Rosetta Core  2014.35
Namespaces | Classes | Typedefs | Functions
core::scoring::rna Namespace Reference

Namespaces

 chemical_shift
 
 data
 

Classes

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_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_JR_SuiteEnergy
 
class  RNA_JR_SuiteEnergyCreator
 
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_SuiteEnergy
 
class  RNA_SuiteEnergyCreator
 
class  RNA_SuitePotential
 
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 numeric::xyzMatrix< RealMatrix
 
typedef
utility::pointer::owning_ptr
< RNA_CentroidInfo
RNA_CentroidInfoOP
 
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_SuitePotential
RNA_SuitePotentialOP
 
typedef
utility::pointer::owning_ptr
< RNA_SuitePotential const > 
RNA_SuitePotentialCOP
 
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_ScoringInfononconst_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

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 
)
Size core::scoring::rna::get_position_in_vector ( utility::vector1< std::string > &  vec,
std::string const  element 
)
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::pose::rna::bases_are_coplanar(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::pose::rna::figure_out_base_pair_orientation(), core::io::rna::RNA_DataReader::fill_rna_data_info(), 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::io::rna::get_rna_data_info(), 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::RNA_PairwiseLowResolutionEnergy::setup_for_scoring(), core::scoring::rna::RG_Energy_RNA::setup_for_scoring(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::scoring::rna::data::RNA_DataBackboneEnergy::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)
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::data::RNA_ChemicalMappingEnergy::calculate_energy(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::data::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::pose::rna::get_number_base_stacks(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status(), core::io::rna::get_rna_data_info(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::rna::RNA_Mg_Energy::residue_pair_energy(), core::scoring::rna::data::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().