#include <CarbohydrateInfo.hh>

Inheritance diagram for core::chemical::carbohydrates::CarbohydrateInfo:

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

	CarbohydrateInfo (CarbohydrateInfo const &object_to_copy, core::chemical::ResidueTypeCAP new_owner)
	Copy constructor. More...

	~CarbohydrateInfo () override

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	linkage_notation () const
	Return the main-chain IUPAC linkage notation for this monosaccharide (for use in polysaccharide sequences). More...

std::string	short_name_w_linkage_notation () const
	Return the abbreviated IUPAC name of the monosaccharide, including main-chain linkage notation (for use in polysaccharide sequences). More...

std::string	basic_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	virtual_anomeric_carbon_index () const
	Return the atom index of the virtual atom that superimposes with the anomeric carbon in this ResidueType or 0, if linear. 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...

core::Size	n_ring_carbons () const
	Get the number of carbons in the ring. More...

core::Size	last_carbon_in_ring () const
	Get the last carbon of the ring. Varies with ketose or aldose. 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...

bool	is_reducing_sugar () const
	Return true if the monosaccharide is a reducing sugar. 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 const i) const
	Return the attachment point of the downstream saccharide residue attached to ith branch off of this residue. More...

bool	has_exocyclic_linkage_to_child_mainchain () const
	Return true if the attachment point of the downstream saccharide (N+1) OF THE MAINCHAIN is on an exocyclic carbon. This residue may still have an exocylic linkage through a branch point. See core::pose::has_exocylic_carbon_linkage to get more specific exocyclic carbon linkage info. More...

core::Real	anomeric_pseudotorsion () const
	Get pseudotorsion of anomeric carbon from ideal residue: defined as the out-of-plane angle of the anomeric O with respect to the Oring-Canomeric-Cadjacent plane w/i the ring. More...

core::Size	anomeric_sidechain_index () const
	Get the index of the non-ring atom bound to the anomeric 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 Attributes
static core::Size const	MAX_C_SIZE_LIMIT = 9

static core::Size const	MIN_C_SIZE_LIMIT = 3

Private Member Functions
	CarbohydrateInfo ()

	CarbohydrateInfo (CarbohydrateInfo const &object_to_copy)

CarbohydrateInfo &	operator= (CarbohydrateInfo const &object_to_copy)

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

void	copy_data (CarbohydrateInfo &object_to_copy_to, CarbohydrateInfo const &object_to_copy_from)

void	read_and_set_properties ()

void	determine_polymer_connections ()

void	determine_anomeric_pseudotorsion ()

void	determine_IUPAC_names ()

Private Attributes
core::chemical::ResidueTypeCAP	residue_type_

std::string	full_name_

std::string	short_name_

std::string	linkage_notation_

core::uint	anomeric_carbon_

std::string	anomeric_carbon_name_

core::uint	anomeric_carbon_index_

core::uint	virtual_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::Real	anomeric_pseudotorsion_

core::Size	anomeric_sidechain_index_

core::uint	mainchain_glycosidic_bond_acceptor_

utility::vector1< core::uint >	branch_points_

bool	has_exocyclic_linkage_to_child_mainchain_

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,
		core::chemical::ResidueTypeCAP	new_owner
	)

Copy constructor.

References copy_data(), and residue_type_.

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

overridedefault

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

private

References init().

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

private

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_.

core::Real core::chemical::carbohydrates::CarbohydrateInfo::anomeric_pseudotorsion ( ) const

Get pseudotorsion of anomeric carbon from ideal residue: defined as the out-of-plane angle of the anomeric O with respect to the Oring-Canomeric-Cadjacent plane w/i the ring.

References anomeric_pseudotorsion_.

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

Get the index of the non-ring atom bound to the anomeric carbon.

Get the index of the non-ring atom bound to the anomeric carbon

Returns: The atom index of the non-ring atom bound to the anomeric carbon. Typically, this is "H1", but not always. 0 if there is no such atom (which happens with virtualized residues)

References anomeric_sidechain_index_.

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

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

References is_amino_sugar(), is_uronic_acid(), residue_type_, and core::chemical::carbohydrates::CarbohydrateInfoManager::root_from_code().

Referenced by show().

core::uint core::chemical::carbohydrates::CarbohydrateInfo::branch_point ( core::uint const 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_, and n_branches().

void core::chemical::carbohydrates::CarbohydrateInfo::copy_data	(	CarbohydrateInfo &	object_to_copy_to,
		CarbohydrateInfo const &	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_anomeric_pseudotorsion ( )

private

References anomeric_pseudotorsion_, anomeric_sidechain_index_, core::conformation::ResidueFactory::create_residue(), and residue_type_.

Referenced by init().

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

private

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

private

References branch_points_, has_exocyclic_linkage_to_child_mainchain_, last_carbon_in_ring(), mainchain_glycosidic_bond_acceptor_, and residue_type_.

Referenced by init().

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

inline

Return the full IUPAC name of the monosaccharide.

References full_name_.

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

inline

Return true if the attachment point of the downstream saccharide (N+1) OF THE MAINCHAIN is on an exocyclic carbon. This residue may still have an exocylic linkage through a branch point. See core::pose::has_exocylic_carbon_linkage to get more specific exocyclic carbon linkage info.

References has_exocyclic_linkage_to_child_mainchain_.

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

private

References anomeric_pseudotorsion_, anomeric_sidechain_index_, cyclic_oxygen_, cyclic_oxygen_index_, cyclic_oxygen_name_, determine_anomeric_pseudotorsion(), determine_IUPAC_names(), determine_polymer_connections(), is_glycoside_, read_and_set_properties(), residue_type_, and virtual_cyclic_oxygen_index_.

Referenced by CarbohydrateInfo().

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

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(), last_carbon_in_ring(), and n_ring_carbons().

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

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

References core::chemical::AMINO_SUGAR, is_N_acetylated(), and residue_type_.

Referenced by basic_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.

References is_glycoside_.

Referenced by is_reducing_sugar().

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

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

References core::chemical::ACETYLAMINO_SUGAR, and residue_type_.

Referenced by is_acetylated(), and is_amino_sugar().

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

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

References core::chemical::ACETYL_SUGAR, and residue_type_.

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_reducing_sugar ( ) const

Return true if the monosaccharide is a reducing sugar.

References is_glycoside(), and residue_type_.

Referenced by show().

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

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

References residue_type_, and core::chemical::URONIC_ACID.

Referenced by basic_name(), and determine_IUPAC_names().

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

inline

Get the last carbon of the ring. Varies with ketose or aldose.

References is_acyclic(), and n_ring_carbons().

Referenced by determine_polymer_connections().

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

inline

Return the main-chain IUPAC linkage notation for this monosaccharide (for use in polysaccharide sequences).

References linkage_notation_.

Referenced by 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_.

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

inline

Get the number of carbons in the ring.

References is_acyclic(), and ring_size_.

Referenced by last_carbon_in_ring().

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

private

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

private

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::short_name ( ) const

inline

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

References short_name_.

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

inline

Return the abbreviated IUPAC name of the monosaccharide, including main-chain linkage notation (for use in polysaccharide sequences).

References linkage_notation_, and short_name_.

Referenced by show().

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_, basic_name(), branch_points_, full_name_, is_aldose(), is_reducing_sugar(), mainchain_glycosidic_bond_acceptor_, modifications_, core::chemical::carbohydrates::CarbohydrateInfoManager::morpheme_from_ring_size(), n_branches(), n_carbons_, ring_size_, short_name_w_linkage_notation(), and stereochem_.

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_.

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

inline

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

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

References virtual_anomeric_carbon_index_.

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(), 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(), 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(), and read_and_set_properties().

core::Real core::chemical::carbohydrates::CarbohydrateInfo::anomeric_pseudotorsion_

private

Referenced by anomeric_pseudotorsion(), determine_anomeric_pseudotorsion(), and init().

core::Size core::chemical::carbohydrates::CarbohydrateInfo::anomeric_sidechain_index_

private

Referenced by anomeric_sidechain_index(), determine_anomeric_pseudotorsion(), and init().

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_to_child_mainchain_

private

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

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

private

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

std::string core::chemical::carbohydrates::CarbohydrateInfo::linkage_notation_

private

Referenced by copy_data(), determine_IUPAC_names(), linkage_notation(), and short_name_w_linkage_notation().

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

static

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

static

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

private

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

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

private

Referenced by copy_data(), determine_IUPAC_names(), 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 basic_name(), CarbohydrateInfo(), determine_anomeric_pseudotorsion(), determine_IUPAC_names(), determine_polymer_connections(), init(), is_amino_sugar(), is_N_acetylated(), is_O_acetylated(), is_reducing_sugar(), is_uronic_acid(), and read_and_set_properties().

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

private

Referenced by copy_data(), determine_IUPAC_names(), is_acyclic(), is_furanose(), is_pyranose(), is_septanose(), n_ring_carbons(), 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 short_name_w_linkage_notation().

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

private

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

core::uint core::chemical::carbohydrates::CarbohydrateInfo::virtual_anomeric_carbon_index_

private

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

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:

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

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

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