Rosetta 3.4
Classes | Typedefs | Enumerations | Functions
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  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. More...
class  RNA_Pairing
class  RNA_StructureParameters

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< RealMatrix
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_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)
void create_rna_vall_torsions (pose::Pose &pose, std::string const outfile)
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)
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 print_internal_coords (core::pose::Pose const &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)
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)
bool in_list (Size const &pos, utility::vector1< Size > const &res_list)

Typedef Documentation

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

Enumeration Type Documentation

Enumerator:
MATCH_ALL 
MATCH_YR 
MATCH_EXACT 

name MATCH_ENUM added for PyRosetta compatability

Enumerator:
MATCH_ALL 
MATCH_YR 
MATCH_EXACT 

Function Documentation

void protocols::rna::assert_phosphate_nomenclature_matches_mini ( pose::Pose const &  pose)
bool protocols::rna::atom_is_acceptor ( core::conformation::Residue const &  rsd,
Size const &  atm 
)
bool protocols::rna::atom_is_polar ( core::conformation::Residue const &  rsd,
Size const &  atm 
)
bool protocols::rna::bases_are_coplanar ( core::pose::Pose pose,
Size const &  i,
Size const &  j 
)
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 
)
void protocols::rna::check_base_pair ( pose::Pose pose,
FArray1D_int &  struct_type 
)
void protocols::rna::check_base_pair ( core::pose::Pose pose,
ObjexxFCL::FArray1D_int &  struct_type 
)
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 
)
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 
)
bool protocols::rna::compare_RNA_char ( char const  char1,
char const  char2 
)
bool protocols::rna::compare_RNA_secstruct ( char const  char1,
char const  char2 
)
std::string const protocols::rna::convert_based_on_match_type ( std::string const  RNA_string,
Size const  type 
)

References MATCH_ALL, and MATCH_YR.

void protocols::rna::create_rna_vall_torsions ( pose::Pose pose,
std::string const  outfile 
)
void protocols::rna::create_rna_vall_torsions ( pose::Pose pose,
utility::io::ozstream &  torsions_out 
)
void protocols::rna::ensure_phosphate_nomenclature_matches_mini ( pose::Pose pose)
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 
)
Size protocols::rna::figure_out_base_pair_orientation ( core::pose::Pose pose,
Size const &  i,
Size const &  j 
)
void protocols::rna::figure_out_number_base_contacts ( conformation::Residue const &  rsd_i,
conformation::Residue const &  rsd_j,
Size edge_classification 
)
void protocols::rna::figure_out_reasonable_rna_fold_tree ( pose::Pose pose)
void protocols::rna::figure_out_secstruct ( pose::Pose pose)
void protocols::rna::get_base_pairing_info ( pose::Pose const &  pose,
Size const &  seqpos,
char &  secstruct,
FArray1D< bool > &  edge_is_base_pairing 
)
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_list ( pose::Pose pose,
utility::vector1< std::pair< Size, Size > > &  base_pairing_list 
)
void protocols::rna::get_base_pairing_list ( core::pose::Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > &  base_pairing_list 
)
core::Size protocols::rna::get_number_base_stacks ( core::pose::Pose const &  pose_input)
core::Real protocols::rna::get_o1p_o2p_sign ( pose::Pose const &  pose)
core::Real protocols::rna::get_o1p_o2p_sign ( pose::Pose const &  pose,
Size  res_num 
)
std::string const & protocols::rna::get_rna_secstruct ( core::pose::Pose pose)
Vector protocols::rna::get_sugar_centroid ( core::conformation::Residue const &  rsd)
bool protocols::rna::heavy_atom_is_polar ( core::conformation::Residue const &  rsd,
Size const &  atm 
)
bool protocols::rna::in_list ( Size const &  pos,
utility::vector1< Size > const &  res_list 
)

Referenced by check_in_base_pair_list().

void protocols::rna::make_coarse_pose ( pose::Pose const &  pose,
pose::Pose coarse_pose 
)
void protocols::rna::make_extended_coarse_pose ( pose::Pose coarse_pose,
std::string const &  full_sequence 
)
void protocols::rna::make_phosphate_nomenclature_matches_mini ( pose::Pose pose)
void protocols::rna::print_internal_coords ( core::pose::Pose const &  pose)
void protocols::rna::remove_cutpoint_closed ( pose::Pose pose,
Size const  i 
)
void protocols::rna::remove_cutpoints_closed ( pose::Pose pose)
bool protocols::rna::residue_is_bulge ( pose::Pose const &  pose,
Size const  i 
)
static numeric::random::RandomGenerator protocols::rna::RG ( 17720  ) [static]
static numeric::random::RandomGenerator protocols::rna::RG ( 12320  ) [static]
static numeric::random::RandomGenerator protocols::rna::RG ( 144621  ) [static]
static numeric::random::RandomGenerator protocols::rna::RG ( 144620  ) [static]
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.

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

Referenced by figure_out_secstruct(), and get_rna_secstruct().

void protocols::rna::setup_base_pair_constraints ( pose::Pose pose,
utility::vector1< std::pair< Size, Size > > const &  pairings 
)
void protocols::rna::setup_base_pair_constraints ( core::pose::Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  pairings 
)
void protocols::rna::setup_coarse_chainbreak_constraints ( pose::Pose pose,
Size const &  n 
)
static basic::Tracer protocols::rna::tr ( "protocols.rna.rna_jump_library"  ) [static]
static basic::Tracer protocols::rna::TR ( "protocols.rna.rna_denovo_protocol"  ) [static]
static basic::Tracer protocols::rna::tr ( "protocols.rna.rna_structure_parameters"  ) [static]
void protocols::rna::update_edge_hbond_numbers ( conformation::Residue const &  rsd,
Size const &  atm,
Size N_W,
Size N_H,
Size N_S 
)
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 
)
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines