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core::scoring::carbohydrates Namespace Reference

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

CHIEnergyFunctionLinkageTypeoperator++ (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

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

Enumeration Type Documentation

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 

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

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, LINKAGE_NA, and core::pose::Pose::residue().

Referenced by core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), get_CHI_energy_function_linkage_type_for_residue_in_pose(), and core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy().

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

utility::vector1< CHIEnergyFunctionLinkageType > core::scoring::carbohydrates::get_linkage_types_for_dihedral ( core::uint  torsion_id)
utility::vector1< CHIEnergyFunctionLinkageType > core::scoring::carbohydrates::get_linkage_types_for_dihedral ( core::Size  torsion)
OmegaPreferenceType core::scoring::carbohydrates::get_omega_preference_for_residue_in_pose ( pose::Pose const &  pose,
core::uint  rsd_num 
)
CHIEnergyFunctionLinkageType & core::scoring::carbohydrates::operator++ ( CHIEnergyFunctionLinkageType &  linkage_type)
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 core::scoring::TR().

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