Classes
struct	CHIDihedralSamplingData
	Struct for CHI-based dihedral sampling. More...

class	CHIEnergyFunction

struct	OmegaPreferenceSamplingData
	Struct for Omega-Preference dihedral sampling. More...

class	OmegaPreferencesFunction

Typedefs
typedef utility::pointer::shared_ptr< CHIEnergyFunction >	CHIEnergyFunctionOP

typedef utility::pointer::shared_ptr< CHIEnergyFunction const >	CHIEnergyFunctionCOP

typedef utility::pointer::shared_ptr< OmegaPreferencesFunction >	OmegaPreferencesFunctionOP

typedef utility::pointer::shared_ptr< OmegaPreferencesFunction const >	OmegaPreferencesFunctionCOP

Enumerations
enum	CHIEnergyFunctionLinkageType { FIRST_LINK_TYPE = 1 , ALPHA_LINKS = 1 , BETA_LINKS , _2AX_3EQ_4AX_LINKS , _2EQ_3AX_4EQ_LINKS , ALPHA6_LINKS , BETA6_LINKS , N_LINK_TYPES = BETA6_LINKS , LINKAGE_NA }
	Labels for the CHI Energy Function linkage type of the carbohydrate phi or psi angle. More...

enum	OmegaPreferenceType { ANTI = 1 , GAUCHE_EFFECT , N_OMEGA_PREFERENCE_TYPES = GAUCHE_EFFECT , PREFERENCE_NA }
	Labels for the omega torsion preference type used to select the proper OmegaPreferencesFunction form. More...

Functions
CHIEnergyFunctionLinkageType &	operator++ (CHIEnergyFunctionLinkageType &linkage_type)

std::map< char, utility::vector1< Real > >	read_Gaussian_parameters_from_database_file (std::string const &filename)
	Return a table of Gaussian parameters read from a database file. More...

CHIEnergyFunctionLinkageType	get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose (pose::Pose const &pose, core::uint rsd_num)
	Get the CHI Energy Function linkage type for phi for a particular residue. More...

CHIEnergyFunctionLinkageType	get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose (pose::Pose const &pose, core::uint rsd_num)
	Get the CHI Energy Function linkage type for psi for a particular residue. More...

OmegaPreferenceType	get_omega_preference_for_residue_in_pose (pose::Pose const &pose, core::uint rsd_num)
	Get the omega preference for a particular residue. More...

CHIEnergyFunctionLinkageType	get_CHI_energy_function_linkage_type_for_residue_in_pose (id::MainchainTorsionType torsion, pose::Pose const &pose, core::uint rsd_num)
	Get the CHI Energy Function linkage type for the given torsion angle of a particular residue. More...

utility::vector1< CHIEnergyFunctionLinkageType >	get_linkage_types_for_dihedral (core::Size torsion)

utility::vector1< CHIEnergyFunctionLinkageType >	get_linkage_types_for_dihedral (core::uint torsion_id)

Typedef Documentation

◆ CHIEnergyFunctionCOP

typedef utility::pointer::shared_ptr< CHIEnergyFunction const> core::scoring::carbohydrates::CHIEnergyFunctionCOP

◆ CHIEnergyFunctionOP

typedef utility::pointer::shared_ptr< CHIEnergyFunction > core::scoring::carbohydrates::CHIEnergyFunctionOP

◆ OmegaPreferencesFunctionCOP

typedef utility::pointer::shared_ptr< OmegaPreferencesFunction const> core::scoring::carbohydrates::OmegaPreferencesFunctionCOP

◆ OmegaPreferencesFunctionOP

typedef utility::pointer::shared_ptr< OmegaPreferencesFunction > core::scoring::carbohydrates::OmegaPreferencesFunctionOP

Enumeration Type Documentation

◆ CHIEnergyFunctionLinkageType

enum core::scoring::carbohydrates::CHIEnergyFunctionLinkageType

Labels for the CHI Energy Function linkage type of the carbohydrate phi or psi angle.

The CHI energy functions depend on the type of linkage.
Parameters for the Gaussian functions that compose the CHI Energy Functions are stored in a vector indexed by these labels.

Enumerator
FIRST_LINK_TYPE
ALPHA_LINKS
BETA_LINKS
_2AX_3EQ_4AX_LINKS
_2EQ_3AX_4EQ_LINKS
ALPHA6_LINKS
BETA6_LINKS
N_LINK_TYPES
LINKAGE_NA

◆ OmegaPreferenceType

enum core::scoring::carbohydrates::OmegaPreferenceType

Labels for the omega torsion preference type used to select the proper OmegaPreferencesFunction form.

In saccharide residues where the hydroxyl group of the carbon atom two carbons previous to the exocyclic carbon is equatorial, the "gauche effect" occurs, in which the exocyclic torsion angle prefers one of the two gauche orientations instead of the expected anti configuration.

Enumerator
ANTI
GAUCHE_EFFECT
N_OMEGA_PREFERENCE_TYPES
PREFERENCE_NA

Function Documentation

◆ get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose()

CHIEnergyFunctionLinkageType core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose	(	pose::Pose const &	pose,
		core::uint	rsd_num
	)

Get the CHI Energy Function linkage type for phi for a particular residue.

Returns: CHIEnergyFunctionLinkageType, which corresponds to one of two particular CHI Energy Functions specific to phi, or LINKAGE_NA if the CHI Energy Function is not applicable to this torsion.

References ALPHA_LINKS, BETA_LINKS, core::conformation::Residue::carbohydrate_info(), core::conformation::Residue::is_carbohydrate(), LINKAGE_NA, core::pose::Pose::residue(), and core::conformation::Residue::seqpos().

Referenced by core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), get_CHI_energy_function_linkage_type_for_residue_in_pose(), and core::energy_methods::SugarBackboneEnergy::residue_energy().

◆ get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose()

CHIEnergyFunctionLinkageType core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose	(	pose::Pose const &	pose,
		core::uint	rsd_num
	)

Get the CHI Energy Function linkage type for psi for a particular residue.

Returns: CHIEnergyFunctionLinkageType, which corresponds to one of four particular CHI Energy Functions specific to psi, or LINKAGE_NA if the CHI Energy Function is not applicable to this torsion.

References _2AX_3EQ_4AX_LINKS, _2EQ_3AX_4EQ_LINKS, ALPHA6_LINKS, core::chemical::rings::AXIAL, BETA6_LINKS, core::chemical::rings::EQUATORIAL, core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::pose::Pose::glycan_tree_set(), core::pose::is_atom_axial_or_equatorial_to_ring(), LINKAGE_NA, core::chemical::rings::NEITHER, core::conformation::position_of_atom_on_ring(), core::pose::Pose::residue(), and core::scoring::TR().

Referenced by core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), get_CHI_energy_function_linkage_type_for_residue_in_pose(), and core::energy_methods::SugarBackboneEnergy::residue_energy().

◆ get_CHI_energy_function_linkage_type_for_residue_in_pose()

CHIEnergyFunctionLinkageType core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_residue_in_pose	(	id::MainchainTorsionType	torsion,
		pose::Pose const &	pose,
		core::uint	rsd_num
	)

Get the CHI Energy Function linkage type for the given torsion angle of a particular residue.

Returns: CHIEnergyFunctionLinkageType, which corresponds to one of six particular CHI Energy Functions specific to the given glycosidic linkage, or LINKAGE_NA if the CHI Energy Function is not applicable to this torsion.

References get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose(), get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose(), LINKAGE_NA, core::id::phi_dihedral, and core::id::psi_dihedral.

Referenced by protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion().

◆ get_linkage_types_for_dihedral() [1/2]

utility::vector1< CHIEnergyFunctionLinkageType > core::scoring::carbohydrates::get_linkage_types_for_dihedral ( core::Size torsion )

Author: Jared Adolf-Bryfogle jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com

References _2AX_3EQ_4AX_LINKS, _2EQ_3AX_4EQ_LINKS, ALPHA6_LINKS, ALPHA_LINKS, BETA6_LINKS, BETA_LINKS, core::id::phi_dihedral, and core::id::psi_dihedral.

◆ get_linkage_types_for_dihedral() [2/2]

utility::vector1< CHIEnergyFunctionLinkageType > core::scoring::carbohydrates::get_linkage_types_for_dihedral ( core::uint torsion_id )

◆ get_omega_preference_for_residue_in_pose()

OmegaPreferenceType core::scoring::carbohydrates::get_omega_preference_for_residue_in_pose	(	pose::Pose const &	pose,
		core::uint	rsd_num
	)

Get the omega preference for a particular residue.

References ANTI, core::chemical::rings::AXIAL, core::pose::Pose::conformation(), core::chemical::rings::EQUATORIAL, core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), GAUCHE_EFFECT, core::pose::Pose::glycan_tree_set(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), core::pose::is_atom_axial_or_equatorial_to_ring(), core::chemical::rings::NEITHER, PREFERENCE_NA, and core::pose::Pose::residue().

Referenced by core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), and core::energy_methods::SugarBackboneEnergy::residue_energy().

◆ operator++()

CHIEnergyFunctionLinkageType & core::scoring::carbohydrates::operator++ ( CHIEnergyFunctionLinkageType & linkage_type )

◆ read_Gaussian_parameters_from_database_file()

std::map< char, utility::vector1< Real > > core::scoring::carbohydrates::read_Gaussian_parameters_from_database_file ( std::string const & filename )

Return a table of Gaussian parameters read from a database file.

References protocols::abinitio::filename(), and core::scoring::TR().

Referenced by core::scoring::carbohydrates::CHIEnergyFunction::init().

Classes

Typedefs

Enumerations

Functions