Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
protocols::farna Namespace Reference

Classes

class  BasePairStep
 
class  BasePairStepLibrary
 
class  BasePairStepSequence
 
class  BasePairType
 
class  ChunkSet
 
class  FragmentLibrary
 
class  FullAtomRNA_Fragments
 
class  MultipleDomainMover
 The RNA de novo structure modeling protocol. More...
 
class  RNA_ChunkLibrary
 
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_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_Pairing
 
class  RNA_PairingTemplate
 
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_StructureParameters
 
class  TorsionSet
 

Typedefs

typedef
utility::pointer::owning_ptr
< BasePairStep
BasePairStepOP
 
typedef
utility::pointer::owning_ptr
< BasePairStep const > 
BasePairStepCOP
 
typedef
utility::pointer::owning_ptr
< BasePairStepLibrary
BasePairStepLibraryOP
 
typedef
utility::pointer::owning_ptr
< BasePairStepLibrary const > 
BasePairStepLibraryCOP
 
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
utility::pointer::owning_ptr
< RNA_ChunkLibrary
RNA_ChunkLibraryOP
 
typedef
utility::pointer::owning_ptr
< ChunkSet
ChunkSetOP
 
typedef
utility::pointer::owning_ptr
< RNA_FragmentMover
RNA_FragmentMoverOP
 
typedef
utility::pointer::owning_ptr
< RNA_Fragments
RNA_FragmentsOP
 
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
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
 
typedef numeric::xyzVector
< core::Length
Vector
 

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

bool check_in_base_pair_list (pose::rna::BasePair const &base_pair, utility::vector1< core::pose::rna::BasePair > const &base_pair_list)
 
std::ostream & operator<< (std::ostream &os, RNA_DeNovoProtocol const &mover)
 
std::ostream & operator<< (std::ostream &os, RNA_Minimizer const &mover)
 
std::string const & get_rna_secstruct (core::pose::Pose &pose)
 
void set_rna_secstruct (core::pose::Pose &pose, std::string const rna_secstruct_string)
 
bool in_list (Size const &pos, utility::vector1< Size > const &res_list)
 
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_op2_op1_sign (pose::Pose const &pose)
 
Real get_op2_op1_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 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)
 
bool involved_in_phosphate_torsion (std::string atomname)
 
void set_output_res_num (pose::Pose &extended_pose, utility::vector1< Size > const &output_res_num)
 
void figure_out_base_pair_partner (pose::Pose &pose, std::map< Size, Size > &partner, bool const strict)
 
void process_input_file (std::string const &input_file, utility::vector1< pose::PoseOP > &pose_list, bool is_pdb, bool coarse_rna)
 
void print_hbonds (pose::Pose &pose)
 
bool moveable_jump (id::AtomID const &jump_atom_id1, id::AtomID const &jump_atom_id2, protocols::toolbox::AllowInsert const &allow_insert)
 
bool moveable_jump (Size const jump_pos1, Size const jump_pos2, protocols::toolbox::AllowInsert const &allow_insert)
 
void get_default_allowed_bulge_res (utility::vector1< core::Size > &allow_bulge_res_list, core::pose::Pose const &pose, bool const verbose)
 
core::Size virtualize_bulges (core::pose::Pose &input_pose, utility::vector1< core::Size > const &in_allow_bulge_res_list, core::scoring::ScoreFunctionCOP const &scorefxn, std::string const &tag, bool const allow_pre_virtualize, bool const allow_consecutive_bulges, bool const verbose)
 
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)
 

Variables

static
numeric::random::RandomGenerator 
RG (12320)
 
static basic::Tracer TR ("protocols.rna.RNA_DeNovoProtocol")
 
static
numeric::random::RandomGenerator 
RG (144621)
 
static basic::Tracer tr ("protocols.rna.RNA_JumpLibrary")
 
static
numeric::random::RandomGenerator 
RG (144620)
 
static basic::Tracer TR ("protocols.farna.RNA_StructureParameters")
 

Typedef Documentation

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::farna::assert_phosphate_nomenclature_matches_mini ( pose::Pose const &  pose)
void protocols::farna::check_base_pair ( core::pose::Pose pose,
ObjexxFCL::FArray1D_int &  struct_type 
)
void protocols::farna::check_base_pair ( pose::Pose pose,
FArray1D_int &  struct_type 
)
bool protocols::farna::check_in_base_pair_list ( pose::rna::BasePair const &  base_pair,
utility::vector1< core::pose::rna::BasePair > const &  base_pair_list 
)
bool protocols::farna::compare_RNA_char ( char const  char1,
char const  char2 
)
bool protocols::farna::compare_RNA_secstruct ( char const  char1,
char const  char2 
)
std::string const protocols::farna::convert_based_on_match_type ( std::string const  RNA_string,
Size const  type 
)
void protocols::farna::create_rna_vall_torsions ( pose::Pose pose,
utility::io::ozstream torsions_out,
utility::vector1< Size > const &  exclude_res_list 
)
void protocols::farna::create_rna_vall_torsions ( pose::Pose pose,
std::string const  outfile,
utility::vector1< Size > const &  exclude_res_list 
)
void protocols::farna::ensure_phosphate_nomenclature_matches_mini ( pose::Pose pose)
void protocols::farna::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::farna::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 protocols::farna::figure_out_base_pair_partner ( pose::Pose pose,
std::map< Size, Size > &  partner,
bool const  strict 
)
void protocols::farna::figure_out_secstruct ( pose::Pose pose)
void protocols::farna::get_base_pairing_info ( core::pose::Pose const &  pose,
core::Size const &  seqpos,
char &  secstruct,
ObjexxFCL::FArray1D< bool > &  edge_is_base_pairing 
)
void protocols::farna::get_base_pairing_info ( pose::Pose const &  pose,
Size const &  seqpos,
char &  secstruct,
FArray1D< bool > &  edge_is_base_pairing 
)
void protocols::farna::get_base_pairing_list ( core::pose::Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > &  base_pairing_list 
)
void protocols::farna::get_base_pairing_list ( pose::Pose pose,
utility::vector1< std::pair< Size, Size > > &  base_pairing_list 
)
void protocols::farna::get_default_allowed_bulge_res ( utility::vector1< core::Size > &  allow_bulge_res_list,
core::pose::Pose const &  pose,
bool const  verbose 
)
core::Real protocols::farna::get_op2_op1_sign ( pose::Pose const &  pose)
core::Real protocols::farna::get_op2_op1_sign ( pose::Pose const &  pose,
Size  res_num 
)
utility::vector1< core::Size > protocols::farna::get_rigid_body_jumps ( core::pose::Pose const &  pose)
std::string const & protocols::farna::get_rna_secstruct ( core::pose::Pose pose)
Vector protocols::farna::get_sugar_centroid ( core::conformation::Residue const &  rsd)
bool protocols::farna::in_list ( Size const &  pos,
utility::vector1< Size > const &  res_list 
)
bool protocols::farna::involved_in_phosphate_torsion ( std::string  atomname)
bool protocols::farna::is_num_in_list ( core::Size const  i,
utility::vector1< core::Size > const &  list 
)
inline
bool protocols::farna::let_rigid_body_jumps_move ( core::kinematics::MoveMap movemap,
pose::Pose const &  pose,
bool const  move_first_rigid_body 
)
void protocols::farna::make_coarse_pose ( pose::Pose const &  pose,
pose::Pose coarse_pose 
)
void protocols::farna::make_extended_coarse_pose ( pose::Pose coarse_pose,
std::string const &  full_sequence 
)
void protocols::farna::make_phosphate_nomenclature_matches_mini ( pose::Pose pose)
bool protocols::farna::moveable_jump ( id::AtomID const &  jump_atom_id1,
id::AtomID const &  jump_atom_id2,
protocols::toolbox::AllowInsert const &  allow_insert 
)
bool protocols::farna::moveable_jump ( Size const  jump_pos1,
Size const  jump_pos2,
protocols::toolbox::AllowInsert const &  allow_insert 
)
std::ostream & protocols::farna::operator<< ( std::ostream &  os,
RNA_Minimizer const &  mover 
)
std::ostream & protocols::farna::operator<< ( std::ostream &  os,
RNA_DeNovoProtocol const &  mover 
)
bool protocols::farna::possible_root ( core::kinematics::FoldTree const &  f,
core::Size const &  n 
)
void protocols::farna::print_hbonds ( pose::Pose pose)
void protocols::farna::print_internal_coords ( core::pose::Pose const &  pose)
void protocols::farna::process_input_file ( std::string const &  input_file,
utility::vector1< pose::PoseOP > &  pose_list,
bool  is_pdb,
bool  coarse_rna 
)
void protocols::farna::remove_cutpoint_closed ( pose::Pose pose,
Size const  i 
)
void protocols::farna::remove_cutpoints_closed ( pose::Pose pose)
void protocols::farna::set_output_res_num ( pose::Pose extended_pose,
utility::vector1< Size > const &  output_res_num 
)
void protocols::farna::set_rna_secstruct ( core::pose::Pose pose,
std::string const  rna_secstruct_string 
)
void protocols::farna::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::farna::setup_base_pair_constraints ( pose::Pose pose,
utility::vector1< std::pair< Size, Size > > const &  pairings,
Real const  suppress_factor 
)
void protocols::farna::setup_coarse_chainbreak_constraints ( pose::Pose pose,
Size const &  n 
)
void protocols::farna::translate_virtual_anchor_to_first_rigid_body ( pose::Pose pose)
core::Size protocols::farna::virtualize_bulges ( core::pose::Pose input_pose,
utility::vector1< core::Size > const &  in_allow_bulge_res_list,
core::scoring::ScoreFunctionCOP const &  scorefxn,
std::string const &  tag,
bool const  allow_pre_virtualize,
bool const  allow_consecutive_bulges,
bool const  verbose 
)

Variable Documentation

numeric::random::RandomGenerator protocols::farna::RG(144621)
static
numeric::random::RandomGenerator protocols::farna::RG(12320)
static
numeric::random::RandomGenerator protocols::farna::RG(144620)
static
basic::Tracer protocols::farna::tr("protocols.rna.RNA_JumpLibrary")
static
basic::Tracer protocols::farna::TR("protocols.rna.RNA_DeNovoProtocol")
static
basic::Tracer protocols::farna::TR("protocols.farna.RNA_StructureParameters")
static