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core::pose::rna Namespace Reference

Namespaces

 secstruct_legacy
 

Classes

struct  Atom_Bin
 
class  BasePair
 
class  BasePairStep
 
class  BaseStack
 
class  principal_angle_degrees
 
class  RNA_DataInfo
 Keep track of RNA chemical mapping data inside the pose. More...
 
class  RNA_Datum
 
class  RNA_FilteredBaseBaseInfo
 Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...
 
class  RNA_IdealCoord
 
class  RNA_RawBaseBaseInfo
 Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! / Also, should probably use EnergyGraph instead of FArrays – much smaller memory footprint (!) /. More...
 
class  RNA_Reactivity
 
class  RNA_SecStruct
 
class  RNA_SuiteAssignment
 
class  RNA_SuiteInfo
 
class  RNA_SuiteName
 
class  VDW_Grid
 
class  VDW_RepScreenInfo
 

Typedefs

typedef
utility::pointer::shared_ptr
< BasePair
BasePairOP
 
typedef
utility::pointer::shared_ptr
< BasePair const > 
BasePairCOP
 
typedef utility::vector1
< BasePair
RNA_BasePairList
 
typedef std::pair< Real, BasePairEnergyBasePair
 
typedef std::list< EnergyBasePairEnergyBasePairList
 
typedef
utility::pointer::shared_ptr
< BasePairStep
BasePairStepOP
 
typedef
utility::pointer::shared_ptr
< BasePairStep const > 
BasePairStepCOP
 
typedef
utility::pointer::shared_ptr
< BaseStack
BaseStackOP
 
typedef
utility::pointer::shared_ptr
< BaseStack const > 
BaseStackCOP
 
typedef utility::vector1
< BaseStack
RNA_BaseStackList
 
typedef std::pair< Real,
BaseStack
EnergyBaseStack
 
typedef std::list
< EnergyBaseStack
EnergyBaseStackList
 
typedef std::map< std::pair
< core::chemical::rna::BaseEdge,
core::chemical::rna::BaseEdge >
, std::map
< core::chemical::rna::BaseDoubletOrientation,
core::chemical::rna::LW_BaseDoubletOrientation > > 
LW_Table
 
using Matrix = numeric::xyzMatrix< Real >
 
typedef
utility::pointer::shared_ptr
< RNA_DataInfo
RNA_DataInfoOP
 
typedef
utility::pointer::weak_ptr
< RNA_DataInfo
RNA_DataInfoAP
 
typedef
utility::pointer::shared_ptr
< RNA_Reactivity
RNA_ReactivityOP
 
typedef
utility::pointer::weak_ptr
< RNA_Reactivity
RNA_ReactivityAP
 
typedef utility::vector1
< RNA_Datum
RNA_Data
 
typedef utility::vector1
< RNA_Reactivity
RNA_Reactivities
 
typedef
utility::pointer::shared_ptr
< RNA_FilteredBaseBaseInfo
RNA_FilteredBaseBaseInfoOP
 
typedef
utility::pointer::shared_ptr
< RNA_IdealCoord
RNA_IdealCoordOP
 
typedef
utility::pointer::shared_ptr
< RNA_RawBaseBaseInfo
RNA_RawBaseBaseInfoOP
 
typedef
utility::pointer::weak_ptr
< RNA_RawBaseBaseInfo
RNA_RawBaseBaseInfoAP
 
typedef
utility::pointer::shared_ptr
< RNA_SecStruct
RNA_SecStructOP
 
typedef
utility::pointer::shared_ptr
< RNA_SecStruct const > 
RNA_SecStructCOP
 
typedef
utility::pointer::shared_ptr
< RNA_SuiteName
RNA_SuiteNameOP
 
typedef
utility::pointer::shared_ptr
< VDW_Grid
VDW_GridOP
 
typedef
utility::pointer::shared_ptr
< VDW_Grid const > 
VDW_GridCOP
 
typedef
utility::pointer::shared_ptr
< VDW_RepScreenInfo
VDW_RepScreenInfoOP
 
typedef
utility::pointer::shared_ptr
< VDW_RepScreenInfo const > 
VDW_RepScreenInfoCOP
 

Enumerations

enum  RNA_ReactivityType {
  NO_REACTIVITY, DMS, CMCT, SHAPE_1M7,
  HRF
}
 
enum  StubStubType { NONE, BASE_CENTROID, O3P_TO_O5P, CHAINBREAK }
 
enum  Terminus { FIVE_PRIME, THREE_PRIME }
 

Functions

bool operator< (BasePair const &lhs, BasePair const &rhs)
 
bool operator== (BasePair const &lhs, BasePair const &rhs)
 
std::ostream & operator<< (std::ostream &out, BasePair const &s)
 
std::ostream & operator<< (std::ostream &os, BasePairStep const &bps)
 
bool operator< (BaseStack const &lhs, BaseStack const &rhs)
 
std::ostream & operator<< (std::ostream &out, BaseStack const &s)
 
LW_BaseDoubletOrientation get_LW_orientation (BaseEdge const &edge1, BaseEdge const &edge2, BaseDoubletOrientation const &orientation)
 
BaseDoubletOrientation get_base_doublet_orientation_from_LW (BaseEdge const &edge1, BaseEdge const &edge2, LW_BaseDoubletOrientation const &lw_orientation)
 
LW_Table const & get_leontis_westhof_table ()
 
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, BaseEdge &edge_classification)
 
BaseDoubletOrientation 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)
 
utility::vector1
< core::pose::rna::BasePair
classify_base_pairs (core::pose::Pose const &pose_input)
 
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)
 
EnergyBaseStackList get_scored_base_stack_list (core::pose::Pose const &pose_input)
 
bool mutate_position (pose::Pose &pose, Size const i, char const new_seq)
 
bool mutate_position (pose::Pose &pose, Size const i, chemical::ResidueType const &rt)
 
bool mutate_position (pose::Pose &pose, Size const i, std::string const &name3)
 
void figure_out_reasonable_rna_fold_tree (pose::Pose &pose, bool force_cut_at_rna_chainbreak)
 
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)
 Returns true if a position is an RNA chainbreak. More...
 
bool is_tna_chainbreak (Pose const &pose, Size const i)
 Returns true if a position is an TNA chainbreak. More...
 
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 position_cutpoint_phosphate_torsions (pose::Pose &current_pose, Size const five_prime_chainbreak, Size three_prime_chainbreak)
 
bool is_cutpoint_closed_by_atom_name (chemical::ResidueType const &rsd_1, chemical::ResidueType const &rsd_2, chemical::ResidueType const &rsd_3, chemical::ResidueType const &rsd_4, id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3, id::AtomID const &id4)
 
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::chemical::ResidueType 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)
 
bool check_in_base_pair_list (pose::rna::BasePair const &base_pair, utility::vector1< core::pose::rna::BasePair > const &base_pair_list)
 
void get_number_base_pairs (pose::Pose const &pose, Size &nwc, Size &nnwc, Size &bs)
 
void add_number_base_pairs (pose::Pose &pose)
 
void add_number_base_pairs (pose::Pose const &pose, io::silent::SilentStruct &s)
 
void get_number_native_base_pairs (pose::Pose &pose, pose::Pose const &native_pose, Size &pN_WC, Size &pN_NWC, Size &pN_BP, Size &pnatWC, Size &pnatNWC, Size &pnatBP, Real &pf_natWC, Real &pf_natNWC, Real &pf_natBP)
 
void add_number_native_base_pairs (pose::Pose &pose, pose::Pose const &native_pose, io::silent::SilentStruct &s)
 
void add_number_native_base_pairs (pose::Pose &pose, pose::Pose const &native_pose)
 
void apply_Aform_torsions (pose::Pose &pose, Size const n)
 
ChiState get_residue_base_state (core::pose::Pose const &pose, Size const seq_num)
 
PuckerState get_residue_pucker_state (core::pose::Pose const &pose, Size const seq_num)
 
utility::vector1< std::pair
< core::id::TorsionID,
core::Real > > 
get_suite_torsion_info (core::pose::Pose const &pose, Size const i)
 'suite' backbone torsion – useful in setting up cutpoint with OVL1, OVL2, OVU atoms More...
 
void apply_suite_torsion_info (core::pose::Pose &pose, utility::vector1< std::pair< core::id::TorsionID, core::Real > > const &suite_torsion_info)
 useful in setting up cutpoint with OVL1, OVL2, OVU atoms More...
 
Real get_op2_op1_sign (pose::Pose const &pose)
 
Real get_op2_op1_sign (pose::Pose const &pose, Size res_num)
 
void make_phosphate_nomenclature_matches_mini (pose::Pose &pose)
 
void add_virtual_O2Prime_hydrogen (core::pose::Pose &pose)
 
Atom_Bin get_atom_bin (numeric::xyzVector< core::Real > const &atom_pos, numeric::xyzVector< core::Real > const &ref_xyz, core::Real const atom_bin_size, int const bin_offset)
 
bool is_atom_bin_in_range (Atom_Bin const &atom_pos_bin, int const bin_max)
 
utility::vector1< std::string > tokenize (std::string const &str, std::string const &delimiters)
 
core::Size string_to_int (std::string const &input_string)
 
std::string remove_bracketed (std::string const &sequence)
 
void remove_and_store_bracketed (std::string const &working_sequence, std::string &working_sequence_clean, std::map< Size, std::string > &special_res)
 
void add_chi_constraints (pose::Pose &pose, core::scoring::func::FuncOP chi_potential_restraint, utility::vector1< Size > const &rna_chi_res)
 
void add_syn_chi_constraints (core::pose::Pose &pose)
 
void add_anti_chi_constraints (core::pose::Pose &pose)
 
void add_syn_anti_chi_constraints (core::pose::Pose &pose)
 
utility::vector1
< core::id::TorsionID
get_suite_torsion_ids (Size const i)
 
void get_stub_stub (conformation::Residue const &rsd1, conformation::Residue const &rsd2, kinematics::Stub &stub1, kinematics::Stub &stub2, StubStubType const &stub_stub_type)
 
void setup_base_pair_constraints (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > const &pairings, Real const scale_factor, bool const use_flat_harmonic)
 
void get_base_pairing_list (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > &base_pairing_list)
 
void assert_phosphate_nomenclature_matches_mini (pose::Pose const &pose)
 
void virtualize_free_rna_moieties (pose::Pose &pose)
 
utility::vector1< booldetect_base_contacts (core::pose::Pose const &pose)
 
bool check_phosphate_contacts_donor (utility::vector1< Vector > const &op_xyz_list, utility::vector1< Vector > const &donor_atom_xyz_list, utility::vector1< Vector > const &donor_base_atom_xyz_list)
 
bool check_phosphate_contacts_donor (pose::Pose const &pose, Size const n)
 
utility::vector1< booldetect_phosphate_contacts (pose::Pose const &pose)
 
void get_phosphate_atom_and_neighbor_list (core::pose::Pose const &pose, Size const n, Terminus const t, utility::vector1< Vector > &donor_atom_xyz_list, utility::vector1< Vector > &donor_base_atom_xyz_list, utility::vector1< Size > &neighbor_copy_dofs)
 
utility::vector1< booldetect_sugar_contacts (pose::Pose const &pose)
 
bool detect_sugar_contacts (pose::Pose const &pose, Size const moving_res, Distance o2prime_contact_distance_cutoff_)
 
void setup_three_prime_phosphate_based_on_next_residue (pose::Pose &pose, Size const n)
 
bool base_pair_step_moving (core::pose::rna::BasePairStep const &base_pair_step, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, pose::Pose const &pose)
 
bool base_pair_moving (core::pose::rna::BasePair const &base_pair, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, core::pose::Pose const &pose)
 
bool moveable_jump (id::AtomID const &jump_atom_id1, id::AtomID const &jump_atom_id2, core::pose::toolbox::AtomLevelDomainMap const &atom_level_domain_map)
 
bool moveable_jump (Size const jump_pos1, Size const jump_pos2, core::pose::toolbox::AtomLevelDomainMap const &atom_level_domain_map)
 
utility::vector1< Sizeget_rigid_body_jumps (core::pose::Pose const &pose)
 
void fill_in_default_jump_atoms (kinematics::FoldTree &f, pose::Pose const &pose)
 
void fill_in_default_jump_atoms (pose::Pose &pose)
 
Vector get_sugar_centroid (core::conformation::Residue const &rsd)
 
void get_base_pairing_info (pose::Pose const &pose, Size const &seqpos, char &secstruct, FArray1D< bool > &edge_is_base_pairing)
 
void output_base_pairs (std::ostream &out, core::pose::rna::RNA_BasePairList const &base_pair_list, core::pose::Pose const &pose)
 Output base pairs detected for RNA, including noncanonicals. Must previously score pose with RNA_LORES. More...
 
void output_base_stacks (std::ostream &out, core::pose::rna::RNA_BaseStackList const &base_stack_list, core::pose::Pose const &pose)
 Output base stacks detected for RNA. Must previously score pose with RNA_LORES. More...
 
void output_stems (std::ostream &out, core::scoring::rna::RNA_Motifs const &rna_motifs, core::pose::Pose const &pose)
 Output stems (>=2 base-pair helices) detected for RNA, including noncanonicals. Must previously score pose with RNA_LORES. More...
 
utility::vector1< std::pair
< char, std::string > > 
figure_out_rna_chains (pose::Pose const &pose, utility::vector1< std::string > const &chains=utility::vector1< std::string >())
 Figure out chains that have RNA in them. Can supply chains from command-line to focus on particular RNA chains. More...
 
pose::Pose extract_rna_chains (pose::Pose const &full_pose, utility::vector1< ChainSegID > const &chain_segids)
 Pull out RNA from pose, in chains specified by chain_segids. More...
 
void update_map (std::map< ChainSegID, std::set< core::Size > > &ligand_map, std::map< ChainSegID, std::string > &ligand_tag, Size const &i, ChainSegID const &chain_segid_j, core::conformation::Residue const &rsd_j)
 
void output_ligands (std::ostream &out, pose::Pose const &pose, utility::vector1< ChainSegID > const &chain_segids)
 Output contacts of RNA chains (specified in chain_segids) to any non-RNA chains ("ligands"). More...
 
void output_other_contacts (std::ostream &out, pose::Pose const &pose)
 Output residue-residue interactions that are not base pairs or base stacks;. More...
 
void figure_out_secstruct (pose::Pose &pose)
 
void remove_upper_lower_variants_from_RNA (pose::Pose &pose)
 get rid of Upper and Lower from RNA; useful for cleaner output of annotated_sequence. More...
 
void apply_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num, utility::vector1< Size > const &working_cutpoint_closed_list, bool const apply_check=true)
 
void apply_suite_torsion_info (core::pose::Pose &pose, utility::vector1< std::pair< id::TorsionID, Real > > const &suite_torsion_info)
 useful in setting up cutpoint with OVL1, OVL2, OVU atoms More...
 
void setup_base_pair_constraints (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const &pairings, core::Real const scale_factor=1.0, bool const use_flat_harmonic=false)
 
void get_base_pairing_list (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &base_pairing_list)
 
bool check_phosphate_contacts_donor (utility::vector1< core::Vector > const &op_xyz_list, utility::vector1< core::Vector > const &donor_atom_xyz_list, utility::vector1< core::Vector > const &donor_base_atom_xyz_list)
 
void get_phosphate_atom_and_neighbor_list (core::pose::Pose const &pose, Size const n, Terminus const t, utility::vector1< core::Vector > &donor_atom_xyz_list, utility::vector1< core::Vector > &donor_base_atom_xyz_list, utility::vector1< core::Size > &neighbor_copy_dofs)
 
void get_base_pairing_info (core::pose::Pose const &pose, core::Size const &seqpos, char &secstruct, ObjexxFCL::FArray1D< bool > &edge_is_base_pairing)
 
pose::Pose extract_rna_chains (pose::Pose const &full_pose, utility::vector1< pose::ChainSegID > const &chain_segids)
 Pull out RNA from pose, in chains specified by chain_segids. More...
 
void output_ligands (std::ostream &out, pose::Pose const &pose, utility::vector1< pose::ChainSegID > const &chain_segids)
 Output contacts of RNA chains (specified in chain_segids) to any non-RNA chains ("ligands"). More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< BasePair const > core::pose::rna::BasePairCOP
typedef utility::pointer::shared_ptr< BasePair > core::pose::rna::BasePairOP
typedef utility::pointer::shared_ptr< BasePairStep const > core::pose::rna::BasePairStepCOP
typedef utility::pointer::shared_ptr< BasePairStep > core::pose::rna::BasePairStepOP
typedef utility::pointer::shared_ptr< BaseStack const > core::pose::rna::BaseStackCOP
typedef utility::pointer::shared_ptr< BaseStack > core::pose::rna::BaseStackOP
using core::pose::rna::Matrix = typedef numeric::xyzMatrix<Real>
typedef utility::vector1< BasePair > core::pose::rna::RNA_BasePairList
typedef utility::vector1< BaseStack > core::pose::rna::RNA_BaseStackList
typedef utility::vector1< RNA_Datum > core::pose::rna::RNA_Data
typedef utility::pointer::weak_ptr< RNA_DataInfo > core::pose::rna::RNA_DataInfoAP
typedef utility::pointer::shared_ptr< RNA_DataInfo > core::pose::rna::RNA_DataInfoOP
typedef utility::pointer::shared_ptr< RNA_IdealCoord > core::pose::rna::RNA_IdealCoordOP
typedef utility::pointer::weak_ptr< RNA_RawBaseBaseInfo > core::pose::rna::RNA_RawBaseBaseInfoAP
typedef utility::pointer::shared_ptr< RNA_RawBaseBaseInfo > core::pose::rna::RNA_RawBaseBaseInfoOP
typedef utility::pointer::weak_ptr< RNA_Reactivity > core::pose::rna::RNA_ReactivityAP
typedef utility::pointer::shared_ptr< RNA_Reactivity > core::pose::rna::RNA_ReactivityOP
typedef utility::pointer::shared_ptr< RNA_SecStruct const > core::pose::rna::RNA_SecStructCOP
typedef utility::pointer::shared_ptr< RNA_SecStruct > core::pose::rna::RNA_SecStructOP
typedef utility::pointer::shared_ptr< RNA_SuiteName > core::pose::rna::RNA_SuiteNameOP
typedef utility::pointer::shared_ptr< VDW_Grid const > core::pose::rna::VDW_GridCOP
typedef utility::pointer::shared_ptr< VDW_Grid > core::pose::rna::VDW_GridOP
typedef utility::pointer::shared_ptr< VDW_RepScreenInfo const > core::pose::rna::VDW_RepScreenInfoCOP
typedef utility::pointer::shared_ptr< VDW_RepScreenInfo > core::pose::rna::VDW_RepScreenInfoOP

Enumeration Type Documentation

Enumerator
NO_REACTIVITY 
DMS 
CMCT 
SHAPE_1M7 
HRF 

O3P_TO_O5P ...-C4'-C3'-O3' to O5'-C5'-C4'-... Centers are O3' and O5'. CHAINBREAK O3'-OVL1-OVL2 to OVU-P-O5', centered on OVL1 and P [overlap means transl = 0, rotation = I ]

Enumerator
NONE 
BASE_CENTROID 
O3P_TO_O5P 
CHAINBREAK 
Enumerator
FIVE_PRIME 
THREE_PRIME 

Function Documentation

void core::pose::rna::add_anti_chi_constraints ( core::pose::Pose pose)
void core::pose::rna::add_chi_constraints ( pose::Pose pose,
core::scoring::func::FuncOP  chi_potential_restraint,
utility::vector1< Size > const &  rna_chi_res 
)
void core::pose::rna::add_number_base_pairs ( pose::Pose pose)
void core::pose::rna::add_number_base_pairs ( pose::Pose const &  pose,
io::silent::SilentStruct s 
)
void core::pose::rna::add_number_native_base_pairs ( pose::Pose pose,
pose::Pose const &  native_pose,
io::silent::SilentStruct s 
)
void core::pose::rna::add_number_native_base_pairs ( pose::Pose pose,
pose::Pose const &  native_pose 
)
void core::pose::rna::add_syn_anti_chi_constraints ( core::pose::Pose pose)
void core::pose::rna::add_syn_chi_constraints ( core::pose::Pose pose)
void core::pose::rna::add_virtual_O2Prime_hydrogen ( core::pose::Pose pose)
void core::pose::rna::apply_Aform_torsions ( pose::Pose pose,
Size const  n 
)
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_suite_torsion_info ( core::pose::Pose pose,
utility::vector1< std::pair< id::TorsionID, Real > > const &  suite_torsion_info 
)
void core::pose::rna::apply_suite_torsion_info ( core::pose::Pose pose,
utility::vector1< std::pair< core::id::TorsionID, core::Real > > const &  suite_torsion_info 
)
void core::pose::rna::apply_virtual_rna_residue_variant_type ( pose::Pose pose,
Size const &  seq_num,
utility::vector1< Size > const &  working_cutpoint_closed_list,
bool const  apply_check = true 
)
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 
)
void core::pose::rna::assert_phosphate_nomenclature_matches_mini ( pose::Pose const &  pose)
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::base_pair_moving ( core::pose::rna::BasePair const &  base_pair,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map,
core::pose::Pose const &  pose 
)
bool core::pose::rna::base_pair_step_moving ( core::pose::rna::BasePairStep const &  base_pair_step,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map,
pose::Pose const &  pose 
)
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 
)
bool core::pose::rna::check_in_base_pair_list ( pose::rna::BasePair const &  base_pair,
utility::vector1< core::pose::rna::BasePair > const &  base_pair_list 
)
bool core::pose::rna::check_phosphate_contacts_donor ( utility::vector1< core::Vector > const &  op_xyz_list,
utility::vector1< core::Vector > const &  donor_atom_xyz_list,
utility::vector1< core::Vector > const &  donor_base_atom_xyz_list 
)
bool core::pose::rna::check_phosphate_contacts_donor ( utility::vector1< Vector > const &  op_xyz_list,
utility::vector1< Vector > const &  donor_atom_xyz_list,
utility::vector1< Vector > const &  donor_base_atom_xyz_list 
)
bool core::pose::rna::check_phosphate_contacts_donor ( pose::Pose const &  pose,
Size const  n 
)
utility::vector1< core::pose::rna::BasePair > core::pose::rna::classify_base_pairs ( core::pose::Pose const &  pose_input)
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 
)
utility::vector1< bool > core::pose::rna::detect_base_contacts ( core::pose::Pose const &  pose)
utility::vector1< bool > core::pose::rna::detect_phosphate_contacts ( pose::Pose const &  pose)
utility::vector1< bool > core::pose::rna::detect_sugar_contacts ( pose::Pose const &  pose)
bool core::pose::rna::detect_sugar_contacts ( pose::Pose const &  pose,
Size const  moving_res,
Distance  o2prime_contact_distance_cutoff_ 
)
pose::Pose core::pose::rna::extract_rna_chains ( pose::Pose const &  full_pose,
utility::vector1< pose::ChainSegID > const &  chain_segids 
)
pose::Pose core::pose::rna::extract_rna_chains ( pose::Pose const &  full_pose,
utility::vector1< ChainSegID > const &  chain_segids 
)
BaseDoubletOrientation 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,
BaseEdge edge_classification 
)
void core::pose::rna::figure_out_reasonable_rna_fold_tree ( pose::Pose pose,
bool  force_cut_at_rna_chainbreak 
)
utility::vector1< std::pair< char, std::string > > core::pose::rna::figure_out_rna_chains ( pose::Pose const &  pose,
utility::vector1< std::string > const &  chains 
)

Figure out chains that have RNA in them. Can supply chains from command-line to focus on particular RNA chains.

References core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

void core::pose::rna::figure_out_secstruct ( pose::Pose pose)
void core::pose::rna::fill_in_default_jump_atoms ( kinematics::FoldTree f,
pose::Pose const &  pose 
)
void core::pose::rna::fill_in_default_jump_atoms ( 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 
)
Atom_Bin core::pose::rna::get_atom_bin ( numeric::xyzVector< core::Real > const &  atom_pos,
numeric::xyzVector< core::Real > const &  ref_xyz,
core::Real const  atom_bin_size,
int const  bin_offset 
)
core::chemical::rna::BaseDoubletOrientation core::pose::rna::get_base_doublet_orientation_from_LW ( BaseEdge const &  edge1,
BaseEdge const &  edge2,
LW_BaseDoubletOrientation const &  lw_orientation 
)
void core::pose::rna::get_base_pairing_info ( core::pose::Pose const &  pose,
core::Size const &  seqpos,
char &  secstruct,
ObjexxFCL::FArray1D< bool > &  edge_is_base_pairing 
)
void core::pose::rna::get_base_pairing_info ( pose::Pose const &  pose,
Size const &  seqpos,
char &  secstruct,
FArray1D< bool > &  edge_is_base_pairing 
)
void core::pose::rna::get_base_pairing_list ( core::pose::Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > &  base_pairing_list 
)
void core::pose::rna::get_base_pairing_list ( pose::Pose pose,
utility::vector1< std::pair< Size, Size > > &  base_pairing_list 
)
LW_Table const & core::pose::rna::get_leontis_westhof_table ( )

From: RNA. 2001 Apr;7(4):499-512. "Geometric nomenclature and classification of RNA base pairs." Leontis NB, Westhof E. Table formatted to match personal communication from N. Leontis to R. Das.

References core::chemical::rna::ANTIPARALLEL, core::chemical::rna::CIS, core::chemical::rna::HOOGSTEEN, core::init::init(), core::chemical::rna::PARALLEL, SUGAR, core::chemical::rna::TRANS, and core::chemical::rna::WATSON_CRICK.

Referenced by get_base_doublet_orientation_from_LW(), and get_LW_orientation().

core::chemical::rna::LW_BaseDoubletOrientation core::pose::rna::get_LW_orientation ( BaseEdge const &  edge1,
BaseEdge const &  edge2,
BaseDoubletOrientation const &  orientation 
)
void core::pose::rna::get_number_base_pairs ( pose::Pose const &  pose,
Size nwc,
Size nnwc,
Size bs 
)
core::Size core::pose::rna::get_number_base_stacks ( core::pose::Pose const &  pose_input)
void core::pose::rna::get_number_native_base_pairs ( pose::Pose pose,
pose::Pose const &  native_pose,
Size pN_WC,
Size pN_NWC,
Size pN_BP,
Size pnatWC,
Size pnatNWC,
Size pnatBP,
Real pf_natWC,
Real pf_natNWC,
Real pf_natBP 
)
Real core::pose::rna::get_op2_op1_sign ( pose::Pose const &  pose)
Real core::pose::rna::get_op2_op1_sign ( pose::Pose const &  pose,
Size  res_num 
)
void core::pose::rna::get_phosphate_atom_and_neighbor_list ( core::pose::Pose const &  pose,
Size const  n,
Terminus const  t,
utility::vector1< core::Vector > &  donor_atom_xyz_list,
utility::vector1< core::Vector > &  donor_base_atom_xyz_list,
utility::vector1< core::Size > &  neighbor_copy_dofs 
)
void core::pose::rna::get_phosphate_atom_and_neighbor_list ( core::pose::Pose const &  pose,
Size const  n,
Terminus const  t,
utility::vector1< Vector > &  donor_atom_xyz_list,
utility::vector1< Vector > &  donor_base_atom_xyz_list,
utility::vector1< Size > &  neighbor_copy_dofs 
)
core::chemical::rna::ChiState core::pose::rna::get_residue_base_state ( core::pose::Pose const &  pose,
Size const  seq_num 
)
core::chemical::rna::PuckerState core::pose::rna::get_residue_pucker_state ( core::pose::Pose const &  pose,
Size const  seq_num 
)
utility::vector1< core::Size > core::pose::rna::get_rigid_body_jumps ( core::pose::Pose const &  pose)
EnergyBaseStackList core::pose::rna::get_scored_base_stack_list ( core::pose::Pose const &  pose_input)
void core::pose::rna::get_stub_stub ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
kinematics::Stub stub1,
kinematics::Stub stub2,
StubStubType const &  stub_stub_type 
)
Vector core::pose::rna::get_sugar_centroid ( core::conformation::Residue const &  rsd)
utility::vector1< core::id::TorsionID > core::pose::rna::get_suite_torsion_ids ( Size const  i)
utility::vector1< std::pair< id::TorsionID, Real > > core::pose::rna::get_suite_torsion_info ( core::pose::Pose const &  pose,
Size const  i 
)

'suite' backbone torsion – useful in setting up cutpoint with OVL1, OVL2, OVU atoms

Could this be made more general? Figured out through knowledge of where side chain atoms connect to polymeric backbone?

References core::id::BB, core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::torsion().

Referenced by core::import_pose::add_cutpoint_closed(), and protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::put_in_cutpoints().

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_atom_bin_in_range ( Atom_Bin const &  atom_pos_bin,
int const  bin_max 
)
bool core::pose::rna::is_cutpoint_closed_atom ( core::chemical::ResidueType const &  rsd,
id::AtomID const &  id 
)
bool core::pose::rna::is_cutpoint_closed_by_atom_name ( chemical::ResidueType const &  rsd_1,
chemical::ResidueType const &  rsd_2,
chemical::ResidueType const &  rsd_3,
chemical::ResidueType const &  rsd_4,
id::AtomID const &  id1,
id::AtomID const &  id2,
id::AtomID const &  id3,
id::AtomID const &  id4 
)

References is_cutpoint_closed_atom().

Referenced by is_torsion_valid().

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 
)

Returns true if a position is an RNA chainbreak.

Returns true if i is greater than pose.size() or less than 1, which is almost certainly designed to account for the semantics of 'chainbreaks' for poses in stepwise/FARFAR contexts.

References core::chemical::rna::RNA_Info::o3prime_atom_index(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::chemical::ResidueType::RNA_info(), core::pose::Pose::size(), core::chemical::rna::TR(), and core::conformation::Residue::type().

Referenced by core::pose::rna::RNA_SuiteName::assign(), core::pose::rna::RNA_SuiteName::closest_suite(), figure_out_reasonable_rna_fold_tree(), and is_torsion_valid().

bool core::pose::rna::is_tna_chainbreak ( Pose const &  pose,
Size const  i 
)

Returns true if a position is an TNA chainbreak.

Returns true if i is greater than pose.size() or less than 1, which is almost certainly designed to account for the semantics of 'chainbreaks' for poses in stepwise/FARFAR contexts.

References core::chemical::rna::RNA_Info::o2prime_index(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::chemical::ResidueType::RNA_info(), core::pose::Pose::size(), core::chemical::rna::TR(), and core::conformation::Residue::type().

Referenced by is_torsion_valid().

bool core::pose::rna::is_torsion_valid ( pose::Pose const &  pose,
id::TorsionID const &  torsion_id,
bool  verbose,
bool  skip_chainbreak_torsions 
)
void core::pose::rna::make_phosphate_nomenclature_matches_mini ( pose::Pose pose)
bool core::pose::rna::moveable_jump ( id::AtomID const &  jump_atom_id1,
id::AtomID const &  jump_atom_id2,
core::pose::toolbox::AtomLevelDomainMap const &  atom_level_domain_map 
)
bool core::pose::rna::moveable_jump ( Size const  jump_pos1,
Size const  jump_pos2,
core::pose::toolbox::AtomLevelDomainMap const &  atom_level_domain_map 
)
bool core::pose::rna::mutate_position ( pose::Pose pose,
Size const  i,
char const  new_seq 
)
bool core::pose::rna::mutate_position ( pose::Pose pose,
Size const  i,
chemical::ResidueType const &  rt 
)
bool core::pose::rna::mutate_position ( pose::Pose pose,
Size const  i,
std::string const &  name3 
)
bool core::pose::rna::operator< ( BaseStack const &  lhs,
BaseStack const &  rhs 
)
bool core::pose::rna::operator< ( BasePair const &  lhs,
BasePair const &  rhs 
)
std::ostream& core::pose::rna::operator<< ( std::ostream &  os,
BasePairStep const &  bps 
)
std::ostream& core::pose::rna::operator<< ( std::ostream &  out,
BaseStack const &  s 
)
std::ostream& core::pose::rna::operator<< ( std::ostream &  out,
BasePair const &  s 
)
bool core::pose::rna::operator== ( BasePair const &  lhs,
BasePair const &  rhs 
)
void core::pose::rna::output_base_pairs ( std::ostream &  out,
core::pose::rna::RNA_BasePairList const &  base_pair_list,
pose::Pose const &  pose 
)

Output base pairs detected for RNA, including noncanonicals. Must previously score pose with RNA_LORES.

References core::chemical::rna::get_edge_from_num(), core::chemical::rna::get_LW_orientation_from_num(), and core::pose::Pose::pdb_info().

void core::pose::rna::output_base_stacks ( std::ostream &  out,
core::pose::rna::RNA_BaseStackList const &  base_stack_list,
pose::Pose const &  pose 
)

Output base stacks detected for RNA. Must previously score pose with RNA_LORES.

References core::chemical::rna::get_orientation_from_num(), core::chemical::rna::get_side_from_num(), and core::pose::Pose::pdb_info().

void core::pose::rna::output_boolean ( std::string const &  tag,
bool  boolean 
)

References protocols::comparative_modeling::features::A, and core::chemical::rna::TR().

Referenced by protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::cluster(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_jump_partners(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), is_torsion_valid(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_fixed_res(), and protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_jump_point_pair_list().

void core::pose::rna::output_ligands ( std::ostream &  out,
pose::Pose const &  pose,
utility::vector1< ChainSegID > const &  chain_segids 
)

Output contacts of RNA chains (specified in chain_segids) to any non-RNA chains ("ligands").

TODO: We should recognize non-RNA bits that are supplied in the PDB with the same chains as the RNA polymers. Happens, e.g., in the glycine riboswitch 3P49 where the glycines are in chain A along with the RNA.

References core::pose::Pose::energies(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), and update_map().

void core::pose::rna::output_ligands ( std::ostream &  out,
pose::Pose const &  pose,
utility::vector1< ChainSegID > const &  chain_segids 
)

Output contacts of RNA chains (specified in chain_segids) to any non-RNA chains ("ligands").

TODO: We should recognize non-RNA bits that are supplied in the PDB with the same chains as the RNA polymers. Happens, e.g., in the glycine riboswitch 3P49 where the glycines are in chain A along with the RNA.

References core::pose::Pose::energies(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), and update_map().

void core::pose::rna::output_other_contacts ( std::ostream &  out,
pose::Pose const &  pose 
)
void core::pose::rna::output_stems ( std::ostream &  out,
RNA_Motifs const &  rna_motifs,
pose::Pose const &  pose 
)
void core::pose::rna::position_cutpoint_phosphate_torsions ( pose::Pose current_pose,
Size const  five_prime_chainbreak,
Size  three_prime_chainbreak 
)
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_and_store_bracketed ( std::string const &  working_sequence,
std::string &  working_sequence_clean,
std::map< Size, std::string > &  special_res 
)
std::string core::pose::rna::remove_bracketed ( std::string const &  sequence)

Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), core::pose::full_model_info::check_full_model_info_OK(), protocols::stepwise::modeler::rna::check_validity_and_get_working_res(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::do_some_clustering(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_chain_boundaries(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_residue_prepend(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_working_sequence_and_mapping(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_working_sequence_and_mapping(), core::import_pose::FullModelPoseBuilder::fill_full_model_info(), core::pose::full_model_info::FullModelParameters::FullModelParameters(), core::sequence::get_conventional_chains_and_numbering(), core::import_pose::get_cutpoints_from_numbering(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::Import_pose(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::initialize_is_fixed_res(), core::pose::full_model_info::initialize_parameters(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_pre_proline(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_fixed_res(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_fixed_residues(), protocols::rna::movers::RNAThreadAndMinimizeMover::set_up_target_sequence(), protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_additional_cutpoint_closed(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_full_model_info(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::legacy::modeler::rna::setup_rna_working_parameters(), protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), core::pose::full_model_info::FullModelParameters::size(), protocols::stepwise::modeler::align::StepWisePoseAligner::update_reference_pose_local(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition().

void core::pose::rna::remove_upper_lower_variants_from_RNA ( pose::Pose pose)
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::setup_base_pair_constraints ( pose::Pose pose,
utility::vector1< std::pair< Size, Size > > const &  pairings,
Real const  scale_factor,
bool const  use_flat_harmonic 
)

Adds 2-3 constraints between donor hydrogen and acceptor across C-G, A-U, or G-U pairs, and asks that C1'-C1' distance be near 10.5 Angstroms (prevents stacking!)

"suppress_factor" reduces strength, in use by FARNA/RNA_DeNovo

use_harmonic is standard 'spring' like function that can pull in bases from very far away to optimal distance of 1.9 Angstroms:

H-bond ( x - 1.9 A )/( 0.25 / scale_factor )^2

C1'-C1' ( x - 10.5 A )/( 1/0 / scale_factor )^2

If use_flat_harmonic is set to true, functions are zero out to tolerance of 1.0 A and 2.0 A, and then go up quadratically. [used in RECCES/free-energy estimation where we want constraint = 0 when base pairs are formed rather than some small number].

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::scoring::base_pair_constraint, core::chemical::rna::RNA_Info::c1prime_atom_index(), core::chemical::rna::CIS, core::chemical::rna::get_base_pair_atoms(), core::chemical::element::I, core::chemical::ResidueType::is_coarse(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueTypeBase::name1(), core::pose::Pose::residue_type(), core::chemical::ResidueType::RNA_info(), core::chemical::rna::TR(), and core::chemical::rna::WATSON_CRICK.

Referenced by protocols::recces::options::RECCES_Options::initialize_from_command_line(), core::import_pose::RNA_HelixAssembler::put_constraints_on_base_step(), protocols::recces::recces_pose_setup(), and core::import_pose::RNA_BasePairHandler::setup_base_pair_constraints().

void core::pose::rna::setup_base_pair_constraints ( pose::Pose pose,
utility::vector1< std::pair< Size, Size > > const &  pairings,
Real const  scale_factor,
bool const  use_flat_harmonic 
)

Adds 2-3 constraints between donor hydrogen and acceptor across C-G, A-U, or G-U pairs, and asks that C1'-C1' distance be near 10.5 Angstroms (prevents stacking!)

"suppress_factor" reduces strength, in use by FARNA/RNA_DeNovo

use_harmonic is standard 'spring' like function that can pull in bases from very far away to optimal distance of 1.9 Angstroms:

H-bond ( x - 1.9 A )/( 0.25 / scale_factor )^2

C1'-C1' ( x - 10.5 A )/( 1/0 / scale_factor )^2

If use_flat_harmonic is set to true, functions are zero out to tolerance of 1.0 A and 2.0 A, and then go up quadratically. [used in RECCES/free-energy estimation where we want constraint = 0 when base pairs are formed rather than some small number].

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::scoring::base_pair_constraint, core::chemical::rna::RNA_Info::c1prime_atom_index(), core::chemical::rna::CIS, core::chemical::rna::get_base_pair_atoms(), core::chemical::element::I, core::chemical::ResidueType::is_coarse(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueTypeBase::name1(), core::pose::Pose::residue_type(), core::chemical::ResidueType::RNA_info(), core::chemical::rna::TR(), and core::chemical::rna::WATSON_CRICK.

Referenced by protocols::recces::options::RECCES_Options::initialize_from_command_line(), core::import_pose::RNA_HelixAssembler::put_constraints_on_base_step(), protocols::recces::recces_pose_setup(), and core::import_pose::RNA_BasePairHandler::setup_base_pair_constraints().

void core::pose::rna::setup_three_prime_phosphate_based_on_next_residue ( pose::Pose pose,
Size const  n 
)
core::Size core::pose::rna::string_to_int ( std::string const &  input_string)
utility::vector1< std::string > core::pose::rna::tokenize ( std::string const &  str,
std::string const &  delimiters 
)
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::update_map ( std::map< ChainSegID, std::set< core::Size > > &  ligand_map,
std::map< ChainSegID, std::string > &  ligand_tag,
Size const &  i,
ChainSegID const &  chain_segid_j,
core::conformation::Residue const &  rsd_j 
)
void core::pose::rna::virtualize_5prime_phosphates ( pose::Pose pose)
void core::pose::rna::virtualize_free_rna_moieties ( pose::Pose pose)