#include <CarbohydrateInfo.hh>

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

Collaboration diagram for core::chemical::carbohydrates::CarbohydrateInfo:

Public Member Functions
	CarbohydrateInfo ()
	Empty constructor. More...

	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 ()

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...

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

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

std::pair < core::id::TorsionType, core::uint >	glycosidic_linkage_id (core::uint torsion_index) const
	Return the BB or CHI identifier for the requested glycosidic linkage torsion angle. More...

std::pair < core::id::TorsionType, core::uint >	nu_id (core::uint subscript) const
	Return the CHI identifier for the requested nu (internal ring torsion) angle. More...

Static Public Attributes
static std::map< std::string, std::string > const	CODE_TO_ROOT_MAP

Private Member Functions
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

void	define_nu_ids ()

Private Attributes
core::chemical::ResidueTypeCAP	residue_type_

std::string	full_name_

std::string	short_name_

core::uint	anomeric_carbon_

core::Size	n_carbons_

char	stereochem_

core::Size	ring_size_

std::string	anomer_

bool	is_glycoside_

bool	is_uronic_acid_

core::uint	mainchain_glycosidic_bond_acceptor_

utility::vector1< core::uint >	branch_points_

bool	has_exocyclic_linkage_

utility::vector1< std::pair < core::id::TorsionType, core::uint > >	glycosidic_linkage_id_

utility::vector1< std::pair < core::id::TorsionType, core::uint > >	nu_id_

Static Private Attributes
static core::Size const	MAX_C_SIZE_LIMIT = 7

static core::Size const	MIN_C_SIZE_LIMIT = 3

Friends
std::ostream &	operator<< (std::ostream &output, CarbohydrateInfo const &object_to_output)

Detailed Description

Definition at line 41 of file CarbohydrateInfo.hh.

Constructor & Destructor Documentation

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

Empty constructor.

Definition at line 95 of file CarbohydrateInfo.cc.

References init().

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

Standard constructor.

Parameters

<residue_type>,: the ResidueType object containing this CarbohydrateInfo

Definition at line 104 of file CarbohydrateInfo.cc.

References init().

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

Copy constructor.

Definition at line 110 of file CarbohydrateInfo.cc.

References copy_data().

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

Definition at line 129 of file CarbohydrateInfo.cc.

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.

Definition at line 278 of file CarbohydrateInfo.hh.

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.

Definition at line 118 of file CarbohydrateInfo.hh.

References anomeric_carbon_.

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

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

Definition at line 207 of file CarbohydrateInfo.cc.

References 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 on the upstream 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()

Remarks: Branches are not yet implemented.

Definition at line 226 of file CarbohydrateInfo.cc.

References branch_points_, and n_branches().

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

private

Definition at line 328 of file CarbohydrateInfo.cc.

References anomer_, anomeric_carbon_, branch_points_, full_name_, glycosidic_linkage_id_, has_exocyclic_linkage_, is_glycoside_, is_uronic_acid_, mainchain_glycosidic_bond_acceptor_, n_carbons_, nu_id_, residue_type_, ring_size_, short_name_, and stereochem_.

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

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

private

Definition at line 592 of file CarbohydrateInfo.cc.

References core::id::CHI, nu_id_, residue_type_, and ring_size_.

Referenced by init().

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

private

Definition at line 525 of file CarbohydrateInfo.cc.

References anomer_, full_name_, is_glycoside_, is_uronic_acid_, mainchain_glycosidic_bond_acceptor_, residue_type_, ring_size_, root_from_code(), short_name_, and stereochem_.

Referenced by init().

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

private

Definition at line 460 of file CarbohydrateInfo.cc.

References anomeric_carbon_, core::id::BB, core::id::CHI, glycosidic_linkage_id_, has_exocyclic_linkage_, is_aldose(), 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.

Definition at line 72 of file CarbohydrateInfo.hh.

References full_name_.

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

private

Definition at line 351 of file CarbohydrateInfo.cc.

References MAX_C_SIZE_LIMIT, MIN_C_SIZE_LIMIT, and residue_type_.

Referenced by init().

std::pair< core::id::TorsionType, core::uint > core::chemical::carbohydrates::CarbohydrateInfo::glycosidic_linkage_id ( core::uint torsion_index) const

Return the BB or CHI identifier for the requested glycosidic linkage torsion angle.

Parameters

<torsion_index>,: an integer corresponding to phi (1), psi (2), or omega (3)

Returns: a pair of values corresponding to the atom tree torsion definitions, in which the first element is either the TorsionID BB or CHI and the second element is an integer

It is crucial to note that this data structure stores information to identify:
phi(n)
psi(n+1), NOT psi(n)
omega(n+1), NOT omega(n)

See Also:
Pose.phi()
Pose.set_phi()
Pose.psi()
Pose.set_psi()
Pose.omega()
Pose.set_omega()

Remarks: An enum would be better than an integer for input to this function; however, static constants phi_torsion, psi_torsion, and omega_torsion were already defined in core/id/types.hh.
The atom tree in Rosetta 3 does not allow for rings, so cyclic carbohydrates are implemented as linear residues. Because of this, the atom tree assigns backbone (BB) torsions to what it considers the main- chain. Thus, only one side of the ring is considered backbone. Side-chain (CHI) angles must be defined in the .params file for the residue; they are not automatically assigned. Glycosidic linkage torsions are not necessarily defined as main chain torsions by the atom tree, so they must be designated here, in some cases with the use of CHI angles.

Definition at line 283 of file CarbohydrateInfo.cc.

References glycosidic_linkage_id_, and has_exocyclic_linkage_.

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.

Definition at line 354 of file CarbohydrateInfo.hh.

References has_exocyclic_linkage_.

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

private

Definition at line 301 of file CarbohydrateInfo.cc.

References anomer_, anomeric_carbon_, define_nu_ids(), determine_IUPAC_names(), determine_polymer_connections(), get_n_carbons(), is_glycoside_, is_uronic_acid_, n_carbons_, read_and_set_properties(), residue_type_, ring_size_, and stereochem_.

Referenced by CarbohydrateInfo().

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

inline

Return true if the monosaccharide is linear.

Definition at line 224 of file CarbohydrateInfo.hh.

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.

Definition at line 91 of file CarbohydrateInfo.hh.

References anomeric_carbon_.

Referenced by determine_polymer_connections(), and 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.

Definition at line 286 of file CarbohydrateInfo.hh.

References anomer_.

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.

Definition at line 297 of file CarbohydrateInfo.hh.

References anomer_.

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

inline

Return true if the monosaccharide is a ring.

Definition at line 234 of file CarbohydrateInfo.hh.

References is_acyclic().

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

inline

Return true if the monosaccharide is a D-sugar.

Definition at line 204 of file CarbohydrateInfo.hh.

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).

Definition at line 242 of file CarbohydrateInfo.hh.

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 implemented

Definition at line 310 of file CarbohydrateInfo.hh.

References is_glycoside_.

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

inline

Return true if the monosaccharide is a heptose.

Definition at line 174 of file CarbohydrateInfo.hh.

References n_carbons_.

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

inline

Return true if the monosaccharide is a hexose.

Definition at line 164 of file CarbohydrateInfo.hh.

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.anomeric_carbon()

Definition at line 106 of file CarbohydrateInfo.hh.

References anomeric_carbon_.

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

inline

Return true if the monosaccharide is an L-sugar.

Definition at line 194 of file CarbohydrateInfo.hh.

References stereochem_.

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

inline

Return true if the monosaccharide is a pentose.

Definition at line 154 of file CarbohydrateInfo.hh.

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).

Definition at line 253 of file CarbohydrateInfo.hh.

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.

Definition at line 264 of file CarbohydrateInfo.hh.

References ring_size_.

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

inline

Return true if the monosaccharide is a tetrose.

Definition at line 144 of file CarbohydrateInfo.hh.

References n_carbons_.

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

inline

Return true if the monosaccharide is a triose.

Definition at line 134 of file CarbohydrateInfo.hh.

References n_carbons_.

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

inline

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

Definition at line 365 of file CarbohydrateInfo.hh.

References is_uronic_acid_.

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()

Definition at line 327 of file CarbohydrateInfo.hh.

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()

Remarks: Branches are not yet implemented.

Definition at line 343 of file CarbohydrateInfo.hh.

References branch_points_.

Referenced by branch_point().

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

inline

Get the number of carbons in the monosaccharide.

Definition at line 127 of file CarbohydrateInfo.hh.

References n_carbons_.

std::pair< core::id::TorsionType, core::uint > core::chemical::carbohydrates::CarbohydrateInfo::nu_id ( core::uint subscript) const

Return the CHI identifier for the requested nu (internal ring torsion) angle.

Parameters

<subscript>,: the subscript for nu, which must be between 1 and 2 less than the ring size, inclusive

Returns: a pair of values corresponding to the atom tree torsion definitions, in which the first element is either the TorsionID BB or CHI and the second element is an integer

Remarks: The atom tree in Rosetta 3 does not allow for rings, so cyclic carbohydrates are implemented as linear residues. Because of this, the atom tree assigns backbone (BB) torsions to what it considers the main- chain. Thus, only one side of the ring is considered backbone. Side-chain (CHI) angles must be defined in the .params file for the residue; they are not automatically assigned. nu angles, which are the torsion angles defining the ring, not considered BB by the atom tree must therefore be defined as CHI angles in the .params file, even though they are not in reality side-chain torsions. Since a ring also has a multiplicity of actual side-chains, the indices for those CHI angles that are actually nu angles will vary.

Definition at line 248 of file CarbohydrateInfo.cc.

References nu_id_, and ring_size_.

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

Definition at line 117 of file CarbohydrateInfo.cc.

References copy_data().

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

private

Definition at line 369 of file CarbohydrateInfo.cc.

References anomer_, anomeric_carbon_, is_uronic_acid_, residue_type_, ring_size_, and stereochem_.

Referenced by init().

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

inline