Rosetta Core  2014.35
Classes | Typedefs | Functions
core::pose::rna Namespace Reference

Classes

class  BasePair
 
class  BaseStack
 
class  RNA_IdealCoord
 
class  RNA_SuiteAssignment
 
class  RNA_SuiteInfo
 
class  RNA_SuiteName
 

Typedefs

typedef std::pair< Real, BasePairEnergyBasePair
 
typedef std::list< EnergyBasePairEnergyBasePairList
 
typedef std::pair< Real,
BaseStack
EnergyBaseStack
 
typedef std::list
< EnergyBaseStack
EnergyBaseStackList
 
typedef numeric::xyzMatrix< RealMatrix
 
typedef
utility::pointer::owning_ptr
< RNA_IdealCoord
RNA_IdealCoordOP
 
typedef
utility::pointer::owning_ptr
< RNA_SuiteName
RNA_SuiteNameOP
 

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::pose::rna::BasePair > &base_pair_list, utility::vector1< bool > &is_bulged)
 
Size get_number_base_stacks (core::pose::Pose const &pose_input)
 
bool mutate_position (pose::Pose &pose, Size const i, char const &new_seq)
 
void figure_out_reasonable_rna_fold_tree (pose::Pose &pose)
 
void virtualize_5prime_phosphates (pose::Pose &pose)
 
bool is_cutpoint_open (Pose const &pose, Size const i)
 
bool is_rna_chainbreak (Pose const &pose, Size const i)
 
void fix_sugar_coords_WORKS_BUT_SLOW (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< utility::vector1< id::DOF_Type > > which_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose &pose, Size const i)
 
void prepare_scratch_residue (core::conformation::ResidueOP &scratch_rsd, core::conformation::Residue const &start_rsd, utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose const &pose)
 
void fix_sugar_coords (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose &pose, Pose const &reference_pose, Size const i)
 
void initialize_atoms_for_which_we_need_new_dofs (utility::vector1< std::string > &atoms_for_which_we_need_new_dofs, Pose const &pose, Size const i)
 
void apply_non_main_chain_sugar_coords (utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose &pose, Pose const &reference_pose, Size const i)
 
void apply_ideal_c2endo_sugar_coords (Pose &pose, Size const i)
 
PuckerState assign_pucker (Pose const &pose, Size const rsd_id)
 
void apply_pucker (Pose &pose, Size const i, PuckerState pucker_state, bool const skip_same_state, bool const idealize_coord)
 
void correctly_position_cutpoint_phosphate_torsions (pose::Pose &current_pose, Size const five_prime_chainbreak)
 
void correctly_add_cutpoint_variants (core::pose::Pose &pose, Size const res_to_add, bool const check_fold_tree)
 
bool is_torsion_valid (pose::Pose const &pose, id::TorsionID const &torsion_id, bool verbose, bool skip_chainbreak_torsions)
 
void print_torsion_info (pose::Pose const &pose, id::TorsionID const &torsion_id)
 
void output_boolean (std::string const &tag, bool boolean)
 
bool is_cutpoint_closed_atom (core::conformation::Residue const &rsd, id::AtomID const &id)
 
bool is_cutpoint_closed_torsion (pose::Pose const &pose, id::TorsionID const &torsion_id)
 
void apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
 
void apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, utility::vector1< core::Size > const &working_cutpoint_closed_list, bool const apply_check)
 
void remove_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
 
bool has_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
 

Typedef Documentation

Function Documentation

void core::pose::rna::apply_ideal_c2endo_sugar_coords ( Pose &  pose,
Size const  i 
)
void core::pose::rna::apply_non_main_chain_sugar_coords ( utility::vector1< Vector > const &  non_main_chain_sugar_coords,
Pose &  pose,
Pose const &  reference_pose,
Size const  i 
)
void core::pose::rna::apply_pucker ( Pose &  pose,
Size const  i,
PuckerState  pucker_state,
bool const  skip_same_state,
bool const  idealize_coord 
)
void core::pose::rna::apply_virtual_rna_residue_variant_type ( core::pose::Pose pose,
core::Size const &  seq_num,
bool const  apply_check 
)
void core::pose::rna::apply_virtual_rna_residue_variant_type ( core::pose::Pose pose,
core::Size const &  seq_num,
utility::vector1< core::Size > const &  working_cutpoint_closed_list,
bool const  apply_check 
)
core::chemical::rna::PuckerState core::pose::rna::assign_pucker ( Pose const &  pose,
Size const  rsd_id 
)
bool core::pose::rna::atom_is_acceptor ( core::conformation::Residue const &  rsd,
Size const &  atm 
)
bool core::pose::rna::atom_is_polar ( core::conformation::Residue const &  rsd,
Size const &  atm 
)
bool core::pose::rna::bases_are_coplanar ( core::pose::Pose pose,
Size const &  i,
Size const &  j 
)
Size core::pose::rna::bases_form_a_hydrogen_bond ( core::scoring::hbonds::HBondSetOP const &  hbond_set,
core::pose::Pose pose,
Size const &  i,
Size const &  j 
)
void core::pose::rna::classify_base_pairs ( core::pose::Pose const &  pose_input,
utility::vector1< core::pose::rna::BasePair > &  base_pair_list,
utility::vector1< bool > &  is_bulged 
)
void core::pose::rna::correctly_add_cutpoint_variants ( core::pose::Pose pose,
Size const  res_to_add,
bool const  check_fold_tree 
)
void core::pose::rna::correctly_position_cutpoint_phosphate_torsions ( pose::Pose &  current_pose,
Size const  five_prime_chainbreak 
)
Size core::pose::rna::figure_out_base_pair_orientation ( core::pose::Pose pose,
Size const &  i,
Size const &  j 
)
void core::pose::rna::figure_out_number_base_contacts ( conformation::Residue const &  rsd_i,
conformation::Residue const &  rsd_j,
Size edge_classification 
)
void core::pose::rna::figure_out_reasonable_rna_fold_tree ( pose::Pose &  pose)
void core::pose::rna::fix_sugar_coords ( utility::vector1< std::string >  atoms_for_which_we_need_new_dofs,
utility::vector1< Vector > const &  non_main_chain_sugar_coords,
Pose &  pose,
Pose const &  reference_pose,
Size const  i 
)
void core::pose::rna::fix_sugar_coords_WORKS_BUT_SLOW ( utility::vector1< std::string >  atoms_for_which_we_need_new_dofs,
utility::vector1< utility::vector1< id::DOF_Type > >  which_dofs,
utility::vector1< Vector > const &  non_main_chain_sugar_coords,
Pose &  pose,
Size const  i 
)
core::Size core::pose::rna::get_number_base_stacks ( core::pose::Pose const &  pose_input)
bool core::pose::rna::has_virtual_rna_residue_variant_type ( pose::Pose &  pose,
Size const &  seq_num 
)
bool core::pose::rna::heavy_atom_is_polar ( core::conformation::Residue const &  rsd,
Size const &  atm 
)
void core::pose::rna::initialize_atoms_for_which_we_need_new_dofs ( utility::vector1< std::string > &  atoms_for_which_we_need_new_dofs,
Pose const &  pose,
Size const  i 
)
bool core::pose::rna::is_cutpoint_closed_atom ( core::conformation::Residue const &  rsd,
id::AtomID const &  id 
)
bool core::pose::rna::is_cutpoint_closed_torsion ( pose::Pose const &  pose,
id::TorsionID const &  torsion_id 
)
bool core::pose::rna::is_cutpoint_open ( Pose const &  pose,
Size const  i 
)
bool core::pose::rna::is_rna_chainbreak ( Pose const &  pose,
Size const  i 
)
bool core::pose::rna::is_torsion_valid ( pose::Pose const &  pose,
id::TorsionID const &  torsion_id,
bool  verbose,
bool  skip_chainbreak_torsions 
)
bool core::pose::rna::mutate_position ( pose::Pose &  pose,
Size const  i,
char const &  new_seq 
)
void core::pose::rna::output_boolean ( std::string const &  tag,
bool  boolean 
)

References core::chemical::rna::TR.

Referenced by is_torsion_valid().

void core::pose::rna::prepare_scratch_residue ( core::conformation::ResidueOP scratch_rsd,
core::conformation::Residue const &  start_rsd,
utility::vector1< Vector > const &  non_main_chain_sugar_coords,
Pose const &  pose 
)
void core::pose::rna::print_torsion_info ( pose::Pose const &  pose,
id::TorsionID const &  torsion_id 
)
void core::pose::rna::remove_virtual_rna_residue_variant_type ( pose::Pose &  pose,
Size const &  seq_num 
)
bool core::pose::rna::residue_is_bulge ( pose::Pose const &  pose,
Size const  i 
)
void core::pose::rna::update_edge_hbond_numbers ( conformation::Residue const &  rsd,
Size const &  atm,
Size N_W,
Size N_H,
Size N_S 
)
void core::pose::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 core::pose::rna::virtualize_5prime_phosphates ( pose::Pose &  pose)