core::scoring::rna Namespace Reference

Namespaces
	chemical_shift

Classes
class	Base_pair
class	Base_stack
class	RG_Energy_RNA
class	RG_Energy_RNACreator
class	RNA_AtomVDW
class	RNA_BaseBaseEnergy
class	RNA_BulgeEnergy
class	RNA_BulgeEnergyCreator
class	RNA_CentroidInfo
	Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...
class	RNA_DataBackboneEnergy
class	RNA_DataBackboneEnergyCreator
class	RNA_DataInfo
	Keep track of RNA centroid information inside the pose. More...
class	RNA_Datum
class	RNA_FilteredBaseBaseInfo
	Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...
class	RNA_FullAtomStackingEnergy
class	RNA_FullAtomStackingEnergyCreator
class	RNA_FullAtomVDW_BasePhosphate
class	RNA_FullAtomVDW_BasePhosphateCreator
class	RNA_LJ_BaseEnergy
class	RNA_LJ_BaseEnergyCreator
class	RNA_LowResolutionPotential
class	RNA_Mg_Energy
class	RNA_Mg_EnergyCreator
class	RNA_Mg_KnowledgeBasedPotential
class	RNA_PairwiseLowResolutionEnergy
class	RNA_PairwiseLowResolutionEnergyCreator
class	RNA_RawBaseBaseInfo
	Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! / Also, should probably use EnergyGraph instead of FArrays – much smaller memory footprint (!) /. More...
class	RNA_ScoringInfo
	Keep track of RNA centroid, useful atom, base-base info inside the pose. More...
class	RNA_SugarCloseEnergy
class	RNA_SugarCloseEnergyCreator
class	RNA_TorsionEnergy
class	RNA_TorsionEnergyCreator
class	RNA_TorsionPotential
class	RNA_VDW_Energy
class	RNA_VDW_EnergyCreator
class	StackElecEnergy
class	StackElecEnergyCreator

Typedefs
typedef utility::pointer::owning_ptr < RNA_AtomVDW >	RNA_AtomVDWOP
typedef utility::pointer::owning_ptr < RNA_AtomVDW const >	RNA_AtomVDWCOP
typedef std::pair< Real, Base_pair >	Energy_base_pair
typedef std::list < Energy_base_pair >	Energy_base_pair_list
typedef std::pair< Real, Base_stack >	Energy_base_stack
typedef std::list < Energy_base_stack >	Energy_base_stack_list
typedef numeric::xyzMatrix< Real >	Matrix
typedef utility::pointer::owning_ptr < RNA_CentroidInfo >	RNA_CentroidInfoOP
typedef numeric::xyzVector < core::Real >	Vector
typedef utility::pointer::owning_ptr < RNA_DataInfo >	RNA_DataInfoOP
typedef utility::pointer::access_ptr < RNA_DataInfo >	RNA_DataInfoAP
typedef utility::vector1 < RNA_Datum >	RNA_Data
typedef utility::pointer::owning_ptr < RNA_FilteredBaseBaseInfo >	RNA_FilteredBaseBaseInfoOP
typedef utility::pointer::owning_ptr < RNA_FullAtomVDW_BasePhosphate >	RNA_FullAtomVDW_BasePhosphateOP
typedef utility::pointer::owning_ptr < RNA_FullAtomVDW_BasePhosphate const >	RNA_FullAtomVDW_BasePhosphateCOP
typedef utility::pointer::owning_ptr < RNA_LowResolutionPotential >	RNA_LowResolutionPotentialOP
typedef utility::pointer::owning_ptr < RNA_Mg_KnowledgeBasedPotential >	RNA_Mg_KnowledgeBasedPotentialOP
typedef utility::pointer::owning_ptr < RNA_Mg_KnowledgeBasedPotential const >	RNA_Mg_KnowledgeBasedPotentialCOP
typedef utility::pointer::owning_ptr < RNA_RawBaseBaseInfo >	RNA_RawBaseBaseInfoOP
typedef utility::pointer::access_ptr < RNA_RawBaseBaseInfo >	RNA_RawBaseBaseInfoAP
typedef utility::pointer::owning_ptr < RNA_ScoringInfo >	RNA_ScoringInfoOP
typedef utility::pointer::owning_ptr < RNA_SugarCloseEnergy >	RNA_SugarCloseEnergyOP
typedef utility::pointer::owning_ptr < RNA_SugarCloseEnergy const >	RNA_SugarCloseEnergyCOP
typedef utility::pointer::owning_ptr < RNA_TorsionEnergy >	RNA_TorsionEnergyOP
typedef utility::pointer::owning_ptr < RNA_TorsionEnergy const >	RNA_TorsionEnergyCOP
typedef utility::pointer::owning_ptr < RNA_TorsionPotential >	RNA_TorsionPotentialOP
typedef utility::pointer::owning_ptr < RNA_TorsionPotential const >	RNA_TorsionPotentialCOP

Functions
Size	rna_residue_name_to_num (char const c)
Size	get_position_in_vector (utility::vector1< std::string > &vec, std::string const element)
RNA_ScoringInfo const &	rna_scoring_info_from_pose (pose::Pose const &pose)
RNA_ScoringInfo &	nonconst_rna_scoring_info_from_pose (pose::Pose &pose)
void	get_fade_correction (Real const z, Real const cutoff_lower, Real const cutoff_upper, Real const fade_zone, Real &fade_value, Real &fade_deriv)

Typedef Documentation

typedef std::pair< Real, Base_pair > core::scoring::rna::Energy_base_pair

typedef std::list< Energy_base_pair > core::scoring::rna::Energy_base_pair_list

typedef std::pair< Real, Base_stack > core::scoring::rna::Energy_base_stack

typedef std::list< Energy_base_stack > core::scoring::rna::Energy_base_stack_list

typedef numeric::xyzMatrix< Real > core::scoring::rna::Matrix

typedef utility::pointer::owning_ptr< RNA_AtomVDW const > core::scoring::rna::RNA_AtomVDWCOP

typedef utility::pointer::owning_ptr< RNA_AtomVDW > core::scoring::rna::RNA_AtomVDWOP

typedef utility::pointer::owning_ptr< RNA_CentroidInfo > core::scoring::rna::RNA_CentroidInfoOP

typedef utility::vector1< RNA_Datum > core::scoring::rna::RNA_Data

typedef utility::pointer::access_ptr< RNA_DataInfo > core::scoring::rna::RNA_DataInfoAP

typedef utility::pointer::owning_ptr< RNA_DataInfo > core::scoring::rna::RNA_DataInfoOP

typedef utility::pointer::owning_ptr< RNA_FilteredBaseBaseInfo > core::scoring::rna::RNA_FilteredBaseBaseInfoOP

typedef utility::pointer::owning_ptr< RNA_FullAtomVDW_BasePhosphate const > core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCOP

typedef utility::pointer::owning_ptr< RNA_FullAtomVDW_BasePhosphate > core::scoring::rna::RNA_FullAtomVDW_BasePhosphateOP

typedef utility::pointer::owning_ptr< RNA_LowResolutionPotential > core::scoring::rna::RNA_LowResolutionPotentialOP

typedef utility::pointer::owning_ptr< RNA_Mg_KnowledgeBasedPotential const > core::scoring::rna::RNA_Mg_KnowledgeBasedPotentialCOP

typedef utility::pointer::owning_ptr< RNA_Mg_KnowledgeBasedPotential > core::scoring::rna::RNA_Mg_KnowledgeBasedPotentialOP

typedef utility::pointer::access_ptr< RNA_RawBaseBaseInfo > core::scoring::rna::RNA_RawBaseBaseInfoAP

typedef utility::pointer::owning_ptr< RNA_RawBaseBaseInfo > core::scoring::rna::RNA_RawBaseBaseInfoOP

typedef utility::pointer::owning_ptr< RNA_ScoringInfo > core::scoring::rna::RNA_ScoringInfoOP

typedef utility::pointer::owning_ptr< RNA_SugarCloseEnergy const > core::scoring::rna::RNA_SugarCloseEnergyCOP

typedef utility::pointer::owning_ptr< RNA_SugarCloseEnergy > core::scoring::rna::RNA_SugarCloseEnergyOP

typedef utility::pointer::owning_ptr< RNA_TorsionEnergy const > core::scoring::rna::RNA_TorsionEnergyCOP

typedef utility::pointer::owning_ptr< RNA_TorsionEnergy > core::scoring::rna::RNA_TorsionEnergyOP

typedef utility::pointer::owning_ptr< RNA_TorsionPotential const > core::scoring::rna::RNA_TorsionPotentialCOP

typedef utility::pointer::owning_ptr< RNA_TorsionPotential > core::scoring::rna::RNA_TorsionPotentialOP

typedef numeric::xyzVector< core::Real > core::scoring::rna::Vector

Function Documentation

void core::scoring::rna::get_fade_correction	(	Real const	z,
		Real const	cutoff_lower,
		Real const	cutoff_upper,
		Real const	fade_zone,
		Real &	fade_value,
		Real &	fade_deriv
	)

Referenced by core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential(), core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential_RNA(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_base_backbone_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy(), and core::scoring::rna::RNA_LowResolutionPotential::get_rna_stack_score().

Size core::scoring::rna::get_position_in_vector	(	utility::vector1< std::string > &	vec,
		std::string const	element
	)

Referenced by core::scoring::rna::RNA_AtomVDW::RNA_AtomVDW().

RNA_ScoringInfo & core::scoring::rna::nonconst_rna_scoring_info_from_pose

(

pose::Pose &

pose

)

Either returns a non-const reference to the rna_scoring object already stored in the pose, or creates a new rna scoring info object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), core::pose::datacache::CacheableDataType::RNA_SCORING_INFO, basic::datacache::BasicDataCache::set(), and core::pose::Pose::total_residue().

Referenced by core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::scoring::rna::RG_Energy_RNA::finalize_total_energy(), core::scoring::rna::RNA_BaseBaseEnergy::finalize_total_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::finalize_total_energy(), core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), core::scoring::rna::RNA_BaseBaseEnergy::setup_for_derivatives(), core::scoring::rna::StackElecEnergy::setup_for_derivatives(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_derivatives(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_packing(), core::scoring::rna::StackElecEnergy::setup_for_packing(), core::scoring::rna::RG_Energy_RNA::setup_for_scoring(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_scoring(), core::scoring::rna::RNA_DataBackboneEnergy::setup_for_scoring(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::scoring::rna::StackElecEnergy::setup_for_scoring(), core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_centroid_info().

Size core::scoring::rna::rna_residue_name_to_num

(

char const

c

)

References core::scoring::tr, and utility_exit_with_message.

Referenced by core::scoring::rna::RNA_AtomVDW::bump_parameter(), and core::scoring::rna::RNA_AtomVDW::RNA_AtomVDW().

RNA_ScoringInfo const & core::scoring::rna::rna_scoring_info_from_pose

(

pose::Pose const &

pose

)

Pose must already contain a rna_scoring_info object or this method will fail.

References core::pose::Pose::data(), basic::datacache::BasicDataCache::get_const_ptr(), basic::datacache::BasicDataCache::has(), and core::pose::datacache::CacheableDataType::RNA_SCORING_INFO.

Referenced by core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::rna::RNA_Mg_Energy::residue_pair_energy(), core::scoring::rna::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::rna::RNA_Mg_Energy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), and core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way().