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core::chemical::rna Namespace Reference

Classes

class  GaussianParameter
 
class  RNA_FittedTorsionInfo
 
class  RNA_Info
 

Typedefs

typedef
utility::pointer::shared_ptr
< RNA_FittedTorsionInfo
RNA_FittedTorsionInfoOP
 
typedef
utility::pointer::weak_ptr
< RNA_Info
RNA_InfoAP
 
typedef
utility::pointer::weak_ptr
< RNA_Info const > 
RNA_InfoCAP
 
typedef
utility::pointer::shared_ptr
< RNA_Info
RNA_InfoOP
 
typedef
utility::pointer::shared_ptr
< RNA_Info const > 
RNA_InfoCOP
 

Enumerations

enum  BaseEdge {
  ANY_BASE_EDGE, WATSON_CRICK, HOOGSTEEN, SUGAR,
  O2PRIME, PHOSPHATE
}
 
enum  RNA_Torsion {
  ANY_TORSION, ALPHA, BETA, GAMMA,
  DELTA, EPSILON, ZETA, CHI,
  NU2, NU1, O2H
}
 
enum  ChiState { ANY_CHI, ANTI, SYN, NO_CHI }
 
enum  PuckerState { ANY_PUCKER, NORTH, SOUTH, NO_PUCKER }
 
enum  BaseDoubletOrientation { ANY_BASE_DOUBLET_ORIENTATION, ANTIPARALLEL, PARALLEL }
 
enum  LW_BaseDoubletOrientation { ANY_LW_BASE_DOUBLET_ORIENTATION, CIS, TRANS }
 
enum  BaseStackWhichSide { ANY_BASE_STACK_SIDE, ABOVE, BELOW }
 

Functions

static basic::Tracer TR ("core.chemical.rna.RNA_Info")
 
void add_values_from_center (utility::vector1< core::Real > &torsions, Real const center, Real const max_range, Real const bin_size)
 
utility::vector1< Realget_full_torsions (Real const bin_size)
 
utility::vector1< Realget_epsilon_torsions (Real const delta, bool const extra_epsilon, Real const bin_size)
 
utility::vector1< Realget_epsilon_torsions (bool const north_pucker, bool const extra_epsilon, Real const )
 
static basic::Tracer TR ("core.chemical.rna")
 
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)
 
BaseEdge get_edge_from_char (char const e)
 
char get_orientation_from_num (Size const num)
 
std::string get_full_orientation_from_num (Size const num)
 
char get_side_from_num (Size const num)
 
std::string get_full_side_from_num (Size const num)
 
BaseDoubletOrientation get_orientation_from_char (char const o)
 
LW_BaseDoubletOrientation get_LW_orientation_from_char (char const o)
 
std::string get_full_LW_orientation_from_num (Size const num)
 
char get_LW_orientation_from_num (Size const num)
 
std::string const first_base_atom (chemical::ResidueType const &rsd)
 
Size first_base_atom_index (chemical::ResidueType const &rsd)
 
std::string const chi1_torsion_atom (chemical::ResidueType const &rsd)
 
Size chi1_torsion_atom_index (chemical::ResidueType const &rsd)
 
std::string const default_jump_atom (chemical::ResidueType 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)
 
std::string get_WC_atom (core::chemical::AA const &res_type)
 
void get_watson_crick_base_pair_atoms (chemical::ResidueType const &rsd_type1, chemical::ResidueType const &rsd_type2, std::string &atom1, std::string &atom2)
 
void get_base_pair_atoms (chemical::ResidueType const &rsd_type1, chemical::ResidueType const &rsd_type2, utility::vector1< std::string > &atom_ids1, utility::vector1< std::string > &atom_ids2, chemical::rna::BaseEdge const edge1, chemical::rna::BaseEdge const edge2, chemical::rna::LW_BaseDoubletOrientation const orientation)
 
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)
 
core::kinematics::Stub get_rna_base_coordinate_system_stub (core::conformation::Residue const &rsd)
 wrapper around get_rna_base_centroid & get_rna_base_coordinate_system More...
 
bool is_base_phosphate_atom_pair (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const atomno_1, Size const atomno_2)
 
ChiState get_residue_base_state (conformation::Residue const &rsd)
 
PuckerState get_residue_pucker_state (conformation::Residue const &rsd)
 
bool rna_dna_match (core::chemical::AA const &aa1, core::chemical::AA const &aa2)
 
std::string const rna_nts ("acgu")
 
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 >
const 
non_main_chain_sugar_atoms = utility::tools::make_vector1( " C2'", " C1'", " O4'" )
 
utility::vector1< std::string >
const 
atoms_involved_in_phosphate_torsion = utility::tools::make_vector1( " P ", " OP2", " OP1", " O5'", " H5'", "H5''" )
 
utility::vector1< std::string >
const 
non_base_atoms
 
utility::vector1< std::string >
const 
sugar_atoms = utility::tools::make_vector1( " C1'", " C2'", " C3'", " C4'", " C5'", " O2'", " O3'", " O4'", " O5'" )
 

Typedef Documentation

typedef utility::pointer::weak_ptr< RNA_Info > core::chemical::rna::RNA_InfoAP
typedef utility::pointer::weak_ptr< RNA_Info const > core::chemical::rna::RNA_InfoCAP
typedef utility::pointer::shared_ptr< RNA_Info const > core::chemical::rna::RNA_InfoCOP
typedef utility::pointer::shared_ptr< RNA_Info > core::chemical::rna::RNA_InfoOP

Enumeration Type Documentation

Enumerator
ANY_BASE_DOUBLET_ORIENTATION 
ANTIPARALLEL 
PARALLEL 
Enumerator
ANY_BASE_EDGE 
WATSON_CRICK 
HOOGSTEEN 
SUGAR 
O2PRIME 
PHOSPHATE 
Enumerator
ANY_BASE_STACK_SIDE 
ABOVE 
BELOW 
Enumerator
ANY_CHI 
ANTI 
SYN 
NO_CHI 
Enumerator
ANY_LW_BASE_DOUBLET_ORIENTATION 
CIS 
TRANS 
Enumerator
ANY_PUCKER 
NORTH 
SOUTH 
NO_PUCKER 
Enumerator
ANY_TORSION 
ALPHA 
BETA 
GAMMA 
DELTA 
EPSILON 
ZETA 
CHI 
NU2 
NU1 
O2H 

Function Documentation

void core::chemical::rna::add_values_from_center ( utility::vector1< core::Real > &  torsions,
Real const  center,
Real const  max_range,
Real const  bin_size 
)
std::string const core::chemical::rna::chi1_torsion_atom ( chemical::ResidueType const &  rsd)
Size core::chemical::rna::chi1_torsion_atom_index ( chemical::ResidueType const &  rsd)
Size core::chemical::rna::convert_acgu_to_1234 ( char const  c)
std::string const core::chemical::rna::default_jump_atom ( chemical::ResidueType const &  rsd)
std::string const core::chemical::rna::first_base_atom ( chemical::ResidueType const &  rsd)
Size core::chemical::rna::first_base_atom_index ( chemical::ResidueType const &  rsd)
void core::chemical::rna::get_base_pair_atoms ( chemical::ResidueType const &  rsd_type1,
chemical::ResidueType const &  rsd_type2,
utility::vector1< std::string > &  atom_ids1,
utility::vector1< std::string > &  atom_ids2,
chemical::rna::BaseEdge const  edge1,
chemical::rna::BaseEdge const  edge2,
chemical::rna::LW_BaseDoubletOrientation const  orientation 
)
BaseEdge core::chemical::rna::get_edge_from_char ( char const  e)
char core::chemical::rna::get_edge_from_num ( Size const  num)
utility::vector1< Real > core::chemical::rna::get_epsilon_torsions ( Real const  delta,
bool const  extra_epsilon,
Real const  bin_size 
)
utility::vector1< Real > core::chemical::rna::get_epsilon_torsions ( bool const  north_pucker,
bool const  extra_epsilon,
Real  const 
)
std::string core::chemical::rna::get_full_edge_from_num ( Size const  num)
std::string core::chemical::rna::get_full_LW_orientation_from_num ( Size const  num)
std::string core::chemical::rna::get_full_orientation_from_num ( Size const  num)
std::string core::chemical::rna::get_full_side_from_num ( Size const  num)

for stacking

References ABOVE, ANY_BASE_STACK_SIDE, and BELOW.

Referenced by core::pose::rna::operator<<().

utility::vector1< Real > core::chemical::rna::get_full_torsions ( Real const  bin_size)
LW_BaseDoubletOrientation core::chemical::rna::get_LW_orientation_from_char ( char const  o)
char core::chemical::rna::get_LW_orientation_from_num ( Size const  num)
BaseDoubletOrientation core::chemical::rna::get_orientation_from_char ( char const  o)
char core::chemical::rna::get_orientation_from_num ( Size const  num)
ChiState core::chemical::rna::get_residue_base_state ( conformation::Residue const &  rsd)
PuckerState core::chemical::rna::get_residue_pucker_state ( conformation::Residue const &  rsd)
numeric::xyzVector< core::Real > core::chemical::rna::get_rna_base_centroid ( conformation::Residue const &  rsd,
bool  verbose 
)

References core::chemical::rna::RNA_Info::atom_is_virtual(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atomic_charge(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_NA(), core::conformation::Residue::is_polymer(), core::chemical::AtomType::is_repulsive(), core::conformation::Residue::is_RNA(), core::chemical::AtomType::name(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name(), core::conformation::Residue::nheavyatoms(), core::chemical::rna::RNA_Info::o2prime_index(), core::conformation::Residue::RNA_info(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::toolbox::sample_around::centroid_dist(), protocols::stepwise::screener::CentroidDistanceScreener::check_screen(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::RNA_CentroidInfo::get_base_centroid(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz(), get_rna_base_coordinate_system_stub(), core::scoring::rna::get_rna_motifs(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResStackEnergy::residue_pair_energy(), protocols::toolbox::rigid_body::set_to_origin(), core::scoring::rna::RNP_LowResEnergy::setup_for_scoring(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker(), and protocols::recces::sampler::rna::MC_RNA_OneJump::update().

numeric::xyzMatrix< core::Real > core::chemical::rna::get_rna_base_coordinate_system ( core::conformation::Residue const &  rsd,
numeric::xyzVector< core::Real > const &  centroid 
)
numeric::xyzMatrix< core::Real > core::chemical::rna::get_rna_base_coordinate_system ( conformation::Residue const &  rsd,
Vector const &  centroid 
)
core::kinematics::Stub core::chemical::rna::get_rna_base_coordinate_system_stub ( core::conformation::Residue const &  rsd)
char core::chemical::rna::get_side_from_num ( Size const  num)
void core::chemical::rna::get_watson_crick_base_pair_atoms ( chemical::ResidueType const &  rsd_type1,
chemical::ResidueType const &  rsd_type2,
std::string &  atom1,
std::string &  atom2 
)
std::string core::chemical::rna::get_WC_atom ( core::chemical::AA const &  res_type)
bool core::chemical::rna::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 core::chemical::rna::NUM_EDGES ( )
Size const core::chemical::rna::NUM_RNA_CHI_TORSIONS ( NUM_RNA_TORSIONS-  NUM_RNA_MAINCHAIN_TORSIONS)
Size const core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS ( )
Size const core::chemical::rna::NUM_RNA_TORSIONS ( 10  )
bool core::chemical::rna::possibly_canonical ( chemical::AA const &  aa1,
chemical::AA const &  aa2 
)
bool core::chemical::rna::possibly_canonical_strict ( chemical::AA const &  aa1,
chemical::AA const &  aa2 
)
bool core::chemical::rna::rna_dna_match ( core::chemical::AA const &  aa1,
core::chemical::AA const &  aa2 
)
std::string const core::chemical::rna::rna_nts ( "acgu"  )
static basic::Tracer core::chemical::rna::TR ( "core.chemical.rna.RNA_Info"  )
static

Referenced by protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::modeler::rna::rigid_body::analyze_base_bin_map(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::pose::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::rna::atom_square_deviation(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), protocols::stepwise::modeler::rna::choose_random_if_unspecified_nucleotide(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::cluster(), core::scoring::rna::RNP_LowResPairDistPotential::convert_aa_to_index(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_tags_map(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_tag(), core::pose::rna::detect_base_contacts(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::do_some_clustering(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), core::pose::rna::figure_out_secstruct(), protocols::stepwise::modeler::rna::freeze_sugar_torsions(), get_base_pair_atoms(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), core::pose::rna::get_rigid_body_jumps(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pose::rna::has_virtual_rna_residue_variant_type(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initial_pose_setup(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose(), core::scoring::rna::RNP_LowResPairDistPotential::initialize_rnp_pair_dist(), core::scoring::rna::RNP_LowResStackData::initialize_rnp_stack_xy(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_sequence_information(), protocols::stepwise::modeler::rna::rigid_body::initialize_xyz_parameters(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_initialization_pdb_numbering_setup(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_pdb_numbering_setup(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_silent_numbering_setup(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), protocols::stepwise::modeler::rna::is_residues_in_contact(), core::pose::rna::is_rna_chainbreak(), core::pose::rna::is_tna_chainbreak(), core::pose::rna::is_torsion_valid(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::stepwise::modeler::rna::o2prime_trials(), core::pose::rna::output_boolean(), protocols::stepwise::modeler::rna::output_rotamer(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::pass_FARFAR_no_auto_bulge_filter(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_rmsd(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_heavy_atoms(), protocols::stepwise::modeler::rna::print_individual_atom_info(), core::pose::rna::print_torsion_info(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::modeler::rna::rescale_scorefxn(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup(), core::pose::rna::setup_base_pair_constraints(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_final_res_lists(), protocols::stepwise::modeler::rna::show_scorefxn_weight_lines(), protocols::stepwise::modeler::rna::suite_rmsd(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::two_stage_clustering(), and core::pose::rna::virtualize_free_rna_moieties().

static basic::Tracer core::chemical::rna::TR ( "core.chemical.rna"  )
static

Variable Documentation

utility::vector1< std::string > const core::chemical::rna::atoms_involved_in_phosphate_torsion = utility::tools::make_vector1( " P ", " OP2", " OP1", " O5'", " H5'", "H5''" )
utility::vector1< std::string > const core::chemical::rna::non_base_atoms
Initial value:
= utility::tools::make_vector1(
" P ", " OP2", " OP1", " O5'", " C4'", " O4'", " C3'", " O3'", " C1'",
" C2'", " O2'", " H5'", "H5''", " H4'", " H3'", " H2'", "HO2'", " H1'" )

Referenced by core::pose::rna::RNA_IdealCoord::apply_coords().

utility::vector1< std::string > const core::chemical::rna::non_main_chain_sugar_atoms = utility::tools::make_vector1( " C2'", " C1'", " O4'" )
utility::vector1< std::string > const core::chemical::rna::sugar_atoms = utility::tools::make_vector1( " C1'", " C2'", " C3'", " C4'", " C5'", " O2'", " O3'", " O4'", " O5'" )