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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< 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_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< Sizeget_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 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 ( core::pose::Pose pose,
ObjexxFCL::FArray1D_int &  struct_type 
)
void protocols::rna::check_base_pair ( pose::Pose pose,
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 
)
void protocols::rna::create_rna_vall_torsions ( pose::Pose pose,
utility::io::ozstream &  torsions_out,
utility::vector1< Size > const &  exclude_res_list 
)
void protocols::rna::create_rna_vall_torsions ( pose::Pose pose,
std::string const  outfile,
utility::vector1< Size > const &  exclude_res_list 
)
Real protocols::rna::distance_4d ( utility::vector1< Real > const &  torsion1,
utility::vector1< Real > const &  torsion2,
Size const (&)  half_width[7] 
)

Referenced by suite_assign().

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

Referenced by suite_assign().

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 ( 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 
)
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 
)
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 
)
utility::vector1< core::Size > protocols::rna::get_rigid_body_jumps ( core::pose::Pose const &  pose)
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 
)
bool protocols::rna::is_in_between ( utility::vector1< Real > const &  target,
utility::vector1< Real > const &  dominant,
utility::vector1< Real > const &  satellite 
)

Referenced by suite_assign().

bool protocols::rna::is_num_in_list ( core::Size const  i,
utility::vector1< core::Size > const &  list 
)
inline
bool protocols::rna::let_rigid_body_jumps_move ( core::kinematics::MoveMap movemap,
pose::Pose const &  pose,
bool const  move_first_rigid_body 
)
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)
bool protocols::rna::possible_root ( core::kinematics::FoldTree const &  f,
core::Size const &  n 
)
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 ( 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
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(), 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 
)
void protocols::rna::setup_coarse_chainbreak_constraints ( pose::Pose pose,
Size const &  n 
)
Size protocols::rna::string_find ( std::string const  input_string,
const std::string *  string_list_first,
const std::string *  string_list_last 
)

Referenced by suite_assign().

std::pair< std::string, std::pair< Size, Real > > protocols::rna::suite_assign ( pose::Pose const &  pose,
Size const  res 
)
static basic::Tracer protocols::rna::tr ( "protocols.rna.rna_jump_library"  )
static
static basic::Tracer protocols::rna::tr ( "protocols.rna.rna_structure_parameters"  )
static
static basic::Tracer protocols::rna::tr ( "protocols.rna.rna_structure_parameters"  )
static
static basic::Tracer protocols::rna::TR ( "protocols.rna.rna_denovo_protocol"  )
static
void protocols::rna::translate_virtual_anchor_to_first_rigid_body ( pose::Pose pose)
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 
)
void protocols::rna::virtualize_5prime_phosphates ( pose::Pose pose)