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protocols::rna Namespace Reference

Classes

class  TorsionSet
 
class  FragmentLibrary
 
class  FullAtomRNA_Fragments
 
class  MultipleDomainMover
 The RNA de novo structure modeling protocol. More...
 
class  ChunkSet
 
class  RNA_ChunkLibrary
 
class  RNA_DataReader
 
class  RNA_DeNovoProtocol
 The RNA de novo structure modeling protocol. More...
 
class  RNA_FragmentMover
 The RNA de novo structure modeling protocol. More...
 
class  RNA_Fragments
 
class  RNA_HelixAssembler
 The RNA de novo structure modeling protocol. More...
 
class  RNA_IdealCoord
 
class  BasePairType
 
class  RNA_PairingTemplate
 
class  RNA_JumpLibrary
 
class  RNA_LoopCloser
 The RNA de novo structure modeling protocol. More...
 
class  RNA_Minimizer
 The RNA de novo structure modeling protocol. More...
 
class  RNA_Relaxer
 The RNA de novo structure modeling protocol. More...
 
class  RNA_SecStructInfo
 Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...
 
class  RNA_Pairing
 
class  RNA_StructureParameters
 
class  suite_info
 
class  RNA_suite_list
 

Typedefs

typedef
utility::pointer::owning_ptr
< FragmentLibrary > 		FragmentLibraryOP
 
typedef std::pair< std::string,
std::string > 		SequenceSecStructPair
 
typedef std::map
< SequenceSecStructPair,
FragmentLibraryOP > 		FragmentLibraryPointerMap
 
typedef
utility::pointer::owning_ptr
< MultipleDomainMover > 		MultipleDomainMoverOP
 
typedef numeric::xyzMatrix< Real > Matrix
 
typedef
utility::pointer::owning_ptr
< RNA_ChunkLibrary > 		RNA_ChunkLibraryOP
 
typedef
utility::pointer::owning_ptr
< ChunkSet > 		ChunkSetOP
 
typedef
utility::pointer::owning_ptr
< RNA_DataReader > 		RNA_DataReaderOP
 
typedef
utility::pointer::owning_ptr
< RNA_FragmentMover > 		RNA_FragmentMoverOP
 
typedef
utility::pointer::owning_ptr
< RNA_Fragments > 		RNA_FragmentsOP
 
typedef
utility::pointer::owning_ptr
< RNA_HelixAssembler > 		RNA_HelixAssemblerOP
 
typedef
utility::pointer::owning_ptr
< RNA_IdealCoord > 		RNA_IdealCoordOP
 
typedef
utility::pointer::access_ptr
< RNA_IdealCoord > 		RNA_IdealCoordAP
 
typedef
utility::pointer::owning_ptr
< RNA_JumpLibrary > 		RNA_JumpLibraryOP
 
typedef
utility::pointer::owning_ptr
< RNA_PairingTemplate > 		RNA_PairingTemplateOP
 
typedef utility::vector1
< RNA_PairingTemplateOP > 		RNA_PairingTemplateList
 
typedef std::map< BasePairType,
RNA_PairingTemplateList > 		RNA_PairingTemplateMap
 
typedef
utility::pointer::owning_ptr
< RNA_LoopCloser > 		RNA_LoopCloserOP
 
typedef
utility::pointer::owning_ptr
< RNA_Minimizer > 		RNA_MinimizerOP
 
typedef numeric::xyzVector
< core::Real > 		Vector
 
typedef
utility::pointer::owning_ptr
< RNA_Relaxer > 		RNA_RelaxerOP
 
typedef
utility::pointer::owning_ptr
< RNA_SecStructInfo > 		RNA_SecStructInfoOP
 
typedef
utility::pointer::owning_ptr
< RNA_StructureParameters > 		RNA_StructureParametersOP
 
typedef utility::vector1
< RNA_Pairing > 		RNA_PairingList
 

Enumerations

enum  MATCH_ENUM { MATCH_ALL, MATCH_YR, MATCH_EXACT }
 name MATCH_ENUM added for PyRosetta compatability More...
 
enum  _RNA_MatchType_ { MATCH_ALL, MATCH_YR, MATCH_EXACT }
 

Functions

void update_edge_hbond_numbers (conformation::Residue const &rsd, Size const &atm, Size &N_W, Size &N_H, Size &N_S)
 
void update_edge_hbond_numbers_careful_hydrogen (conformation::Residue const &rsd, Size const &atm, conformation::Residue const &other_rsd, Size const &other_atm, Size &N_W, Size &N_H, Size &N_S)
 
bool atom_is_polar (core::conformation::Residue const &rsd, Size const &atm)
 
bool heavy_atom_is_polar (core::conformation::Residue const &rsd, Size const &atm)
 
bool atom_is_acceptor (core::conformation::Residue const &rsd, Size const &atm)
 
void figure_out_number_base_contacts (conformation::Residue const &rsd_i, conformation::Residue const &rsd_j, Size &edge_classification)
 
Size figure_out_base_pair_orientation (core::pose::Pose &pose, Size const &i, Size const &j)
 
bool residue_is_bulge (pose::Pose const &pose, Size const i)
 
Size bases_form_a_hydrogen_bond (core::scoring::hbonds::HBondSetOP const &hbond_set, core::pose::Pose &pose, Size const &i, Size const &j)
 
bool bases_are_coplanar (core::pose::Pose &pose, Size const &i, Size const &j)
 
void classify_base_pairs (core::pose::Pose const &pose_input, utility::vector1< core::scoring::rna::Base_pair > &base_pair_list, utility::vector1< bool > &is_bulged)
 
Size get_number_base_stacks (core::pose::Pose const &pose_input)
 
static basic::Tracer tr ("protocols.rna.rna_structure_parameters")
 
static
numeric::random::RandomGenerator 		RG (12320)
 
static basic::Tracer TR ("protocols.rna.rna_denovo_protocol")
 
bool check_in_base_pair_list (scoring::rna::Base_pair const &base_pair, utility::vector1< core::scoring::rna::Base_pair > const &base_pair_list)
 
static
numeric::random::RandomGenerator 		RG (17720)
 
static
numeric::random::RandomGenerator 		RG (144621)
 
static basic::Tracer tr ("protocols.rna.rna_jump_library")
 
void figure_out_reasonable_rna_fold_tree (pose::Pose &pose)
 
void get_base_pairing_info (pose::Pose const &pose, Size const &seqpos, char &secstruct, FArray1D< bool > &edge_is_base_pairing)
 
void get_base_pairing_list (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > &base_pairing_list)
 
void figure_out_secstruct (pose::Pose &pose)
 
void create_rna_vall_torsions (pose::Pose &pose, utility::io::ozstream &torsions_out, utility::vector1< Size > const &exclude_res_list)
 
void create_rna_vall_torsions (pose::Pose &pose, std::string const outfile, utility::vector1< Size > const &exclude_res_list)
 
Real get_o1p_o2p_sign (pose::Pose const &pose)
 
Real get_o1p_o2p_sign (pose::Pose const &pose, Size res_num)
 
void assert_phosphate_nomenclature_matches_mini (pose::Pose const &pose)
 
void ensure_phosphate_nomenclature_matches_mini (pose::Pose &pose)
 
void make_phosphate_nomenclature_matches_mini (pose::Pose &pose)
 
void export_packer_results (utility::vector1< std::pair< Real, std::string > > &results, utility::vector1< pose::PoseOP > pose_list, scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dump)
 
void check_base_pair (pose::Pose &pose, FArray1D_int &struct_type)
 
void setup_base_pair_constraints (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > const &pairings, Real const suppress_factor)
 
void setup_coarse_chainbreak_constraints (pose::Pose &pose, Size const &n)
 
std::string const convert_based_on_match_type (std::string const RNA_string, Size const type)
 
bool compare_RNA_char (char const char1, char const char2)
 
bool compare_RNA_secstruct (char const char1, char const char2)
 
Vector get_sugar_centroid (core::conformation::Residue const &rsd)
 
void make_extended_coarse_pose (pose::Pose &coarse_pose, std::string const &full_sequence)
 
void make_coarse_pose (pose::Pose const &pose, pose::Pose &coarse_pose)
 
void remove_cutpoint_closed (pose::Pose &pose, Size const i)
 
void remove_cutpoints_closed (pose::Pose &pose)
 
void virtualize_5prime_phosphates (pose::Pose &pose)
 
void print_internal_coords (core::pose::Pose const &pose)
 
bool possible_root (core::kinematics::FoldTree const &f, core::Size const &n)
 
utility::vector1< Size > get_rigid_body_jumps (core::pose::Pose const &pose)
 
bool let_rigid_body_jumps_move (core::kinematics::MoveMap &movemap, pose::Pose const &pose, bool const move_first_rigid_body)
 
void translate_virtual_anchor_to_first_rigid_body (pose::Pose &pose)
 
void get_base_pairing_info (core::pose::Pose const &pose, core::Size const &seqpos, char &secstruct, ObjexxFCL::FArray1D< bool > &edge_is_base_pairing)
 
void get_base_pairing_list (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &base_pairing_list)
 
void export_packer_results (utility::vector1< std::pair< core::Real, std::string > > &results, utility::vector1< core::pose::PoseOP > pose_list, core::scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dumo=false)
 
void check_base_pair (core::pose::Pose &pose, ObjexxFCL::FArray1D_int &struct_type)
 
void setup_base_pair_constraints (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const &pairings, core::Real const suppress_factor=1.0)
 
bool is_num_in_list (core::Size const i, utility::vector1< core::Size > const &list)
 
std::string const & get_rna_secstruct (core::pose::Pose &pose)
 
void set_rna_secstruct (core::pose::Pose &pose, std::string const rna_secstruct_string)
 
static
numeric::random::RandomGenerator 		RG (144620)
 
static basic::Tracer tr ("protocols.rna.rna_structure_parameters")
 
bool in_list (Size const &pos, utility::vector1< Size > const &res_list)
 
Real distance_4d (utility::vector1< Real > const &torsion1, utility::vector1< Real > const &torsion2, Size const (&half_width)[7])
 
Real distance_7d (utility::vector1< Real > const &torsion1, utility::vector1< Real > const &torsion2, Size const (&half_width)[7])
 
Size string_find (std::string const input_string, const std::string *string_list_first, const std::string *string_list_last)
 
bool is_in_between (utility::vector1< Real > const &target, utility::vector1< Real > const &dominant, utility::vector1< Real > const &satellite)
 
std::pair< std::string,
std::pair< Size, Real > > 		suite_assign (pose::Pose const &pose, Size const res)
 

Typedef Documentation

typedef utility::pointer::owning_ptr< ChunkSet > protocols::rna::ChunkSetOP

Definition at line 31 of file RNA_ChunkLibrary.fwd.hh.

typedef utility::pointer::owning_ptr< FragmentLibrary > protocols::rna::FragmentLibraryOP

Definition at line 24 of file FullAtomRNA_Fragments.fwd.hh.

typedef std::map< SequenceSecStructPair, FragmentLibraryOP > protocols::rna::FragmentLibraryPointerMap

Definition at line 122 of file FullAtomRNA_Fragments.hh.

typedef numeric::xyzMatrix< Real > protocols::rna::Matrix

Definition at line 349 of file RNA_BasePairClassifier.cc.

typedef utility::pointer::owning_ptr< MultipleDomainMover > protocols::rna::MultipleDomainMoverOP

Definition at line 23 of file MultipleDomainMover.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_ChunkLibrary > protocols::rna::RNA_ChunkLibraryOP

Definition at line 28 of file RNA_ChunkLibrary.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_DataReader > protocols::rna::RNA_DataReaderOP

Definition at line 22 of file RNA_DataReader.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_FragmentMover > protocols::rna::RNA_FragmentMoverOP

Definition at line 24 of file RNA_FragmentMover.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_Fragments > protocols::rna::RNA_FragmentsOP

Definition at line 22 of file RNA_Fragments.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_HelixAssembler > protocols::rna::RNA_HelixAssemblerOP

Definition at line 22 of file RNA_HelixAssembler.fwd.hh.

typedef utility::pointer::access_ptr< RNA_IdealCoord > protocols::rna::RNA_IdealCoordAP

Definition at line 28 of file RNA_IdealCoord.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_IdealCoord > protocols::rna::RNA_IdealCoordOP

Definition at line 26 of file RNA_IdealCoord.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_JumpLibrary > protocols::rna::RNA_JumpLibraryOP

Definition at line 22 of file RNA_JumpLibrary.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_LoopCloser > protocols::rna::RNA_LoopCloserOP

Definition at line 21 of file RNA_LoopCloser.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_Minimizer > protocols::rna::RNA_MinimizerOP

Definition at line 19 of file RNA_Minimizer.fwd.hh.

typedef utility::vector1< RNA_Pairing > protocols::rna::RNA_PairingList

Definition at line 50 of file RNA_StructureParameters.hh.

typedef utility::vector1< RNA_PairingTemplateOP > protocols::rna::RNA_PairingTemplateList

Definition at line 114 of file RNA_JumpLibrary.hh.

typedef std::map< BasePairType, RNA_PairingTemplateList > protocols::rna::RNA_PairingTemplateMap

Definition at line 115 of file RNA_JumpLibrary.hh.

typedef utility::pointer::owning_ptr< RNA_PairingTemplate > protocols::rna::RNA_PairingTemplateOP

Definition at line 110 of file RNA_JumpLibrary.hh.

typedef utility::pointer::owning_ptr< RNA_Relaxer > protocols::rna::RNA_RelaxerOP

Definition at line 21 of file RNA_Relaxer.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_SecStructInfo > protocols::rna::RNA_SecStructInfoOP

Definition at line 31 of file RNA_SecStructInfo.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_StructureParameters > protocols::rna::RNA_StructureParametersOP

Definition at line 22 of file RNA_StructureParameters.fwd.hh.

typedef std::pair< std::string, std::string > protocols::rna::SequenceSecStructPair

Definition at line 121 of file FullAtomRNA_Fragments.hh.

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

Definition at line 43 of file RNA_ProtocolUtil.hh.

Enumeration Type Documentation

enum protocols::rna::_RNA_MatchType_
Enumerator
MATCH_ALL 
MATCH_YR 
MATCH_EXACT 

Definition at line 48 of file RNA_MatchType.hh.

enum protocols::rna::MATCH_ENUM

name MATCH_ENUM added for PyRosetta compatability

Enumerator
MATCH_ALL 
MATCH_YR 
MATCH_EXACT 

Definition at line 56 of file RNA_FragmentsClasses.hh.

Function Documentation

void protocols::rna::assert_phosphate_nomenclature_matches_mini ( pose::Pose const &  pose)

Definition at line 467 of file RNA_ProtocolUtil.cc.

References get_o1p_o2p_sign(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

bool protocols::rna::atom_is_acceptor ( core::conformation::Residue const &  rsd,
Size const &  atm 
)

Definition at line 247 of file RNA_BasePairClassifier.cc.

References core::conformation::Residue::accpt_pos().

Referenced by figure_out_number_base_contacts().

bool protocols::rna::atom_is_polar ( core::conformation::Residue const &  rsd,
Size const &  atm 
)

Definition at line 219 of file RNA_BasePairClassifier.cc.

References core::conformation::Residue::Hpos_polar().

bool protocols::rna::bases_are_coplanar ( core::pose::Pose &  pose,
Size const &  i,
Size const &  j 
)

Definition at line 503 of file RNA_BasePairClassifier.cc.

References core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().

Referenced by classify_base_pairs().

Size protocols::rna::bases_form_a_hydrogen_bond ( core::scoring::hbonds::HBondSetOP const &  hbond_set,
core::pose::Pose &  pose,
Size const &  i,
Size const &  j 
)

Definition at line 407 of file RNA_BasePairClassifier.cc.

References core::conformation::Residue::atom_base(), core::scoring::hbonds::HBond::don_res(), core::conformation::Residue::first_sidechain_atom(), and core::pose::Pose::residue().

Referenced by classify_base_pairs().

void protocols::rna::check_base_pair ( core::pose::Pose &  pose,
ObjexxFCL::FArray1D_int &  struct_type 
)
void protocols::rna::check_base_pair ( pose::Pose &  pose,
FArray1D_int &  struct_type 
)

Definition at line 604 of file RNA_ProtocolUtil.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, core::scoring::rna::Base_pair::orientation, core::scoring::rna::possibly_canonical(), core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, core::pose::Pose::residue(), core::scoring::RNA_LORES_WTS, core::scoring::rna::rna_scoring_info_from_pose(), core::pose::Pose::total_residue(), and core::scoring::rna::WATSON_CRICK.

bool protocols::rna::check_in_base_pair_list ( scoring::rna::Base_pair const &  base_pair,
utility::vector1< core::scoring::rna::Base_pair > const &  base_pair_list 
)

Definition at line 1067 of file RNA_DeNovoProtocol.cc.

References core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, in_list(), core::scoring::rna::Base_pair::orientation, core::scoring::rna::Base_pair::res1, and core::scoring::rna::Base_pair::res2.

Referenced by protocols::rna::RNA_DeNovoProtocol::add_number_native_base_pairs().

void protocols::rna::classify_base_pairs ( core::pose::Pose const &  pose_input,
utility::vector1< core::scoring::rna::Base_pair > &  base_pair_list,
utility::vector1< bool > &  is_bulged 
)

Definition at line 560 of file RNA_BasePairClassifier.cc.

References bases_are_coplanar(), bases_form_a_hydrogen_bond(), figure_out_base_pair_orientation(), figure_out_number_base_contacts(), core::scoring::hbonds::fill_hbond_set(), core::scoring::rna::get_edge_from_num(), core::scoring::hbond_sc, residue_is_bulge(), and core::scoring::ScoreFunction::set_weight().

Referenced by protocols::rna::RNA_DeNovoProtocol::add_number_base_pairs(), protocols::rna::RNA_DeNovoProtocol::add_number_native_base_pairs(), and protocols::swa::RigidBodySampler::assign_WC_edges_to_base_pair12().

bool protocols::rna::compare_RNA_char ( char const  char1,
char const  char2 
)

Definition at line 908 of file RNA_ProtocolUtil.cc.

Referenced by protocols::rna::RNA_Fragments::pick_fragment_library().

bool protocols::rna::compare_RNA_secstruct ( char const  char1,
char const  char2 
)

Definition at line 921 of file RNA_ProtocolUtil.cc.

Referenced by protocols::rna::RNA_Fragments::pick_fragment_library().

std::string const protocols::rna::convert_based_on_match_type ( std::string const  RNA_string,
Size const  type 
)

Definition at line 879 of file RNA_ProtocolUtil.cc.

References MATCH_ALL, MATCH_YR, and core::io::serialization::size().

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::pick_random_fragment(), and protocols::rna::RNA_Fragments::pick_random_fragment().

void protocols::rna::create_rna_vall_torsions ( pose::Pose &  pose,
utility::io::ozstream &  torsions_out,
utility::vector1< Size > const &  exclude_res_list 
)

Definition at line 298 of file RNA_ProtocolUtil.cc.

References core::pose::Pose::append_residue_by_bond(), core::id::BB, core::id::CHI, protocols::idealize::IdealizeMover::fast(), figure_out_reasonable_rna_fold_tree(), core::pose::Pose::fold_tree(), get_base_pairing_info(), core::scoring::rna::initialize_non_main_chain_sugar_atoms(), core::kinematics::FoldTree::is_cutpoint(), is_num_in_list(), core::conformation::Residue::name1(), core::scoring::rna::non_main_chain_sugar_atoms, core::scoring::rna::NUM_RNA_CHI_TORSIONS(), core::scoring::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::pose::Pose::residue(), core::scoring::rna_base_pair, core::pose::Pose::torsion(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by create_rna_vall_torsions().

void protocols::rna::create_rna_vall_torsions ( pose::Pose &  pose,
std::string const  outfile,
utility::vector1< Size > const &  exclude_res_list 
)

Definition at line 413 of file RNA_ProtocolUtil.cc.

References create_rna_vall_torsions().

Real protocols::rna::distance_4d ( utility::vector1< Real > const &  torsion1,
utility::vector1< Real > const &  torsion2,
Size const (&)  half_width[7] 
)

Definition at line 129 of file RNA_SuiteAssign.cc.

Referenced by suite_assign().

Real protocols::rna::distance_7d ( utility::vector1< Real > const &  torsion1,
utility::vector1< Real > const &  torsion2,
Size const (&)  half_width[7] 
)

Definition at line 148 of file RNA_SuiteAssign.cc.

Referenced by suite_assign().

void protocols::rna::ensure_phosphate_nomenclature_matches_mini ( pose::Pose &  pose)

Definition at line 501 of file RNA_ProtocolUtil.cc.

References get_o1p_o2p_sign(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::pose::Pose::set_xyz(), and core::pose::Pose::total_residue().

Referenced by protocols::rna::RNA_ChunkLibrary::process_input_file().

void protocols::rna::export_packer_results ( utility::vector1< std::pair< core::Real, std::string > > &  results,
utility::vector1< core::pose::PoseOP >  pose_list,
core::scoring::ScoreFunctionOP &  scorefxn,
std::string const &  outfile,
bool const  dumo = false 
)
void protocols::rna::export_packer_results ( utility::vector1< std::pair< Real, std::string > > &  results,
utility::vector1< pose::PoseOP >  pose_list,
scoring::ScoreFunctionOP &  scorefxn,
std::string const &  outfile,
bool const  dump 
)

Definition at line 570 of file RNA_ProtocolUtil.cc.

References core::pose::Pose::dump_pdb().

Size protocols::rna::figure_out_base_pair_orientation ( core::pose::Pose &  pose,
Size const &  i,
Size const &  j 
)

Definition at line 353 of file RNA_BasePairClassifier.cc.

References core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().

Referenced by classify_base_pairs().

void protocols::rna::figure_out_number_base_contacts ( conformation::Residue const &  rsd_i,
conformation::Residue const &  rsd_j,
Size &  edge_classification 
)

Definition at line 265 of file RNA_BasePairClassifier.cc.

References atom_is_acceptor(), core::conformation::Residue::first_sidechain_atom(), heavy_atom_is_polar(), core::scoring::rna::HOOGSTEEN, core::conformation::Residue::nheavyatoms(), core::scoring::rna::SUGAR, update_edge_hbond_numbers(), update_edge_hbond_numbers_careful_hydrogen(), core::scoring::rna::WATSON_CRICK, and core::conformation::Residue::xyz().

Referenced by classify_base_pairs().

void protocols::rna::figure_out_reasonable_rna_fold_tree ( pose::Pose &  pose)

Definition at line 87 of file RNA_ProtocolUtil.cc.

References core::scoring::rna::chi1_torsion_atom(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_RNA(), core::scoring::rna::is_rna_chainbreak(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::residue(), core::kinematics::FoldTree::set_jump_atoms(), and core::pose::Pose::total_residue().

Referenced by create_rna_vall_torsions(), and protocols::rna::RNA_ChunkLibrary::process_input_file().

void protocols::rna::figure_out_secstruct ( pose::Pose &  pose)

Definition at line 272 of file RNA_ProtocolUtil.cc.

References get_base_pairing_info(), core::scoring::rna_base_pair, set_rna_secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::initialize_frag_source_pose().

void protocols::rna::get_base_pairing_info ( core::pose::Pose const &  pose,
core::Size const &  seqpos,
char &  secstruct,
ObjexxFCL::FArray1D< bool > &  edge_is_base_pairing 
)
void protocols::rna::get_base_pairing_info ( pose::Pose const &  pose,
Size const &  seqpos,
char &  secstruct,
FArray1D< bool > &  edge_is_base_pairing 
)

Definition at line 135 of file RNA_ProtocolUtil.cc.

References core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, core::scoring::rna::get_watson_crick_base_pair_atoms(), core::scoring::rna::Base_pair::orientation, core::scoring::rna::possibly_canonical(), core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::rna::rna_scoring_info_from_pose(), and core::scoring::rna::WATSON_CRICK.

Referenced by create_rna_vall_torsions(), and figure_out_secstruct().

void protocols::rna::get_base_pairing_list ( core::pose::Pose &  pose,
utility::vector1< std::pair< core::Size, core::Size > > &  base_pairing_list 
)
void protocols::rna::get_base_pairing_list ( pose::Pose &  pose,
utility::vector1< std::pair< Size, Size > > &  base_pairing_list 
)

Definition at line 205 of file RNA_ProtocolUtil.cc.

References core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, core::scoring::rna::get_watson_crick_base_pair_atoms(), core::scoring::rna::Base_pair::orientation, core::scoring::rna::possibly_canonical(), core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, core::pose::Pose::residue(), core::scoring::rna_base_pair, core::scoring::rna::rna_scoring_info_from_pose(), and core::scoring::rna::WATSON_CRICK.

core::Size protocols::rna::get_number_base_stacks ( core::pose::Pose const &  pose_input)

Definition at line 640 of file RNA_BasePairClassifier.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::RNA_LORES_WTS, core::scoring::rna::rna_scoring_info_from_pose(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::size().

Referenced by protocols::rna::RNA_DeNovoProtocol::add_number_base_pairs().

core::Real protocols::rna::get_o1p_o2p_sign ( pose::Pose const &  pose)

Definition at line 426 of file RNA_ProtocolUtil.cc.

References core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by assert_phosphate_nomenclature_matches_mini(), ensure_phosphate_nomenclature_matches_mini(), and make_phosphate_nomenclature_matches_mini().

core::Real protocols::rna::get_o1p_o2p_sign ( pose::Pose const &  pose,
Size  res_num 
)

Definition at line 451 of file RNA_ProtocolUtil.cc.

References core::pose::Pose::residue(), and core::pose::Pose::total_residue().

utility::vector1< core::Size > protocols::rna::get_rigid_body_jumps ( core::pose::Pose const &  pose)

Definition at line 1204 of file RNA_ProtocolUtil.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by let_rigid_body_jumps_move(), protocols::rna::RNA_DeNovoProtocol::randomize_rigid_body_orientations(), protocols::rna::RNA_StructureParameters::setup_jumps(), protocols::rna::RNA_DeNovoProtocol::setup_monte_carlo_cycles(), and translate_virtual_anchor_to_first_rigid_body().

std::string const & protocols::rna::get_rna_secstruct ( core::pose::Pose &  pose)

Pose must already contain a core::pose::datacache::CacheableDataType::RNA_SCORING_INFO object or this method will fail.

Definition at line 52 of file RNA_SecStructInfo.cc.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::RNA_SECSTRUCT_INFO, set_rna_secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::initialize_frag_source_pose(), protocols::coarse_rna::CoarseRNA_Fragments::pick_random_fragment(), protocols::rna::RNA_Fragments::pick_random_fragment(), protocols::rna::FullAtomRNA_Fragments::pick_random_fragment(), and protocols::rna::RNA_StructureParameters::setup_jumps().

Vector protocols::rna::get_sugar_centroid ( core::conformation::Residue const &  rsd)

Definition at line 931 of file RNA_ProtocolUtil.cc.

References core::conformation::Residue::atom_index(), and core::conformation::Residue::xyz().

Referenced by make_coarse_pose().

bool protocols::rna::heavy_atom_is_polar ( core::conformation::Residue const &  rsd,
Size const &  atm 
)

Definition at line 233 of file RNA_BasePairClassifier.cc.

References core::conformation::Residue::atom_base(), and core::conformation::Residue::Hpos_polar().

Referenced by figure_out_number_base_contacts().

bool protocols::rna::in_list ( Size const &  pos,
utility::vector1< Size > const &  res_list 
)

Definition at line 489 of file RNA_StructureParameters.cc.

Referenced by check_in_base_pair_list(), and protocols::rna::RNA_StructureParameters::check_in_chain_connections().

bool protocols::rna::is_in_between ( utility::vector1< Real > const &  target,
utility::vector1< Real > const &  dominant,
utility::vector1< Real > const &  satellite 
)

Definition at line 181 of file RNA_SuiteAssign.cc.

Referenced by suite_assign().

bool protocols::rna::is_num_in_list ( core::Size const  i,
utility::vector1< core::Size > const &  list 
)
inline

Definition at line 139 of file RNA_ProtocolUtil.hh.

Referenced by create_rna_vall_torsions().

bool protocols::rna::let_rigid_body_jumps_move ( core::kinematics::MoveMap &  movemap,
pose::Pose const &  pose,
bool const  move_first_rigid_body 
)

Definition at line 1231 of file RNA_ProtocolUtil.cc.

References get_rigid_body_jumps(), core::kinematics::MoveMap::set_jump(), and protocols::loops::start.

Referenced by protocols::rna::RNA_Minimizer::setup_movemap(), and protocols::rna::RNA_DeNovoProtocol::setup_rigid_body_mover().

void protocols::rna::make_coarse_pose ( pose::Pose const &  pose,
pose::Pose &  coarse_pose 
)

Definition at line 963 of file RNA_ProtocolUtil.cc.

References core::chemical::COARSE_RNA, core::pose::Pose::fold_tree(), core::chemical::ChemicalManager::get_instance(), get_sugar_centroid(), core::kinematics::Stub::M, make_extended_coarse_pose(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), core::chemical::ChemicalManager::residue_type_set(), core::pose::Pose::sequence(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by protocols::rna::RNA_ChunkLibrary::process_input_file().

void protocols::rna::make_extended_coarse_pose ( pose::Pose &  coarse_pose,
std::string const &  full_sequence 
)

Definition at line 944 of file RNA_ProtocolUtil.cc.

References core::id::BB, core::chemical::COARSE_RNA, core::chemical::ChemicalManager::get_instance(), core::pose::make_pose_from_sequence(), core::chemical::ChemicalManager::residue_type_set(), core::pose::Pose::set_torsion(), and core::pose::Pose::total_residue().

Referenced by make_coarse_pose().

void protocols::rna::make_phosphate_nomenclature_matches_mini ( pose::Pose &  pose)

Definition at line 534 of file RNA_ProtocolUtil.cc.

References get_o1p_o2p_sign(), core::conformation::Residue::is_RNA(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::pose::Pose::set_xyz(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::InputStreamWithResidueInfo::cleanup_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_rep_screen_pose(), protocols::swa::StepWisePoseSetup::get_working_pose(), protocols::swa::rna::StepWiseRNA_PoseSetup::Import_pose(), and protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose().

bool protocols::rna::possible_root ( core::kinematics::FoldTree const &  f,
core::Size const &  n 
)

Definition at line 1193 of file RNA_ProtocolUtil.cc.

References core::kinematics::FoldTree::is_cutpoint(), and core::kinematics::FoldTree::nres().

Referenced by protocols::swa::StepWisePoseSetup::reroot_fold_tree(), and protocols::rna::RNA_StructureParameters::setup_jumps().

void protocols::rna::print_internal_coords ( core::pose::Pose const &  pose)

Definition at line 1108 of file RNA_ProtocolUtil.cc.

References protocols::comparative_modeling::features::A, core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::D, core::kinematics::AtomTree::dof(), core::conformation::Residue::name3(), core::id::PHI, core::pose::Pose::residue(), core::id::THETA, and core::pose::Pose::total_residue().

Referenced by protocols::coarse_rna::CoarseRNA_DeNovoProtocol::apply().

void protocols::rna::remove_cutpoint_closed ( pose::Pose &  pose,
Size const  i 
)

Definition at line 1001 of file RNA_ProtocolUtil.cc.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::partition_by_jump(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::total_residue(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by remove_cutpoints_closed().

void protocols::rna::remove_cutpoints_closed ( pose::Pose &  pose)

Definition at line 1074 of file RNA_ProtocolUtil.cc.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), remove_cutpoint_closed(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::rna::RNA_ChunkLibrary::process_input_file().

bool protocols::rna::residue_is_bulge ( pose::Pose const &  pose,
Size const  i 
)

Definition at line 383 of file RNA_BasePairClassifier.cc.

References core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by classify_base_pairs().

static numeric::random::RandomGenerator protocols::rna::RG ( 144621  )
static
static numeric::random::RandomGenerator protocols::rna::RG ( 17720  )
static
static numeric::random::RandomGenerator protocols::rna::RG ( 144620  )
static
static numeric::random::RandomGenerator protocols::rna::RG ( 12320  )
static

Referenced by protocols::rna::MultipleDomainMover::apply_and_return_jump(), protocols::rna::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff(), protocols::rna::RNA_JumpLibrary::get_random_base_pair_jump(), protocols::rna::RNA_ChunkLibrary::initialize_random_chunks(), protocols::rna::RNA_Relaxer::lores_monte_carlo(), protocols::rna::RNA_ChunkLibrary::random_chunk_insertion(), protocols::rna::RNA_FragmentMover::random_fragment_insertion(), protocols::rna::RNA_StructureParameters::random_jump_change(), protocols::rna::RNA_DeNovoProtocol::random_jump_trial(), protocols::rna::RNA_DeNovoProtocol::RNA_move_trial(), protocols::rna::RNA_StructureParameters::sample_alternative_chain_connection(), and protocols::rna::RNA_StructureParameters::setup_jumps().

void protocols::rna::set_rna_secstruct ( core::pose::Pose &  pose,
std::string const  rna_secstruct_string 
)

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.

Definition at line 67 of file RNA_SecStructInfo.cc.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RNA_SECSTRUCT_INFO.

Referenced by figure_out_secstruct(), get_rna_secstruct(), protocols::rna::RNA_StructureParameters::initialize_secstruct(), and protocols::rna::RNA_StructureParameters::override_secstruct().

void protocols::rna::setup_base_pair_constraints ( core::pose::Pose &  pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  pairings,
core::Real const  suppress_factor = 1.0 
)
void protocols::rna::setup_base_pair_constraints ( pose::Pose &  pose,
utility::vector1< std::pair< Size, Size > > const &  pairings,
Real const  suppress_factor 
)

Definition at line 677 of file RNA_ProtocolUtil.cc.

References core::conformation::Residue::aa(), core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), core::scoring::rna::get_watson_crick_base_pair_atoms(), core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), core::pose::Pose::residue(), core::TR(), and core::conformation::Residue::type().

Referenced by protocols::rna::RNA_HelixAssembler::put_constraints_on_base_step(), and protocols::rna::RNA_StructureParameters::setup_base_pair_constraints().

void protocols::rna::setup_coarse_chainbreak_constraints ( pose::Pose &  pose,
Size const &  n 
)

Definition at line 805 of file RNA_ProtocolUtil.cc.

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

Size protocols::rna::string_find ( std::string const  input_string,
const std::string *  string_list_first,
const std::string *  string_list_last 
)

Definition at line 167 of file RNA_SuiteAssign.cc.

Referenced by suite_assign().

std::pair< std::string, std::pair< Size, Real > > protocols::rna::suite_assign ( pose::Pose const &  pose,
Size const  res 
)

Definition at line 196 of file RNA_SuiteAssign.cc.

References core::scoring::rna::ALPHA, core::scoring::rna::BETA, core::scoring::rna::DELTA, distance_4d(), distance_7d(), core::scoring::rna::EPSILON, protocols::rna::RNA_suite_list::full_list(), core::scoring::rna::GAMMA, is_in_between(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), string_find(), and core::scoring::rna::ZETA.

static basic::Tracer protocols::rna::tr ( "protocols.rna.rna_jump_library"  )
static
static basic::Tracer protocols::rna::tr ( "protocols.rna.rna_structure_parameters"  )
static

Referenced by protocols::rna::RNA_StructureParameters::check_base_pairs(), protocols::rna::RNA_DataReader::read_data_from_file(), protocols::rna::RNA_JumpLibrary::read_jumps_from_file(), protocols::rna::RNA_StructureParameters::read_parameters_from_file(), protocols::rna::RNA_StructureParameters::setup_base_pair_constraints(), and protocols::rna::RNA_StructureParameters::setup_fold_tree_and_jumps_and_variants().

static basic::Tracer protocols::rna::tr ( "protocols.rna.rna_structure_parameters"  )
static
static basic::Tracer protocols::rna::TR ( "protocols.rna.rna_denovo_protocol"  )
static

Referenced by protocols::rna::RNA_Minimizer::apply(), protocols::rna::RNA_LoopCloser::apply(), protocols::rna::RNA_Relaxer::apply(), protocols::rna::RNA_DeNovoProtocol::apply(), protocols::rna::RNA_DeNovoProtocol::calc_rmsds(), protocols::rna::RNA_DeNovoProtocol::check_score_filter(), protocols::rna::RNA_DeNovoProtocol::do_random_moves(), protocols::rna::RNA_ChunkLibrary::fill_res_map(), protocols::rna::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff(), protocols::rna::RNA_ChunkLibrary::find_res_maps(), protocols::rna::RNA_ChunkLibrary::get_component_sequences(), protocols::rna::RNA_ChunkLibrary::get_sequence_matches(), protocols::rna::RNA_LoopCloser::local_minimize_at_chainbreaks(), protocols::rna::RNA_Relaxer::lores_monte_carlo(), protocols::rna::RNA_Minimizer::o2star_trials(), protocols::rna::RNA_DeNovoProtocol::output_silent_struct(), protocols::rna::RNA_DeNovoProtocol::output_to_silent_file(), protocols::rna::RNA_LoopCloser::passes_fast_scan(), protocols::rna::RNA_LoopCloser::rna_ccd_close(), protocols::rna::RNA_DeNovoProtocol::setup_monte_carlo_cycles(), protocols::rna::RNA_DeNovoProtocol::setup_rigid_body_mover(), protocols::rna::RNA_ChunkLibrary::test_matches(), protocols::rna::RNA_DeNovoProtocol::update_frag_size(), and protocols::rna::RNA_DeNovoProtocol::update_pose_constraints().

void protocols::rna::translate_virtual_anchor_to_first_rigid_body ( pose::Pose &  pose)

Definition at line 1247 of file RNA_ProtocolUtil.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), get_rigid_body_jumps(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), core::kinematics::FoldTree::upstream_jump_residue(), and core::pose::Pose::xyz().

Referenced by protocols::rna::RNA_DeNovoProtocol::do_random_moves().

void protocols::rna::update_edge_hbond_numbers ( conformation::Residue const &  rsd,
Size const &  atm,
Size &  N_W,
Size &  N_H,
Size &  N_S 
)

Definition at line 78 of file RNA_BasePairClassifier.cc.

References core::conformation::Residue::aa(), core::conformation::Residue::atom_name(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.

Referenced by figure_out_number_base_contacts().

void protocols::rna::update_edge_hbond_numbers_careful_hydrogen ( conformation::Residue const &  rsd,
Size const &  atm,
conformation::Residue const &  other_rsd,
Size const &  other_atm,
Size &  N_W,
Size &  N_H,
Size &  N_S 
)

Definition at line 174 of file RNA_BasePairClassifier.cc.

References core::conformation::Residue::aa(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::conformation::Residue::xyz().

Referenced by figure_out_number_base_contacts().

void protocols::rna::virtualize_5prime_phosphates ( pose::Pose &  pose)

Definition at line 1090 of file RNA_ProtocolUtil.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::rna::RNA_ChunkLibrary::process_input_file().

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