core::pose::rna Namespace Reference

Namespaces
	secstruct_legacy

Classes
class	BasePair
class	BasePairStep
class	BaseStack
class	RNA_Datum
class	RNA_Reactivity
class	RNA_DataInfo
	Keep track of RNA chemical mapping data inside the pose. More...
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_SecStruct
class	principal_angle_degrees
class	RNA_SuiteAssignment
class	RNA_SuiteInfo
class	RNA_SuiteName
struct	Atom_Bin
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, BasePair >	EnergyBasePair
typedef std::list< EnergyBasePair >	EnergyBasePairList
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)
Real	get_inf_base_pairs (pose::Pose &pose, pose::Pose const &native_pose)
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< bool >	detect_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< bool >	detect_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< bool >	detect_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< Size >	get_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

BasePairCOP

typedef utility::pointer::shared_ptr< BasePair const > core::pose::rna::BasePairCOP

BasePairOP

typedef utility::pointer::shared_ptr< BasePair > core::pose::rna::BasePairOP

BasePairStepCOP

typedef utility::pointer::shared_ptr< BasePairStep const > core::pose::rna::BasePairStepCOP

BasePairStepOP

typedef utility::pointer::shared_ptr< BasePairStep > core::pose::rna::BasePairStepOP

BaseStackCOP

typedef utility::pointer::shared_ptr< BaseStack const > core::pose::rna::BaseStackCOP

BaseStackOP

typedef utility::pointer::shared_ptr< BaseStack > core::pose::rna::BaseStackOP

EnergyBasePair

typedef std::pair< Real, BasePair > core::pose::rna::EnergyBasePair

EnergyBasePairList

typedef std::list< EnergyBasePair > core::pose::rna::EnergyBasePairList

EnergyBaseStack

typedef std::pair< Real, BaseStack > core::pose::rna::EnergyBaseStack

EnergyBaseStackList

typedef std::list< EnergyBaseStack > core::pose::rna::EnergyBaseStackList

LW_Table

typedef std::map< std::pair< core::chemical::rna::BaseEdge, core::chemical::rna::BaseEdge >, std::map< core::chemical::rna::BaseDoubletOrientation, core::chemical::rna::LW_BaseDoubletOrientation > > core::pose::rna::LW_Table

Matrix

using core::pose::rna::Matrix = typedef numeric::xyzMatrix<Real>

RNA_BasePairList

typedef utility::vector1< BasePair > core::pose::rna::RNA_BasePairList

RNA_BaseStackList

typedef utility::vector1< BaseStack > core::pose::rna::RNA_BaseStackList

RNA_Data

typedef utility::vector1< RNA_Datum > core::pose::rna::RNA_Data

RNA_DataInfoAP

typedef utility::pointer::weak_ptr< RNA_DataInfo > core::pose::rna::RNA_DataInfoAP

RNA_DataInfoOP

typedef utility::pointer::shared_ptr< RNA_DataInfo > core::pose::rna::RNA_DataInfoOP

RNA_FilteredBaseBaseInfoOP

typedef utility::pointer::shared_ptr< RNA_FilteredBaseBaseInfo > core::pose::rna::RNA_FilteredBaseBaseInfoOP

RNA_IdealCoordOP

typedef utility::pointer::shared_ptr< RNA_IdealCoord > core::pose::rna::RNA_IdealCoordOP

RNA_RawBaseBaseInfoAP

typedef utility::pointer::weak_ptr< RNA_RawBaseBaseInfo > core::pose::rna::RNA_RawBaseBaseInfoAP

RNA_RawBaseBaseInfoOP

typedef utility::pointer::shared_ptr< RNA_RawBaseBaseInfo > core::pose::rna::RNA_RawBaseBaseInfoOP

RNA_Reactivities

typedef utility::vector1< RNA_Reactivity > core::pose::rna::RNA_Reactivities

RNA_ReactivityAP

typedef utility::pointer::weak_ptr< RNA_Reactivity > core::pose::rna::RNA_ReactivityAP

RNA_ReactivityOP

typedef utility::pointer::shared_ptr< RNA_Reactivity > core::pose::rna::RNA_ReactivityOP

RNA_SecStructCOP

typedef utility::pointer::shared_ptr< RNA_SecStruct const > core::pose::rna::RNA_SecStructCOP

RNA_SecStructOP

typedef utility::pointer::shared_ptr< RNA_SecStruct > core::pose::rna::RNA_SecStructOP

RNA_SuiteNameOP

typedef utility::pointer::shared_ptr< RNA_SuiteName > core::pose::rna::RNA_SuiteNameOP

VDW_GridCOP

typedef utility::pointer::shared_ptr< VDW_Grid const > core::pose::rna::VDW_GridCOP

VDW_GridOP

typedef utility::pointer::shared_ptr< VDW_Grid > core::pose::rna::VDW_GridOP

VDW_RepScreenInfoCOP

typedef utility::pointer::shared_ptr< VDW_RepScreenInfo const > core::pose::rna::VDW_RepScreenInfoCOP

VDW_RepScreenInfoOP

typedef utility::pointer::shared_ptr< VDW_RepScreenInfo > core::pose::rna::VDW_RepScreenInfoOP

Enumeration Type Documentation

RNA_ReactivityType

enum core::pose::rna::RNA_ReactivityType

Enumerator
NO_REACTIVITY
DMS
CMCT
SHAPE_1M7
HRF

StubStubType

enum core::pose::rna::StubStubType

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

Terminus

enum core::pose::rna::Terminus

Enumerator
FIVE_PRIME
THREE_PRIME

Function Documentation

add_anti_chi_constraints()

void core::pose::rna::add_anti_chi_constraints

(

core::pose::Pose &

pose

)

References add_chi_constraints(), core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), and core::chemical::rings::q.

Referenced by add_syn_anti_chi_constraints().

add_chi_constraints()

void core::pose::rna::add_chi_constraints	(	pose::Pose &	pose,
		core::scoring::func::FuncOP	chi_potential_restraint,
		utility::vector1< Size > const &	rna_chi_res
	)

References core::pose::Pose::add_constraint(), core::id::CHI, core::pose::Pose::conformation(), core::pose::full_model_info::const_full_model_info(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue_type(), and core::scoring::rna_torsion.

Referenced by add_anti_chi_constraints(), and add_syn_chi_constraints().

add_number_base_pairs() [1/2]

void core::pose::rna::add_number_base_pairs

(

pose::Pose &

pose

)

References get_number_base_pairs(), core::pose::setPoseExtraScore(), and core::id::to_string().

Referenced by protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), protocols::rna::denovo::RNA_DeNovoProtocol::output_silent_struct(), protocols::stepwise::monte_carlo::prepare_silent_struct(), and protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::write_output().

add_number_base_pairs() [2/2]

void core::pose::rna::add_number_base_pairs	(	pose::Pose const &	pose,
		io::silent::SilentStruct &	s
	)

References core::io::silent::SilentStruct::add_string_value(), get_number_base_pairs(), and core::chemical::element::I.

add_number_native_base_pairs() [1/2]

void core::pose::rna::add_number_native_base_pairs	(	pose::Pose &	pose,
		pose::Pose const &	native_pose
	)

References get_number_native_base_pairs(), core::pose::setPoseExtraScore(), and core::id::to_string().

add_number_native_base_pairs() [2/2]

void core::pose::rna::add_number_native_base_pairs	(	pose::Pose &	pose,
		pose::Pose const &	native_pose,
		io::silent::SilentStruct &	s
	)

References core::io::silent::SilentStruct::add_energy(), core::io::silent::SilentStruct::add_string_value(), get_number_native_base_pairs(), and core::chemical::element::I.

Referenced by protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), protocols::rna::denovo::RNA_DeNovoProtocol::output_silent_struct(), protocols::stepwise::monte_carlo::prepare_silent_struct(), and protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::write_output().

add_syn_anti_chi_constraints()

void core::pose::rna::add_syn_anti_chi_constraints

(

core::pose::Pose &

pose

)

References add_anti_chi_constraints(), add_syn_chi_constraints(), and core::pose::full_model_info::full_model_info_defined().

Referenced by protocols::rna::denovo::movers::RNA_Minimizer::apply(), and protocols::stepwise::modeler::StepWiseMinimizer::do_minimize().

add_syn_chi_constraints()

void core::pose::rna::add_syn_chi_constraints

(

core::pose::Pose &

pose

)

References add_chi_constraints(), core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), and core::chemical::rings::q.

Referenced by add_syn_anti_chi_constraints().

add_virtual_O2Prime_hydrogen()

void core::pose::rna::add_virtual_O2Prime_hydrogen

(

core::pose::Pose &

pose

)

References core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::chemical::VIRTUAL_O2PRIME_HYDROGEN.

Referenced by protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::read_in_VDW_rep_screen_pose(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

apply_Aform_torsions()

void core::pose::rna::apply_Aform_torsions	(	pose::Pose &	pose,
		Size const	n
	)

References core::chemical::rna::RNA_FittedTorsionInfo::alpha_aform(), apply_pucker(), core::id::BB, core::chemical::rna::RNA_FittedTorsionInfo::beta_aform(), core::chemical::rna::RNA_FittedTorsionInfo::delta_north(), core::chemical::rna::RNA_FittedTorsionInfo::epsilon_aform(), core::chemical::rna::RNA_FittedTorsionInfo::gamma_aform(), core::chemical::rna::NORTH, core::pose::Pose::set_torsion(), and core::chemical::rna::RNA_FittedTorsionInfo::zeta_aform().

apply_ideal_c2endo_sugar_coords()

void core::pose::rna::apply_ideal_c2endo_sugar_coords	(	Pose &	pose,
		Size const	i
	)

References apply_non_main_chain_sugar_coords(), apply_pucker(), core::id::BB, core::id::CHI, core::pose::Pose::set_torsion(), and core::chemical::rna::SOUTH.

Referenced by protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker().

apply_non_main_chain_sugar_coords()

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
	)

References core::id::BB, core::id::CHI, fix_sugar_coords(), initialize_atoms_for_which_we_need_new_dofs(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::chemical::rna::NUM_RNA_TORSIONS(), core::pose::Pose::set_torsion(), and core::pose::Pose::torsion().

Referenced by apply_ideal_c2endo_sugar_coords(), core::io::silent::RNA_SilentStruct::fill_pose(), and core::fragment::rna::FullAtomRNA_Fragments::insert_fragment().

apply_pucker()

void core::pose::rna::apply_pucker	(	Pose &	pose,
		Size const	i,
		PuckerState	pucker_state,
		bool const	skip_same_state,
		bool const	idealize_coord
	)

References core::chemical::rna::ANY_PUCKER, core::pose::rna::RNA_IdealCoord::apply_pucker(), assign_pucker(), core::id::BB, core::id::CHI, core::chemical::rna::RNA_FittedTorsionInfo::delta_north(), core::chemical::rna::RNA_FittedTorsionInfo::delta_south(), core::chemical::rna::NORTH, core::chemical::rna::RNA_FittedTorsionInfo::nu1_north(), core::chemical::rna::RNA_FittedTorsionInfo::nu1_south(), core::chemical::rna::RNA_FittedTorsionInfo::nu2_north(), core::chemical::rna::RNA_FittedTorsionInfo::nu2_south(), core::pose::Pose::set_torsion(), and torsion_info.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply(), apply_Aform_torsions(), apply_ideal_c2endo_sugar_coords(), protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), and core::import_pose::RNA_HelixAssembler::set_Aform_torsions().

apply_suite_torsion_info() [1/2]

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

References core::pose::Pose::set_torsion().

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

apply_suite_torsion_info() [2/2]

void core::pose::rna::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

References core::pose::Pose::set_torsion().

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

apply_virtual_rna_residue_variant_type() [1/3]

void core::pose::rna::apply_virtual_rna_residue_variant_type	(	core::pose::Pose &	pose,
		core::Size const &	seq_num,
		bool const	apply_check
	)

References apply_virtual_rna_residue_variant_type().

Referenced by protocols::stepwise::modeler::rna::bulge::BulgeApplyMover::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_the_modeler(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::restore_pose_variants_after_chain_closure(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters(), and protocols::rna::denovo::virtualize_bulges().

apply_virtual_rna_residue_variant_type() [2/3]

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
	)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::annotated_sequence(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), protocols::stepwise::modeler::is_cutpoint_closed(), is_cutpoint_open(), core::chemical::PROTONATED_N1, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::chemical::rna::TR(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by apply_virtual_rna_residue_variant_type().

apply_virtual_rna_residue_variant_type() [3/3]

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
	)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::annotated_sequence(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), protocols::stepwise::modeler::is_cutpoint_closed(), is_cutpoint_open(), core::chemical::PROTONATED_N1, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::chemical::rna::TR(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by apply_virtual_rna_residue_variant_type().

assert_phosphate_nomenclature_matches_mini()

void core::pose::rna::assert_phosphate_nomenclature_matches_mini

(

pose::Pose const &

pose

)

References get_op2_op1_sign(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::make_pose_from_sequence(), core::chemical::ResidueTypeBase::mode(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), and core::pose::Pose::size().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

assign_pucker()

core::chemical::rna::PuckerState core::pose::rna::assign_pucker	(	Pose const &	pose,
		Size const	rsd_id
	)

References core::id::BB, core::chemical::rna::RNA_FittedTorsionInfo::delta_cutoff(), core::chemical::rna::NORTH, core::chemical::rna::SOUTH, core::pose::Pose::torsion(), and torsion_info.

Referenced by protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::apply(), apply_pucker(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::get_next_valid_bb(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::init(), protocols::recces::sampler::rna::MC_RNA_Suite::set_init_from_pose(), and protocols::stepwise::sampler::rna::setup_sampler().

atom_is_acceptor()

bool core::pose::rna::atom_is_acceptor	(	core::conformation::Residue const &	rsd,
		Size const	atm
	)

References core::conformation::Residue::accpt_pos().

Referenced by figure_out_number_base_contacts().

atom_is_polar()

bool core::pose::rna::atom_is_polar	(	core::conformation::Residue const &	rsd,
		Size const	atm
	)

References core::conformation::Residue::Hpos_polar().

base_pair_moving()

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
	)

References core::pose::rna::BasePair::res1(), and core::pose::rna::BasePair::res2().

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

base_pair_step_moving()

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
	)

References core::pose::rna::BasePairStep::i(), core::pose::rna::BasePairStep::i_next(), core::pose::rna::BasePairStep::j(), and core::pose::rna::BasePairStep::j_next().

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::setup_base_pair_step_chunks(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

bases_are_coplanar()

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

References core::scoring::rna::RNA_CentroidInfo::base_centroids(), core::scoring::rna::RNA_CentroidInfo::base_stubs(), core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().

Referenced by classify_base_pairs().

bases_form_a_hydrogen_bond()

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
	)

References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_base(), core::conformation::Residue::first_sidechain_atom(), core::scoring::hbond, core::conformation::Residue::Hpos_polar(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by classify_base_pairs().

check_in_base_pair_list()

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
	)

Referenced by get_inf_base_pairs(), and get_number_native_base_pairs().

check_phosphate_contacts_donor() [1/3]

bool core::pose::rna::check_phosphate_contacts_donor	(	pose::Pose const &	pose,
		Size const	n
	)

References FIVE_PRIME, get_phosphate_atom_and_neighbor_list(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by detect_phosphate_contacts().

check_phosphate_contacts_donor() [2/3]

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
	)

check_phosphate_contacts_donor() [3/3]

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
	)

Referenced by protocols::stepwise::modeler::rna::phosphate::PhosphateMover::check_phosphate_contacts_donor().

classify_base_pairs() [1/2]

utility::vector1< core::pose::rna::BasePair > core::pose::rna::classify_base_pairs

(

core::pose::Pose const &

pose_input

)

Referenced by get_inf_base_pairs(), get_number_base_pairs(), get_number_native_base_pairs(), and core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status().

classify_base_pairs() [2/2]

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
	)

References core::chemical::rna::ANY_BASE_EDGE, core::scoring::rna::RNA_CentroidInfo::base_centroids(), core::pose::rna::RNA_RawBaseBaseInfo::base_pair_array(), core::scoring::rna::RNA_CentroidInfo::base_stubs(), bases_are_coplanar(), bases_form_a_hydrogen_bond(), core::pose::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering(), figure_out_base_pair_orientation(), figure_out_number_base_contacts(), core::scoring::hbonds::fill_hbond_set(), core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array(), core::chemical::rna::get_edge_from_num(), core::scoring::hbond_sc, core::chemical::ResidueTypeBase::is_RNA(), core::kinematics::Stub::M, core::conformation::Residue::name1(), core::conformation::Residue::nbr_atom_xyz(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), residue_is_bulge(), core::pose::Pose::residue_type(), core::pose::rna::RNA_RawBaseBaseInfo::resize(), core::pose::Pose::size(), and core::scoring::rna::RNA_CentroidInfo::update().

detect_base_contacts()

utility::vector1< bool > core::pose::rna::detect_base_contacts

(

core::pose::Pose const &

pose

)

References core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_virtual(), core::chemical::ResidueTypeBase::name1(), core::conformation::Residue::nbr_atom_xyz(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::chemical::rna::TR(), and core::conformation::Residue::xyz().

Referenced by virtualize_free_rna_moieties().

detect_phosphate_contacts()

utility::vector1< bool > core::pose::rna::detect_phosphate_contacts

(

pose::Pose const &

pose

)

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

Referenced by virtualize_free_rna_moieties().

detect_sugar_contacts() [1/2]

utility::vector1< bool > core::pose::rna::detect_sugar_contacts

(

pose::Pose const &

pose

)

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

Referenced by protocols::stepwise::screener::SugarInstantiator::check_moving_sugar().

detect_sugar_contacts() [2/2]

bool core::pose::rna::detect_sugar_contacts	(	pose::Pose const &	pose,
		Size const	moving_res,
		Distance	o2prime_contact_distance_cutoff_
	)

References core::chemical::ResidueType::heavyatom_has_polar_hydrogens(), core::chemical::ResidueType::heavyatom_is_an_acceptor(), core::chemical::ResidueType::is_virtual(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by detect_sugar_contacts(), and virtualize_free_rna_moieties().

extract_rna_chains() [1/2]

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.

References figure_out_reasonable_rna_fold_tree(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::pdb_info(), protocols::magnesium::pdbslice(), remove_upper_lower_variants_from_RNA(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

extract_rna_chains() [2/2]

pose::Pose core::pose::rna::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.

References figure_out_reasonable_rna_fold_tree(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::pdb_info(), protocols::magnesium::pdbslice(), remove_upper_lower_variants_from_RNA(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

figure_out_base_pair_orientation()

BaseDoubletOrientation core::pose::rna::figure_out_base_pair_orientation	(	core::pose::Pose &	pose,
		Size const &	i,
		Size const &	j
	)

References core::chemical::rna::ANTIPARALLEL, core::scoring::rna::RNA_CentroidInfo::base_stubs(), core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::chemical::rna::PARALLEL, core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().

Referenced by classify_base_pairs().

figure_out_number_base_contacts()

void core::pose::rna::figure_out_number_base_contacts	(	conformation::Residue const &	rsd_i,
		conformation::Residue const &	rsd_j,
		BaseEdge &	edge_classification
	)

References atom_is_acceptor(), core::conformation::Residue::first_sidechain_atom(), heavy_atom_is_polar(), core::chemical::rna::HOOGSTEEN, core::conformation::Residue::nheavyatoms(), core::chemical::rna::SUGAR, update_edge_hbond_numbers(), update_edge_hbond_numbers_careful_hydrogen(), core::chemical::rna::WATSON_CRICK, and core::conformation::Residue::xyz().

Referenced by classify_base_pairs().

figure_out_reasonable_rna_fold_tree()

void core::pose::rna::figure_out_reasonable_rna_fold_tree	(	pose::Pose &	pose,
		bool	force_cut_at_rna_chainbreak
	)

References core::chemical::rna::chi1_torsion_atom(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), is_rna_chainbreak(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::size(), and core::chemical::rna::TR().

Referenced by core::import_pose::cleanup(), protocols::rna::denovo::create_rna_vall_torsions(), extract_rna_chains(), protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries(), and core::import_pose::process_input_file().

figure_out_rna_chains()

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().

figure_out_secstruct()

void core::pose::rna::figure_out_secstruct

(

pose::Pose &

pose

)

References get_base_pairing_info(), core::scoring::rna_base_pair, core::pose::rna::secstruct_legacy::set_rna_secstruct_legacy(), core::pose::Pose::size(), and core::chemical::rna::TR().

Referenced by protocols::rna::denovo::coarse::CoarseRNA_Fragments::initialize_frag_source_pose().

fill_in_default_jump_atoms() [1/2]

void core::pose::rna::fill_in_default_jump_atoms	(	kinematics::FoldTree &	f,
		pose::Pose const &	pose
	)

References core::chemical::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library(), core::import_pose::RNA_JumpMover::sample_alternative_chain_connection(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps().

fill_in_default_jump_atoms() [2/2]

void core::pose::rna::fill_in_default_jump_atoms

(

pose::Pose &

pose

)

References core::pose::Pose::fold_tree().

fix_sugar_coords()

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
	)

References core::kinematics::AtomTree::atom_dont_do_update(), core::pose::Pose::atom_tree(), core::id::D, core::kinematics::tree::Atom::get_self_ptr(), core::chemical::rings::PHI, prepare_scratch_residue(), core::pose::Pose::residue(), core::pose::Pose::set_dof(), core::chemical::rings::THETA, and core::conformation::Residue::type().

Referenced by apply_non_main_chain_sugar_coords().

get_atom_bin()

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
	)

References core::pose::rna::Atom_Bin::x, core::pose::rna::Atom_Bin::y, and core::pose::rna::Atom_Bin::z.

Referenced by protocols::scoring::VDW_GridEnergy::finalize_total_energy(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen().

get_base_doublet_orientation_from_LW()

core::chemical::rna::BaseDoubletOrientation core::pose::rna::get_base_doublet_orientation_from_LW	(	BaseEdge const &	edge1,
		BaseEdge const &	edge2,
		LW_BaseDoubletOrientation const &	lw_orientation
	)

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

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), core::import_pose::RNA_DeNovoParameters::get_pairings_from_line(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::refine_working_obligate_pairs().

get_base_pairing_info() [1/2]

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
	)

get_base_pairing_info() [2/2]

void core::pose::rna::get_base_pairing_info	(	pose::Pose const &	pose,
		Size const &	seqpos,
		char &	secstruct,
		FArray1D< bool > &	edge_is_base_pairing
	)

References core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, core::chemical::rna::ANY_BASE_EDGE, core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), core::chemical::rna::get_watson_crick_base_pair_atoms(), core::conformation::Residue::is_coarse(), core::pose::rna::BasePair::orientation(), core::chemical::rna::possibly_canonical(), core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::rna::rna_scoring_info_from_pose(), core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list(), core::conformation::Residue::type(), core::chemical::rna::WATSON_CRICK, and core::conformation::Residue::xyz().

Referenced by protocols::rna::denovo::create_rna_vall_torsions(), core::fragment::rna::figure_out_secstruct(), and figure_out_secstruct().

get_base_pairing_list() [1/2]

void core::pose::rna::get_base_pairing_list	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > &	base_pairing_list
	)

References core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, core::chemical::rna::ANY_BASE_EDGE, core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), core::chemical::rna::get_watson_crick_base_pair_atoms(), core::conformation::Residue::is_coarse(), core::pose::rna::BasePair::orientation(), core::chemical::rna::possibly_canonical(), core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), core::pose::Pose::residue(), core::scoring::rna_base_pair, core::scoring::rna::rna_scoring_info_from_pose(), core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list(), core::conformation::Residue::type(), core::chemical::rna::WATSON_CRICK, and core::conformation::Residue::xyz().

Referenced by protocols::recces::recces_pose_setup().

get_base_pairing_list() [2/2]

void core::pose::rna::get_base_pairing_list	(	pose::Pose &	pose,
		utility::vector1< std::pair< Size, Size > > &	base_pairing_list
	)

References core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, core::chemical::rna::ANY_BASE_EDGE, core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), core::chemical::rna::get_watson_crick_base_pair_atoms(), core::conformation::Residue::is_coarse(), core::pose::rna::BasePair::orientation(), core::chemical::rna::possibly_canonical(), core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), core::pose::Pose::residue(), core::scoring::rna_base_pair, core::scoring::rna::rna_scoring_info_from_pose(), core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list(), core::conformation::Residue::type(), core::chemical::rna::WATSON_CRICK, and core::conformation::Residue::xyz().

Referenced by protocols::recces::recces_pose_setup().

get_inf_base_pairs()

Real core::pose::rna::get_inf_base_pairs	(	pose::Pose &	pose,
		pose::Pose const &	native_pose
	)

References check_in_base_pair_list(), classify_base_pairs(), core::pose::Pose::pdb_info(), core::pose::rna::BasePair::set_res1(), core::pose::rna::BasePair::set_res2(), and core::pose::Pose::size().

get_leontis_westhof_table()

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().

get_LW_orientation()

core::chemical::rna::LW_BaseDoubletOrientation core::pose::rna::get_LW_orientation	(	BaseEdge const &	edge1,
		BaseEdge const &	edge2,
		BaseDoubletOrientation const &	orientation
	)

References core::chemical::rna::ANTIPARALLEL, get_leontis_westhof_table(), core::chemical::rna::HOOGSTEEN, core::chemical::rna::PARALLEL, SUGAR, and core::chemical::rna::WATSON_CRICK.

Referenced by core::pose::rna::BasePair::derive_LW_orientation(), and core::scoring::constraints::BasePairConstraint::read_def().

get_number_base_pairs()

void core::pose::rna::get_number_base_pairs	(	pose::Pose const &	pose,
		Size &	nwc,
		Size &	nnwc,
		Size &	bs
	)

References core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, classify_base_pairs(), core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), get_number_base_stacks(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::rna::BasePair::orientation(), core::chemical::rna::possibly_canonical(), core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), core::pose::Pose::residue(), core::conformation::Residue::type(), core::chemical::VIRTUAL_RNA_RESIDUE, and core::chemical::rna::WATSON_CRICK.

Referenced by add_number_base_pairs().

get_number_base_stacks()

core::Size core::pose::rna::get_number_base_stacks

(

core::pose::Pose const &

pose_input

)

References get_scored_base_stack_list().

Referenced by get_number_base_pairs().

get_number_native_base_pairs()

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
	)

References core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, check_in_base_pair_list(), classify_base_pairs(), core::chemical::rna::get_edge_from_num(), core::chemical::ResidueTypeBase::name1(), core::pose::rna::BasePair::orientation(), core::pose::Pose::pdb_info(), core::chemical::rna::possibly_canonical(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::rna::BasePair::set_res1(), core::pose::rna::BasePair::set_res2(), core::pose::Pose::size(), and core::chemical::rna::WATSON_CRICK.

Referenced by add_number_native_base_pairs().

get_op2_op1_sign() [1/2]

Real core::pose::rna::get_op2_op1_sign

(

pose::Pose const &

pose

)

References core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by assert_phosphate_nomenclature_matches_mini(), and protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini().

get_op2_op1_sign() [2/2]

Real core::pose::rna::get_op2_op1_sign	(	pose::Pose const &	pose,
		Size	res_num
	)

References core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by make_phosphate_nomenclature_matches_mini().

get_phosphate_atom_and_neighbor_list() [1/2]

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
	)

get_phosphate_atom_and_neighbor_list() [2/2]

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
	)

References core::chemical::ResidueType::atom_base(), FIVE_PRIME, core::chemical::ResidueType::Hpos_polar(), core::conformation::Residue::nbr_atom_xyz(), core::chemical::rings::q, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::hybridization::t, and core::conformation::Residue::xyz().

Referenced by check_phosphate_contacts_donor(), and protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_atom_and_neighbor_list().

get_residue_base_state()

core::chemical::rna::ChiState core::pose::rna::get_residue_base_state	(	core::pose::Pose const &	pose,
		Size const	seq_num
	)

References core::chemical::rna::get_residue_base_state(), and core::pose::Pose::residue().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list().

get_residue_pucker_state()

core::chemical::rna::PuckerState core::pose::rna::get_residue_pucker_state	(	core::pose::Pose const &	pose,
		Size const	seq_num
	)

References core::chemical::rna::get_residue_pucker_state(), and core::pose::Pose::residue().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), and protocols::stepwise::legacy::modeler::rna::is_same_sugar_pucker().

get_rigid_body_jumps()

utility::vector1< core::Size > core::pose::rna::get_rigid_body_jumps

(

core::pose::Pose const &

pose

)

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::chemical::rna::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by core::import_pose::get_anchor_rsd(), protocols::rna::denovo::let_rigid_body_jumps_move(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rigid_body_orientations(), protocols::rna::denovo::movers::RNA_HelixMover::set_pose(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps(), protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_monte_carlo_cycles(), and protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap().

get_scored_base_stack_list()

EnergyBaseStackList core::pose::rna::get_scored_base_stack_list

(

core::pose::Pose const &

pose_input

)

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::RNA_LORES_WTS, core::scoring::rna::rna_scoring_info_from_pose(), and core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_stack_list().

Referenced by get_number_base_stacks().

get_stub_stub()

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
	)

References BASE_CENTROID, CHAINBREAK, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::rna::get_rna_base_coordinate_system_stub(), core::conformation::Residue::has_variant_type(), core::kinematics::Stub::M, core::conformation::Residue::mainchain_atoms(), O3P_TO_O5P, and core::conformation::Residue::xyz().

Referenced by protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::get_output_jump_stub_stub(), and core::energy_methods::RNA_StubCoordinateEnergy::residue_pair_energy().

get_sugar_centroid()

Vector core::pose::rna::get_sugar_centroid

(

core::conformation::Residue const &

rsd

)

References core::chemical::rna::RNA_Info::c1prime_atom_index(), core::chemical::rna::RNA_Info::c2prime_atom_index(), core::chemical::rna::RNA_Info::c3prime_atom_index(), core::chemical::rna::RNA_Info::c4prime_atom_index(), core::chemical::rna::RNA_Info::o4prime_atom_index(), core::chemical::ResidueType::RNA_info(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::import_pose::make_coarse_pose().

get_suite_torsion_ids()

utility::vector1< core::id::TorsionID > core::pose::rna::get_suite_torsion_ids

(

Size const

i

)

References core::chemical::rna::ALPHA, core::id::BB, core::chemical::rna::BETA, core::chemical::rna::EPSILON, core::chemical::rna::GAMMA, and core::chemical::rna::ZETA.

Referenced by protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::find(), protocols::recces::set_gaussian_stdevs_recces_turner_from_secstruct(), and protocols::recces::set_gaussian_stdevs_recces_turner_legacy().

get_suite_torsion_info()

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().

has_virtual_rna_residue_variant_type()

bool core::pose::rna::has_virtual_rna_residue_variant_type	(	pose::Pose &	pose,
		Size const &	seq_num
	)

References core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::chemical::rna::TR(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

heavy_atom_is_polar()

bool core::pose::rna::heavy_atom_is_polar	(	core::conformation::Residue const &	rsd,
		Size const	atm
	)

References core::conformation::Residue::atom_base(), and core::conformation::Residue::Hpos_polar().

Referenced by figure_out_number_base_contacts().

initialize_atoms_for_which_we_need_new_dofs()

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
	)

References core::kinematics::AtomTree::atom(), core::chemical::ResidueType::atom_name(), core::pose::Pose::atom_tree(), core::chemical::rna::RNA_Info::c1prime_atom_index(), core::chemical::rna::RNA_Info::c2prime_atom_index(), core::chemical::rna::first_base_atom_index(), core::kinematics::tree::Atom::get_self_ptr(), core::chemical::rna::RNA_Info::o2prime_index(), core::chemical::rna::RNA_Info::o4prime_atom_index(), core::pose::Pose::residue_type(), and core::chemical::ResidueType::RNA_info().

Referenced by apply_non_main_chain_sugar_coords().

is_atom_bin_in_range()

bool core::pose::rna::is_atom_bin_in_range	(	Atom_Bin const &	atom_pos_bin,
		int const	bin_max
	)

References core::pose::rna::Atom_Bin::x, core::pose::rna::Atom_Bin::y, and core::pose::rna::Atom_Bin::z.

Referenced by protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::check_atom_bin_in_range(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin().

is_cutpoint_closed_atom()

bool core::pose::rna::is_cutpoint_closed_atom	(	core::chemical::ResidueType const &	rsd,
		id::AtomID const &	id
	)

References core::chemical::ResidueType::atom_name().

Referenced by is_cutpoint_closed_by_atom_name().

is_cutpoint_closed_by_atom_name()

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().

is_cutpoint_closed_torsion()

bool core::pose::rna::is_cutpoint_closed_torsion	(	pose::Pose const &	pose,
		id::TorsionID const &	torsion_id
	)

References core::chemical::rna::ALPHA, core::id::BB, core::chemical::rna::BETA, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::rna::DELTA, core::chemical::rna::EPSILON, core::chemical::rna::GAMMA, core::scoring::methods::get_lower_cutpoint_partner_for_upper(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), core::id::TorsionID::type(), and core::chemical::rna::ZETA.

Referenced by is_torsion_valid().

is_cutpoint_open()

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

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by apply_virtual_rna_residue_variant_type(), and core::import_pose::RNA_BasePairHandler::check_base_pairs().

is_rna_chainbreak()

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::conformation::Residue::atom(), core::conformation::Residue::is_RNA(), core::chemical::rna::RNA_Info::o3prime_atom_index(), core::chemical::rna::RNA_Info::p_atom_index(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::chemical::ResidueType::RNA_info(), core::pose::Pose::size(), core::chemical::rna::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

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().

is_tna_chainbreak()

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::conformation::Residue::atom(), core::conformation::Residue::is_TNA(), core::chemical::rna::RNA_Info::o2prime_index(), core::chemical::rna::RNA_Info::p_atom_index(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::chemical::ResidueType::RNA_info(), core::pose::Pose::size(), core::chemical::rna::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by is_torsion_valid().

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
	)

References core::id::AtomID::atomno(), core::pose::Pose::conformation(), core::chemical::FIVEPRIME_CAP, core::pose::Pose::fold_tree(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), is_cutpoint_closed_by_atom_name(), is_cutpoint_closed_torsion(), core::chemical::ResidueTypeBase::is_RNA(), is_rna_chainbreak(), core::chemical::ResidueType::is_TNA(), is_tna_chainbreak(), core::chemical::ResidueType::is_virtual(), output_boolean(), print_torsion_info(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), and core::chemical::rna::TR().

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::rna::TNA_SuitePotential::eval_score(), core::scoring::rna::RNA_TorsionPotential::get_f1_f2(), core::energy_methods::RNA_JR_SuiteEnergy::residue_pair_energy(), and core::scoring::rna::RNA_TorsionPotential::residue_pair_energy().

make_phosphate_nomenclature_matches_mini()

void core::pose::rna::make_phosphate_nomenclature_matches_mini

(

pose::Pose &

pose

)

References core::conformation::Residue::atom_index(), get_op2_op1_sign(), core::conformation::Residue::is_RNA(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::cleanup_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::Import_pose(), protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::read_in_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class(), and protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters().

moveable_jump() [1/2]

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
	)

References core::pose::toolbox::AtomLevelDomainMap::get(), and core::pose::toolbox::AtomLevelDomainMap::get_domain().

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps(), core::import_pose::RNA_JumpMover::random_jump_change(), and protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap().

moveable_jump() [2/2]

bool core::pose::rna::moveable_jump	(	Size const	jump_pos1,
		Size const	jump_pos2,
		core::pose::toolbox::AtomLevelDomainMap const &	atom_level_domain_map
	)

References core::pose::toolbox::AtomLevelDomainMap::get(), and core::pose::toolbox::AtomLevelDomainMap::get_domain().

mutate_position() [1/3]

bool core::pose::rna::mutate_position	(	pose::Pose &	pose,
		Size const	i,
		char const	new_seq
	)

References core::chemical::ResidueTypeFinder::base_property(), core::pose::Pose::chi(), core::pose::Pose::conformation(), core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeFinder::name1(), core::chemical::NO_PROPERTY, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::chemical::RNA, core::pose::Pose::sequence(), core::pose::Pose::set_chi(), core::chemical::ResidueTypeBase::variant_types(), and core::chemical::ResidueTypeFinder::variants().

Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::rna::movers::RNAThreadAndMinimizeMover::long_mutate_strategy(), protocols::rna::movers::RNAThreadAndMinimizeMover::mutate_all_at_once(), protocols::stepwise::modeler::rna::mutate_res_if_allowed(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_reference_pose_local().

mutate_position() [2/3]

bool core::pose::rna::mutate_position	(	pose::Pose &	pose,
		Size const	i,
		chemical::ResidueType const &	rt
	)

References core::pose::Pose::chi(), core::pose::Pose::conformation(), core::chemical::ResidueTypeBase::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::set_chi().

mutate_position() [3/3]

bool core::pose::rna::mutate_position	(	pose::Pose &	pose,
		Size const	i,
		std::string const &	name3
	)

References core::pose::Pose::annotated_sequence(), core::chemical::ResidueTypeFinder::base_property(), core::pose::Pose::chi(), core::pose::Pose::conformation(), core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeFinder::name3(), core::chemical::NO_PROPERTY, remove_and_store_bracketed(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::chemical::RNA, core::pose::Pose::set_chi(), core::chemical::ResidueTypeBase::variant_types(), and core::chemical::ResidueTypeFinder::variants().

operator<() [1/2]

bool core::pose::rna::operator<	(	BasePair const &	lhs,
		BasePair const &	rhs
	)

operator<() [2/2]

bool core::pose::rna::operator<	(	BaseStack const &	lhs,
		BaseStack const &	rhs
	)

operator<<() [1/3]

std::ostream& core::pose::rna::operator<<	(	std::ostream &	os,
		BasePairStep const &	bps
	)

operator<<() [2/3]

std::ostream& core::pose::rna::operator<<	(	std::ostream &	out,
		BasePair const &	s
	)

operator<<() [3/3]

std::ostream& core::pose::rna::operator<<	(	std::ostream &	out,
		BaseStack const &	s
	)

operator==()

bool core::pose::rna::operator==	(	BasePair const &	lhs,
		BasePair const &	rhs
	)

output_base_pairs()

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(), core::conformation::membrane::out, and core::pose::Pose::pdb_info().

output_base_stacks()

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(), core::conformation::membrane::out, and core::pose::Pose::pdb_info().

output_boolean()

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().

output_ligands() [1/2]

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::conformation::Residue::nheavyatoms(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), update_map(), and core::conformation::Residue::xyz().

output_ligands() [2/2]

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::conformation::Residue::nheavyatoms(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), update_map(), and core::conformation::Residue::xyz().

output_other_contacts()

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;.

References core::conformation::Residue::atom_name(), core::pose::Pose::energies(), core::conformation::Residue::nheavyatoms(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::rna::rna_scoring_info_from_pose(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Residue::xyz().

output_stems()

void core::pose::rna::output_stems	(	std::ostream &	out,
		RNA_Motifs const &	rna_motifs,
		pose::Pose const &	pose
	)

Output stems (>=2 base-pair helices) detected for RNA, including noncanonicals. Must previously score pose with RNA_LORES.

References core::pose::Pose::fold_tree(), core::scoring::rna::RNA_Motifs::get_motifs(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::pose::Pose::size(), protocols::loops::loop_closure::ccd::strand, and core::scoring::rna::WC_STACKED_PAIR.

position_cutpoint_phosphate_torsions()

void core::pose::rna::position_cutpoint_phosphate_torsions	(	pose::Pose &	current_pose,
		Size const	five_prime_chainbreak,
		Size	three_prime_chainbreak
	)

References core::id::BB, core::conformation::ResidueFactory::create_residue(), core::pose::Pose::delete_polymer_residue(), core::chemical::FULL_ATOM_t, core::chemical::na_rad, core::pose::Pose::prepend_polymer_residue_before_seqpos(), core::pose::Pose::residue_type_set_for_pose(), and core::pose::Pose::set_torsion().

Referenced by core::pose::correctly_add_2prime_connection_variants(), and core::pose::correctly_add_cutpoint_variants().

prepare_scratch_residue()

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
	)

References core::pose::Pose::conformation(), core::kinematics::Stub::local2global(), core::chemical::rna::non_main_chain_sugar_atoms, and core::conformation::Residue::xyz().

Referenced by fix_sugar_coords().

print_torsion_info()

void core::pose::rna::print_torsion_info	(	pose::Pose const &	pose,
		id::TorsionID const &	torsion_id
	)

References core::chemical::ResidueType::atom_charge(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::ResidueType::atom_type_index(), core::id::AtomID::atomno(), core::pose::Pose::conformation(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::chemical::AtomType::name(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), and core::chemical::rna::TR().

Referenced by is_torsion_valid().

remove_and_store_bracketed()

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
	)

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_working_sequence_and_mapping(), mutate_position(), and protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree().

remove_bracketed()

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::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().

remove_upper_lower_variants_from_RNA()

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.

References core::chemical::ResidueTypeBase::is_RNA(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by extract_rna_chains().

remove_virtual_rna_residue_variant_type()

void core::pose::rna::remove_virtual_rna_residue_variant_type	(	pose::Pose &	pose,
		Size const &	seq_num
	)

References core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::size(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::initialize_pose_variants_for_chain_closure(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::instantiate_residue_if_rebuilding_bulge().

residue_is_bulge()

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

References core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by classify_base_pairs().

setup_base_pair_constraints() [1/2]

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().

setup_base_pair_constraints() [2/2]

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().

setup_three_prime_phosphate_based_on_next_residue()

void core::pose::rna::setup_three_prime_phosphate_based_on_next_residue	(	pose::Pose &	pose,
		Size const	n
	)

References core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), core::chemical::THREE_PRIME_PHOSPHATE, core::chemical::VIRTUAL_PHOSPHATE, core::chemical::VIRTUAL_RNA_RESIDUE, and core::conformation::Residue::xyz().

Referenced by virtualize_free_rna_moieties().

string_to_int()

core::Size core::pose::rna::string_to_int

(

std::string const &

input_string

)

References core::conformation::membrane::in, and core::conformation::membrane::out.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose_from_options(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_jump_point_pair_list(), protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters(), and protocols::stepwise::modeler::rna::string_to_int().

tokenize()

utility::vector1< std::string > core::pose::rna::tokenize	(	std::string const &	str,
		std::string const &	delimiters
	)

References protocols::kinmatch::str().

Referenced by protocols::stepwise::legacy::modeler::rna::get_silent_file_tags(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose_from_options(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_jump_point_pair_list(), protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters(), and protocols::stepwise::modeler::rna::tokenize().

update_edge_hbond_numbers()

void core::pose::rna::update_edge_hbond_numbers	(	conformation::Residue const &	rsd,
		Size const &	atm,
		Size &	N_W,
		Size &	N_H,
		Size &	N_S
	)

References core::conformation::Residue::aa(), core::conformation::Residue::atom_name(), core::chemical::na_ade, core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name1(), core::chemical::name_from_aa(), and core::conformation::Residue::type().

Referenced by figure_out_number_base_contacts().

update_edge_hbond_numbers_careful_hydrogen()

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
	)

References core::conformation::Residue::aa(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::has(), core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by figure_out_number_base_contacts().

update_map()

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
	)

References core::chemical::ResidueTypeBase::is_DNA(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::conformation::Residue::name(), and core::conformation::Residue::type().

Referenced by output_ligands().

virtualize_5prime_phosphates()

void core::pose::rna::virtualize_5prime_phosphates

(

pose::Pose &

pose

)

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::FIVE_PRIME_PACKABLE_TRIPHOSPHATE, core::chemical::FIVEPRIME_CAP, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by core::import_pose::cleanup(), protocols::recces::pose_setup_turner(), and core::import_pose::process_input_file().

virtualize_free_rna_moieties()

void core::pose::rna::virtualize_free_rna_moieties

(

pose::Pose &

pose

)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::annotated_sequence(), protocols::sparta::contains(), detect_base_contacts(), detect_phosphate_contacts(), detect_sugar_contacts(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_RNA(), core::conformation::Residue::is_virtual_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), setup_three_prime_phosphate_based_on_next_residue(), core::pose::Pose::size(), core::chemical::rna::TR(), core::chemical::VIRTUAL_BASE, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by core::import_pose::initialize_native_and_align_pose().