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core::scoring::rna Namespace Reference

Namespaces

 chemical_shift
 

Classes

class  Gaussian_parameter
 
class  RG_Energy_RNA
 
class  RG_Energy_RNACreator
 
class  RNA_AtomVDW
 
class  RNA_BaseBaseEnergy
 
class  Base_pair
 
class  Base_stack
 
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_Datum
 
class  RNA_DataInfo
 Keep track of RNA centroid information inside the pose. More...
 
class  RNA_FA_Stack
 
class  RNA_FilteredBaseBaseInfo
 Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...
 
class  RNA_FittedTorsionInfo
 
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
 

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< RealMatrix
 
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::vector1
< Gaussian_parameter
Gaussian_parameter_set
 
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
 

Enumerations

enum  _RNA_FittedTorsionInfo_ {
  WHATEVER, ALPHA, BETA, GAMMA,
  DELTA, EPSILON, ZETA, CHI,
  NU2, NU1, O2H
}
 
enum  __RNA_UTIL__ {
  X, WATSON_CRICK, HOOGSTEEN, SUGAR,
  O2STAR, PHOSPHATE
}
 

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)
 
Size convert_acgu_to_1234 (char const c)
 
char get_edge_from_num (Size const num)
 
std::string get_full_edge_from_num (Size const num)
 
char get_orientation_from_num (Size const num)
 
std::string get_full_orientation_from_num (Size const num)
 
std::string get_full_LW_orientation_from_num (Size const num)
 
std::string const first_base_atom (conformation::Residue const &rsd)
 
bool is_purine (conformation::Residue const &rsd)
 
Size first_base_atom_index (conformation::Residue const &rsd)
 
std::string const chi1_torsion_atom (conformation::Residue const &rsd)
 
Size chi1_torsion_atom_index (conformation::Residue const &rsd)
 
std::string const default_jump_atom (conformation::Residue const &rsd)
 
bool possibly_canonical (chemical::AA const &aa1, chemical::AA const &aa2)
 
bool possibly_canonical_strict (chemical::AA const &aa1, chemical::AA const &aa2)
 
void get_watson_crick_base_pair_atoms (chemical::AA const &aa1, chemical::AA const &aa2, std::string &atom1, std::string &atom2)
 
void get_watson_crick_base_pair_atoms (chemical::AA const &aa1, chemical::AA const &aa2, utility::vector1< std::string > &atom_ids1, utility::vector1< std::string > &atom_ids2)
 
bool is_cutpoint_open (core::pose::Pose const &pose, Size const i)
 
bool is_rna_chainbreak (core::pose::Pose const &pose, Size const i)
 
void initialize_non_main_chain_sugar_atoms ()
 
void fix_sugar_coords_WORKS_BUT_SLOW (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< utility::vector1< id::DOF_Type > > which_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::Size const &i)
 
void prepare_scratch_residue (core::conformation::ResidueOP &scratch_rsd, core::conformation::Residue const &start_rsd, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose const &pose)
 
void fix_sugar_coords (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::pose::Pose const &reference_pose, core::Size const &i)
 
void initialize_atoms_for_which_we_need_new_dofs (utility::vector1< std::string > &atoms_for_which_we_need_new_dofs, pose::Pose const &pose, Size const &i)
 
void apply_non_main_chain_sugar_coords (utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::pose::Pose const &reference_pose, core::Size const &i)
 
void apply_ideal_c2endo_sugar_coords (core::pose::Pose &pose, core::Size const &i)
 
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)
 
Vector get_rna_base_centroid (conformation::Residue const &rsd, bool verbose)
 
numeric::xyzMatrix< core::Realget_rna_base_coordinate_system (conformation::Residue const &rsd, Vector const &centroid)
 
bool Is_base_phosphate_atom_pair (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const atomno_1, Size const atomno_2)
 
Size const NUM_EDGES (3)
 
Size const NUM_RNA_TORSIONS (10)
 
Size const NUM_RNA_MAINCHAIN_TORSIONS (6)
 
Size const NUM_RNA_CHI_TORSIONS (NUM_RNA_TORSIONS-NUM_RNA_MAINCHAIN_TORSIONS)
 
numeric::xyzMatrix< core::Realget_rna_base_coordinate_system (core::conformation::Residue const &rsd, numeric::xyzVector< core::Real > const &centroid)
 

Variables

utility::vector1< std::string > non_main_chain_sugar_atoms
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
X 
WATSON_CRICK 
HOOGSTEEN 
SUGAR 
O2STAR 
PHOSPHATE 
Enumerator
WHATEVER 
ALPHA 
BETA 
GAMMA 
DELTA 
EPSILON 
ZETA 
CHI 
NU2 
NU1 
O2H 

Function Documentation

void core::scoring::rna::apply_ideal_c2endo_sugar_coords ( core::pose::Pose pose,
core::Size const &  i 
)
void core::scoring::rna::apply_non_main_chain_sugar_coords ( utility::vector1< Vector > const &  non_main_chain_sugar_coords,
core::pose::Pose pose,
core::pose::Pose const &  reference_pose,
core::Size const &  i 
)
std::string const core::scoring::rna::chi1_torsion_atom ( conformation::Residue const &  rsd)
Size core::scoring::rna::chi1_torsion_atom_index ( conformation::Residue const &  rsd)
Size core::scoring::rna::convert_acgu_to_1234 ( char const  c)
std::string const core::scoring::rna::default_jump_atom ( conformation::Residue const &  rsd)
std::string const core::scoring::rna::first_base_atom ( conformation::Residue const &  rsd)
Size core::scoring::rna::first_base_atom_index ( conformation::Residue const &  rsd)
void core::scoring::rna::fix_sugar_coords ( utility::vector1< std::string >  atoms_for_which_we_need_new_dofs,
utility::vector1< Vector > const &  non_main_chain_sugar_coords,
core::pose::Pose pose,
core::pose::Pose const &  reference_pose,
core::Size const &  i 
)
void core::scoring::rna::fix_sugar_coords_WORKS_BUT_SLOW ( utility::vector1< std::string >  atoms_for_which_we_need_new_dofs,
utility::vector1< utility::vector1< id::DOF_Type > >  which_dofs,
utility::vector1< Vector > const &  non_main_chain_sugar_coords,
core::pose::Pose pose,
core::Size const &  i 
)
char core::scoring::rna::get_edge_from_num ( Size const  num)
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 
)
std::string core::scoring::rna::get_full_edge_from_num ( Size const  num)
std::string core::scoring::rna::get_full_LW_orientation_from_num ( Size const  num)
std::string core::scoring::rna::get_full_orientation_from_num ( Size const  num)
char core::scoring::rna::get_orientation_from_num ( Size const  num)
Size core::scoring::rna::get_position_in_vector ( utility::vector1< std::string > &  vec,
std::string const  element 
)
numeric::xyzVector< core::Real > core::scoring::rna::get_rna_base_centroid ( conformation::Residue const &  rsd,
bool  verbose 
)
numeric::xyzMatrix< core::Real > core::scoring::rna::get_rna_base_coordinate_system ( core::conformation::Residue const &  rsd,
numeric::xyzVector< core::Real > const &  centroid 
)
numeric::xyzMatrix< core::Real > core::scoring::rna::get_rna_base_coordinate_system ( conformation::Residue const &  rsd,
Vector const &  centroid 
)
void core::scoring::rna::get_watson_crick_base_pair_atoms ( chemical::AA const &  aa1,
chemical::AA const &  aa2,
std::string &  atom1,
std::string &  atom2 
)
void core::scoring::rna::get_watson_crick_base_pair_atoms ( chemical::AA const &  aa1,
chemical::AA const &  aa2,
utility::vector1< std::string > &  atom_ids1,
utility::vector1< std::string > &  atom_ids2 
)
void core::scoring::rna::initialize_atoms_for_which_we_need_new_dofs ( utility::vector1< std::string > &  atoms_for_which_we_need_new_dofs,
pose::Pose const &  pose,
Size const &  i 
)
void core::scoring::rna::initialize_non_main_chain_sugar_atoms ( )
bool core::scoring::rna::Is_base_phosphate_atom_pair ( conformation::Residue const &  rsd_1,
conformation::Residue const &  rsd_2,
Size const  atomno_1,
Size const  atomno_2 
)
bool core::scoring::rna::is_cutpoint_open ( core::pose::Pose const &  pose,
Size const  i 
)
bool core::scoring::rna::is_purine ( conformation::Residue const &  rsd)
bool core::scoring::rna::is_rna_chainbreak ( core::pose::Pose const &  pose,
Size const  i 
)
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(), core::pose::datacache::CacheableDataType::RNA_SCORING_INFO, and core::pose::Pose::total_residue().

Referenced by protocols::rna::bases_are_coplanar(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), protocols::rna::figure_out_base_pair_orientation(), core::scoring::rna::RG_Energy_RNA::finalize_total_energy(), core::scoring::rna::RNA_BaseBaseEnergy::finalize_total_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::finalize_total_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), core::scoring::rna::RNA_BaseBaseEnergy::setup_for_derivatives(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_derivatives(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_packing(), core::scoring::rna::RG_Energy_RNA::setup_for_scoring(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::scoring::rna::RNA_DataBackboneEnergy::setup_for_scoring(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_scoring(), core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation(), protocols::rna::RNA_DataReader::setup_rna_data(), 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 const core::scoring::rna::NUM_EDGES ( )
Size const core::scoring::rna::NUM_RNA_CHI_TORSIONS ( NUM_RNA_TORSIONS-  NUM_RNA_MAINCHAIN_TORSIONS)
Size const core::scoring::rna::NUM_RNA_MAINCHAIN_TORSIONS ( )
Size const core::scoring::rna::NUM_RNA_TORSIONS ( 10  )
bool core::scoring::rna::possibly_canonical ( chemical::AA const &  aa1,
chemical::AA const &  aa2 
)
bool core::scoring::rna::possibly_canonical_strict ( chemical::AA const &  aa1,
chemical::AA const &  aa2 
)
void core::scoring::rna::prepare_scratch_residue ( core::conformation::ResidueOP scratch_rsd,
core::conformation::Residue const &  start_rsd,
utility::vector1< Vector > const &  non_main_chain_sugar_coords,
core::pose::Pose const &  pose 
)
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)

Variable Documentation

utility::vector1< std::string > core::scoring::rna::non_main_chain_sugar_atoms