util.cc File Reference

#include <core/pose/rna/util.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeFinder.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/chemical/rna/RNA_Info.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/id/TorsionID.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Stub.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/pose/rna/RNA_IdealCoord.hh>
#include <core/pose/rna/BasePair.hh>
#include <core/pose/rna/BasePairStep.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.hh>
#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <core/pose/rna/VDW_Grid.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/CircularSplineFunc.hh>
#include <core/scoring/methods/chainbreak_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/FlatHarmonicFunc.hh>
#include <core/scoring/func/FadeFunc.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/pose/rna/secstruct_legacy/RNA_SecStructLegacyInfo.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <core/scoring/rna/RNA_Motif.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <utility/vector1.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <map>

Namespaces
	core
	A class for reading in the atom type properties.
	core::pose
	core::pose::rna

Functions
static basic::Tracer	TR ("core.pose.rna.RNA_Util")
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)
void	core::pose::rna::figure_out_reasonable_rna_fold_tree (pose::Pose &pose, bool force_cut_at_rna_chainbreak)
void	core::pose::rna::virtualize_5prime_phosphates (pose::Pose &pose)
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. More...
bool	core::pose::rna::is_tna_chainbreak (Pose const &pose, Size const i)
	Returns true if a position is an TNA chainbreak. More...
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::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::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	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_ideal_c2endo_sugar_coords (Pose &pose, Size const i)
PuckerState	core::pose::rna::assign_pucker (Pose const &pose, Size const rsd_id)
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::position_cutpoint_phosphate_torsions (pose::Pose &current_pose, Size const five_prime_chainbreak, Size three_prime_chainbreak)
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)
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::print_torsion_info (pose::Pose const &pose, id::TorsionID const &torsion_id)
void	core::pose::rna::output_boolean (std::string const &tag, bool boolean)
bool	core::pose::rna::is_cutpoint_closed_atom (core::chemical::ResidueType const &rsd, id::AtomID const &id)
bool	core::pose::rna::is_cutpoint_closed_torsion (pose::Pose const &pose, id::TorsionID const &torsion_id)
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::remove_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
bool	core::pose::rna::has_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
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)
void	core::pose::rna::get_number_base_pairs (pose::Pose const &pose, Size &nwc, Size &nnwc, Size &bs)
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::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_inf_base_pairs (pose::Pose &pose, pose::Pose const &native_pose)
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::apply_Aform_torsions (pose::Pose &pose, Size const n)
ChiState	core::pose::rna::get_residue_base_state (core::pose::Pose const &pose, Size const seq_num)
PuckerState	core::pose::rna::get_residue_pucker_state (core::pose::Pose const &pose, Size const seq_num)
utility::vector1< std::pair < core::id::TorsionID, core::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 More...
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)
	useful in setting up cutpoint with OVL1, OVL2, OVU atoms More...
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::make_phosphate_nomenclature_matches_mini (pose::Pose &pose)
void	core::pose::rna::add_virtual_O2Prime_hydrogen (core::pose::Pose &pose)
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)
bool	core::pose::rna::is_atom_bin_in_range (Atom_Bin const &atom_pos_bin, int const bin_max)
utility::vector1< std::string >	core::pose::rna::tokenize (std::string const &str, std::string const &delimiters)
core::Size	core::pose::rna::string_to_int (std::string const &input_string)
std::string	core::pose::rna::remove_bracketed (std::string const &sequence)
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)
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_syn_chi_constraints (core::pose::Pose &pose)
void	core::pose::rna::add_anti_chi_constraints (core::pose::Pose &pose)
void	core::pose::rna::add_syn_anti_chi_constraints (core::pose::Pose &pose)
utility::vector1 < core::id::TorsionID >	core::pose::rna::get_suite_torsion_ids (Size const i)
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)
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)
void	core::pose::rna::get_base_pairing_list (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > &base_pairing_list)
void	core::pose::rna::assert_phosphate_nomenclature_matches_mini (pose::Pose const &pose)
void	core::pose::rna::virtualize_free_rna_moieties (pose::Pose &pose)
utility::vector1< bool >	core::pose::rna::detect_base_contacts (core::pose::Pose const &pose)
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< bool >	core::pose::rna::detect_phosphate_contacts (pose::Pose const &pose)
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)
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_)
void	core::pose::rna::setup_three_prime_phosphate_based_on_next_residue (pose::Pose &pose, Size const n)
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::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::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)
utility::vector1< Size >	core::pose::rna::get_rigid_body_jumps (core::pose::Pose const &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)
Vector	core::pose::rna::get_sugar_centroid (core::conformation::Residue const &rsd)
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::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	core::pose::rna::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	core::pose::rna::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 > >	core::pose::rna::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	core::pose::rna::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	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::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	core::pose::rna::output_other_contacts (std::ostream &out, pose::Pose const &pose)
	Output residue-residue interactions that are not base pairs or base stacks;. More...
void	core::pose::rna::figure_out_secstruct (pose::Pose &pose)
void	core::pose::rna::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...

Variables
static const RNA_FittedTorsionInfo	torsion_info

Function Documentation

static basic::Tracer TR ( "core.pose.rna.RNA_Util"  )

static

Variable Documentation

const RNA_FittedTorsionInfo torsion_info

static

Referenced by protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::apply(), core::pose::rna::apply_pucker(), core::pose::rna::assign_pucker(), core::chemical::rna::get_epsilon_torsions(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::init(), core::pose::rna::RNA_IdealCoord::init(), protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_fast(), protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard(), and protocols::recces::sampler::rna::MC_RNA_Suite::MC_RNA_Suite().