxygen_, cyclic_oxygen_index_, cyclic_oxygen_name_, determine_IUPAC_names(), determine_polymer_connections(), get_n_carbons(), is_glycoside_, n_carbons_, read_and_set_properties(), residue_type_, ring_size_, stereochem_, and virtual_cyclic_oxygen_index_.

Referenced by CarbohydrateInfo().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_acetylated ( ) const

inline

Return true if the sugar has been acetylated at any position.

References is_N_acetylated(), and is_O_acetylated().

Referenced by determine_IUPAC_names().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_acyclic ( ) const

inline

Return true if the monosaccharide is linear.

References ring_size_.

Referenced by is_cyclic().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_aldose ( ) const

inline

Return true if the monosaccharide is an aldose.

An aldose sugar is an aldehyde derivative. See also:
CarbohydrateInfo.is_ketose() CarbohydrateInfo.is_ulose() CarbohydrateInfo.anomeric_carbon()

References anomeric_carbon_.

Referenced by show().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_alpha_sugar ( ) const

inline

Return true if the cyclic monosaccharide is an alpha sugar.

"alpha" and "beta" designate the stereochemistry at the anomeric carbon of a cyclic sugar.

References anomer_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_amino_sugar ( ) const

inline

Return true if any hydroxyl group has been modified to an amino group or an acetylated amino group.

References modifications_.

Referenced by base_name(), and determine_IUPAC_names().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_beta_sugar ( ) const

inline

Return true if the cyclic monosaccharide is a beta sugar.

"alpha" and "beta" designate the stereochemistry at the anomeric carbon of a cyclic sugar.

References anomer_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_cyclic ( ) const

inline

Return true if the monosaccharide is a ring.

References is_acyclic().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_D_sugar ( ) const

inline

Return true if the monosaccharide is a D-sugar.

References stereochem_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_furanose ( ) const

inline

Return true if the monosaccharide is a furanose.

A furanose has a five-membered ring (like furan).

References ring_size_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_glycoside ( ) const

inline

Return true if the monosaccharide is attached to something at the anomeric carbon.

Remarks: not yet fully implemented

References is_glycoside_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_heptose ( ) const

inline

Return true if the monosaccharide is a heptose.

References n_carbons_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_hexose ( ) const

inline

Return true if the monosaccharide is a hexose.

References n_carbons_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_ketose ( ) const

inline

Return true if the monosaccharide is a ketose.

A ketose sugar is a ketone derivative.
Does not distinguish between 2-ketoses (uloses) and 3-ketoses.

See also:
CarbohydrateInfo.is_aldose() CarbohydrateInfo.is_ulose() CarbohydrateInfo.anomeric_carbon()

References anomeric_carbon_.

Referenced by is_ulose().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_ketose ( core::uint const n ) const

inline

Return true if the monosaccharide is an n-ketose.

A ketose sugar is a ketone derivative.
See also:
CarbohydrateInfo.is_aldose() CarbohydrateInfo.is_ulose() CarbohydrateInfo.anomeric_carbon()

References anomeric_carbon_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_L_sugar ( ) const

inline

Return true if the monosaccharide is an L-sugar.

References stereochem_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_N_acetylated ( ) const

inline

Return true if any hydroxyl group has been modified to an acetylated amino group.

References modifications_.

Referenced by is_acetylated().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_nonose ( ) const

inline

Return true if the monosaccharide is a nonose.

References n_carbons_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_O_acetylated ( ) const

inline

Return true if any hydroxyl group has been modified by acetylation.

References modifications_.

Referenced by is_acetylated().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_octose ( ) const

inline

Return true if the monosaccharide is an octose.

References n_carbons_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_pentose ( ) const

inline

Return true if the monosaccharide is a pentose.

References n_carbons_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_pyranose ( ) const

inline

Return true if the monosaccharide is a pyranose.

A pyranose has a six-membered ring (like pyran).

References ring_size_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_septanose ( ) const

inline

Return true if the monosaccharide is a septanose.

A septanose has a seven-membered ring.

References ring_size_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_tetrose ( ) const

inline

Return true if the monosaccharide is a tetrose.

References n_carbons_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_triose ( ) const

inline

Return true if the monosaccharide is a triose.

References n_carbons_.

bool core::chemical::carbohydrates::CarbohydrateInfo::is_ulose ( ) const

inline

Return true if the monosaccharide is a 2-ketose.

References is_ketose().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_uronic_acid ( ) const

inline

Return true if the primary hydroxyl group is oxidized to the acid.

References modifications_.

Referenced by base_name(), and determine_IUPAC_names().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::mainchain_glycosidic_bond_acceptor ( ) const

inline

Return the attachment point of the downstream saccharide residue of the main chain.

Returns: an integer n of (1->n) of polysaccharide nomenclature, where n specifies the attachment point on the upstream monosaccharide residue; e.g., 4 specifies O4; n = 0 specifies an upper terminus

A monosaccharide with a group linked to it at one position is a distinct residue type from the same monosaccharide with the same group linked to it at another position. For example, Rosetta treats (1->4)-beta- D-glucopyranose as an entirely distinct residue type from (1->3)-beta-D-glucopyranose, with separate .params files for each.

See also:
CarbohydrateInfo.n_branches()
CarbohydrateInfo.branch_point()

References mainchain_glycosidic_bond_acceptor_.

core::Size core::chemical::carbohydrates::CarbohydrateInfo::n_branches ( ) const

inline

Return the number of branches off of this residue.

A monosaccharide with a group linked to it at one position is a distinct residue type from the same monosaccharide with the same group linked to it at another position. For example, Rosetta treats (1->4)-beta- D-glucopyranose as an entirely distinct residue type from (1->3)-beta-D-glucopyranose, with separate .params files for each.

See also:
CarbohydrateInfo.mainchain_glycosidic_bond_acceptor()
CarbohydrateInfo.branch_point()

References branch_points_.

Referenced by branch_point(), and show().

core::Size core::chemical::carbohydrates::CarbohydrateInfo::n_carbons ( ) const

inline

Get the number of carbons in the monosaccharide.

This ignores carbons found in modifications to the base sugar.

References n_carbons_.

CarbohydrateInfo & core::chemical::carbohydrates::CarbohydrateInfo::operator= ( CarbohydrateInfo const & object_to_copy )

References copy_data().

void core::chemical::carbohydrates::CarbohydrateInfo::read_and_set_properties ( )

private

References anomer_, anomeric_carbon_, anomeric_carbon_index_, anomeric_carbon_name_, cyclic_oxygen_, cyclic_oxygen_index_, cyclic_oxygen_name_, modifications_, n_carbons_, residue_type_, ring_size_, stereochem_, utility_exit_with_message, and virtual_cyclic_oxygen_index_.

Referenced by init().

core::Size core::chemical::carbohydrates::CarbohydrateInfo::ring_size ( ) const

inline

Get the size of the carbohydrate ring.

A linear monosaccharide has a ring size of zero.

References ring_size_.

std::string core::chemical::carbohydrates::CarbohydrateInfo::root_from_code ( std::string code ) const

inlineprivate

References code_to_root_map().

Referenced by base_name(), and determine_IUPAC_names().

std::string core::chemical::carbohydrates::CarbohydrateInfo::short_name ( ) const

inline

Return the abbreviated IUPAC name of the monosaccharide (for use in polysaccharide sequences).

References short_name_.

void core::chemical::carbohydrates::CarbohydrateInfo::show ( std::ostream & output = std::cout ) const

virtual

Generate string representation of CarbohydrateInfo for debugging purposes.

References anomer_, anomeric_carbon_, base_name(), branch_points_, full_name_, is_aldose(), mainchain_glycosidic_bond_acceptor_, modifications_, n_branches(), n_carbons_, prefix, ring_size_, short_name_, stereochem_, and suffix.

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

char core::chemical::carbohydrates::CarbohydrateInfo::stereochem ( ) const

inline

Get the stereochemical designation for the monosaccharide.

Returns: 'L' or 'D'

References stereochem_.

utility::vector1< std::string > const & core::chemical::carbohydrates::CarbohydrateInfo::sugar_properties ( )

static

A list of allowed properties in carbohydrate .params and patch files.

References basic::options::OptionKeys::in::path::database, basic::options::option, and core::chemical::carbohydrates::read_properties_from_database_file().

Referenced by core::chemical::ResidueType::add_property().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::virtual_cyclic_oxygen_index ( ) const

inline

Return the atom index of the virtual atom that superimposes with the cyclic oxygen in this ResidueType or 0, if linear.

This atom is used as a reference atom for certain torsion angles.
See also:
CarbohydrateInfo.cyclic_oxygen_index()

References virtual_cyclic_oxygen_index_.

Member Data Documentation

std::string core::chemical::carbohydrates::CarbohydrateInfo::anomer_

private

Referenced by anomer(), copy_data(), determine_IUPAC_names(), init(), is_alpha_sugar(), is_beta_sugar(), read_and_set_properties(), and show().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon_

private

Referenced by anomeric_carbon(), copy_data(), determine_polymer_connections(), init(), is_aldose(), is_ketose(), read_and_set_properties(), and show().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon_index_

private

Referenced by anomeric_carbon_index(), copy_data(), and read_and_set_properties().

std::string core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon_name_

private

Referenced by anomeric_carbon_name(), copy_data(), init(), and read_and_set_properties().

utility::vector1<core::uint> core::chemical::carbohydrates::CarbohydrateInfo::branch_points_

private

Referenced by branch_point(), copy_data(), determine_polymer_connections(), n_branches(), and show().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen_

private

Referenced by copy_data(), cyclic_oxygen(), init(), and read_and_set_properties().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen_index_

private

Referenced by copy_data(), cyclic_oxygen_index(), init(), and read_and_set_properties().

std::string core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen_name_

private

Referenced by copy_data(), cyclic_oxygen_name(), init(), and read_and_set_properties().

std::string core::chemical::carbohydrates::CarbohydrateInfo::full_name_

private

Referenced by copy_data(), determine_IUPAC_names(), full_name(), and show().

bool core::chemical::carbohydrates::CarbohydrateInfo::has_exocyclic_linkage_

private

Referenced by copy_data(), determine_polymer_connections(), and has_exocyclic_linkage().

bool core::chemical::carbohydrates::CarbohydrateInfo::is_glycoside_

private

Referenced by copy_data(), determine_IUPAC_names(), init(), and is_glycoside().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::mainchain_glycosidic_bond_acceptor_

private

Referenced by copy_data(), determine_IUPAC_names(), determine_polymer_connections(), mainchain_glycosidic_bond_acceptor(), and show().

core::Size const core::chemical::carbohydrates::CarbohydrateInfo::MAX_C_SIZE_LIMIT = 9

staticprivate

Referenced by get_n_carbons().

core::Size const core::chemical::carbohydrates::CarbohydrateInfo::MIN_C_SIZE_LIMIT = 3

staticprivate

Referenced by get_n_carbons().

utility::vector1<std::string> core::chemical::carbohydrates::CarbohydrateInfo::modifications_

private

Referenced by copy_data(), determine_IUPAC_names(), is_amino_sugar(), is_N_acetylated(), is_O_acetylated(), is_uronic_acid(), read_and_set_properties(), and show().

core::Size core::chemical::carbohydrates::CarbohydrateInfo::n_carbons_

private

Referenced by copy_data(), determine_IUPAC_names(), init(), is_heptose(), is_hexose(), is_nonose(), is_octose(), is_pentose(), is_tetrose(), is_triose(), n_carbons(), read_and_set_properties(), and show().

core::chemical::ResidueTypeCAP core::chemical::carbohydrates::CarbohydrateInfo::residue_type_

private

Referenced by base_name(), copy_data(), determine_IUPAC_names(), determine_polymer_connections(), get_n_carbons(), init(), and read_and_set_properties().

core::Size core::chemical::carbohydrates::CarbohydrateInfo::ring_size_

private

Referenced by copy_data(), determine_IUPAC_names(), determine_polymer_connections(), init(), is_acyclic(), is_furanose(), is_pyranose(), is_septanose(), read_and_set_properties(), ring_size(), and show().

std::string core::chemical::carbohydrates::CarbohydrateInfo::short_name_

private

Referenced by copy_data(), determine_IUPAC_names(), short_name(), and show().

char core::chemical::carbohydrates::CarbohydrateInfo::stereochem_

private

Referenced by copy_data(), determine_IUPAC_names(), init(), is_D_sugar(), is_L_sugar(), read_and_set_properties(), show(), and stereochem().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::virtual_cyclic_oxygen_index_

private

Referenced by copy_data(), init(), read_and_set_properties(), and virtual_cyclic_oxygen_index().

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

symlinks/rosetta/src/core/chemical/carbohydrates/CarbohydrateInfo.hh
symlinks/rosetta/src/core/chemical/carbohydrates/CarbohydrateInfo.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation