util.cc File Reference

Util functions for Stepwise Assembly RNA. More...

#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_Classes.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh>
#include <protocols/stepwise/modeler/rna/phosphate/util.hh>
#include <protocols/stepwise/modeler/rna/sugar/util.hh>
#include <protocols/stepwise/modeler/rna/bulge/util.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/modeler/output_util.hh>
#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <protocols/farna/util.hh>
#include <protocols/toolbox/rigid_body/util.hh>
#include <core/pose/rna/RNA_BaseDoubletClasses.hh>
#include <core/scoring/ScoreType.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueProperties.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/pose/util.hh>
#include <core/pose/util.tmpl.hh>
#include <core/pose/rna/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/func/FadeFunc.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <protocols/toolbox/AllowInsert.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/TorsionID.hh>
#include <numeric/conversions.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <utility/tools/make_vector1.hh>
#include <iostream>
#include <fstream>
#include <sstream>
#include <ObjexxFCL/format.hh>
#include <set>
#include <time.h>
#include <map>
#include <stdio.h>
#include <ios>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::stepwise
	protocols::stepwise::modeler
	protocols::stepwise::modeler::rna

Functions
static thread_local basic::Tracer	TR ("protocols.stepwise.modeler.rna.util")
void	protocols::stepwise::modeler::rna::minimize_with_constraints (core::pose::Pose &pose, core::kinematics::MoveMap const &mm, core::scoring::ScoreFunctionOP const &scorefxn, core::optimization::MinimizerOptions const &options)
void	protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
void	protocols::stepwise::modeler::rna::remove_all_variant_types (pose::Pose &pose)
utility::vector1< Size >	protocols::stepwise::modeler::rna::apply_full_to_sub_mapping (utility::vector1< Size > const &res_vector, utility::vector1< core::Size > const &is_working_res, std::map< core::Size, core::Size > const &full_to_sub)
utility::vector1< Size >	protocols::stepwise::modeler::rna::apply_full_to_sub_mapping (utility::vector1< Size > const &res_vector, working_parameters::StepWiseWorkingParametersCOP working_parameters)
utility::vector1< Size >	protocols::stepwise::modeler::rna::apply_sub_to_full_mapping (utility::vector1< Size > const &working_res_vector, working_parameters::StepWiseWorkingParametersCOP working_parameters)
void	protocols::stepwise::modeler::rna::ensure_valid_full_seq_num (Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
bool	protocols::stepwise::modeler::rna::check_is_working_res (Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
core::Size	protocols::stepwise::modeler::rna::check_validity_and_get_working_res (Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
std::map< core::Size, core::Size >	protocols::stepwise::modeler::rna::create_full_to_input_res_map (utility::vector1< core::Size > const &input_res_vector)
core::Size	protocols::stepwise::modeler::rna::string_to_int (std::string const input_string)
core::Real	protocols::stepwise::modeler::rna::string_to_real (std::string const input_string)
utility::vector1< std::string >	protocols::stepwise::modeler::rna::tokenize (std::string const str, std::string delimiters)
bool	protocols::stepwise::modeler::rna::is_virtual_base (conformation::Residue const &rsd)
void	protocols::stepwise::modeler::rna::setup_suite_atom_id_map (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
void	protocols::stepwise::modeler::rna::setup_suite_atom_id_map (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const res_num_1, Size const res_num_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
void	protocols::stepwise::modeler::rna::setup_suite_atom_id_map (pose::Pose const &pose_1, pose::Pose const &pose_2, Size const base_res, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
void	protocols::stepwise::modeler::rna::setup_suite_atom_id_map (pose::Pose const &pose_1, pose::Pose const &pose_2, Size const base_res_1, Size const base_res_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
id::AtomID_Map< id::AtomID >	protocols::stepwise::modeler::rna::create_aligment_id_map_legacy (pose::Pose &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &rmsd_residue_list, bool const base_only)
void	protocols::stepwise::modeler::rna::align_poses (core::pose::Pose &moving_pose, std::string const moving_tag, core::pose::Pose const &static_pose, std::string const static_tag, utility::vector1< core::Size > const &working_best_alignment, bool const base_only)
bool	protocols::stepwise::modeler::rna::seq_num_sort_criterion (core::Size seq_num_1, core::Size seq_num_2)
void	protocols::stepwise::modeler::rna::sort_seq_num_list (utility::vector1< core::Size > &seq_num_list)
void	protocols::stepwise::modeler::rna::output_seq_num_list (std::string const tag, utility::vector1< core::Size > const &seq_num_list, std::ostream &outstream, core::Size const spacing)
void	protocols::stepwise::modeler::rna::output_title_text (std::string const title, std::ostream &outstream)
bool	protocols::stepwise::modeler::rna::file_exists (std::string const &file_name)
void	protocols::stepwise::modeler::rna::remove_file (std::string const &file_name)
void	protocols::stepwise::modeler::rna::output_rotamer (utility::vector1< Real > &rotamer)
void	protocols::stepwise::modeler::rna::add_virtual_O2Prime_hydrogen (core::pose::Pose &pose)
void	protocols::stepwise::modeler::rna::check_instantiated_O2Prime_hydrogen (core::pose::Pose const &pose)
bool	protocols::stepwise::modeler::rna::remove_virtual_O2Prime_hydrogen (pose::Pose &pose)
Real	protocols::stepwise::modeler::rna::suite_rmsd (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_num, bool const prepend_res, bool const ignore_virtual_atom)
Real	protocols::stepwise::modeler::rna::rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &residue_list, std::map< core::Size, core::Size > const &full_to_sub, std::map< core::Size, bool > const &is_prepend_map, bool const verbose, bool const ignore_virtual_atom)
Real	protocols::stepwise::modeler::rna::rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, working_parameters::StepWiseWorkingParametersCOP working_parameters_, bool const ignore_virtual_atom)
void	protocols::stepwise::modeler::rna::print_heavy_atoms (Size const &suite_num_1, Size const &suite_num_2, pose::Pose const &pose1, pose::Pose const &pose2)
Size	protocols::stepwise::modeler::rna::get_num_side_chain_atom_from_res_name (chemical::AA const &res_aa, bool const verbose)
Real	protocols::stepwise::modeler::rna::atom_square_deviation (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const &atomno_1, Size const &atomno_2, bool verbose)
void	protocols::stepwise::modeler::rna::base_atoms_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
void	protocols::stepwise::modeler::rna::phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
core::Real	protocols::stepwise::modeler::rna::phosphate_base_phosphate_rmsd (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_num, bool const ignore_virtual_atom)
void	protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
void	protocols::stepwise::modeler::rna::suite_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, bool const &prepend_res, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
void	protocols::stepwise::modeler::rna::freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const total_residue)
utility::vector1< core::Size >	protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res, bool verbose)
void	protocols::stepwise::modeler::rna::o2prime_trials (pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn, bool const pack_virtual_o2prime_hydrogen)
void	protocols::stepwise::modeler::rna::o2prime_trials (pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn, utility::vector1< core::Size > const &O2prime_pack_seq_num, bool const pack_virtual_o2prime_hydrogen)
pack::task::PackerTaskOP	protocols::stepwise::modeler::rna::create_standard_o2prime_pack_task (pose::Pose const &pose, utility::vector1< core::Size > const &O2prime_pack_seq_num, bool const pack_virtual_o2prime_hydrogen)
void	protocols::stepwise::modeler::rna::setup_chain_break_variants (core::pose::Pose &pose, Size const cutpoint)
void	protocols::stepwise::modeler::rna::remove_chain_break_variants (core::pose::Pose &pose, Size const &cutpoint)
utility::vector1< bool >	protocols::stepwise::modeler::rna::get_partition_definition_floating_base (pose::Pose const &pose, Size const &moving_res)
Size	protocols::stepwise::modeler::rna::get_anchor_res (Size const rebuild_res, pose::Pose const &pose)
bool	protocols::stepwise::modeler::rna::check_for_messed_up_structure (core::pose::Pose const &pose, std::string const &tag)
void	protocols::stepwise::modeler::rna::sleep (core::Size mseconds)
bool	protocols::stepwise::modeler::rna::is_residues_in_contact (core::Size const &res_ONE, core::pose::Pose const &pose_ONE, core::Size const &res_TWO, core::pose::Pose const &pose_TWO, core::Real const atom_atom_overlap_dist_cutoff, core::Size const num_atom_contacts_cutoff, bool const verbose)
void	protocols::stepwise::modeler::rna::set_CCD_torsions_to_zero (core::pose::Pose &pose, Size const five_prime_res)
void	protocols::stepwise::modeler::rna::print_atom_info (pose::Pose const &pose, Size const seq_num, std::string const pose_name)
void	protocols::stepwise::modeler::rna::print_individual_atom_info (core::conformation::Residue const &rsd, Size const atomno, std::string const rsd_name)
void	protocols::stepwise::modeler::rna::print_base_state (std::string const tag, core::Size const base_state, std::ostream &outstream)
void	protocols::stepwise::modeler::rna::print_sugar_pucker_state (std::string const tag, core::Size const pucker_state, std::ostream &outstream)
scoring::ScoreFunctionOP	protocols::stepwise::modeler::rna::get_modeler_scorefxn (scoring::ScoreFunctionCOP scorefxn)
void	protocols::stepwise::modeler::rna::copy_all_o2prime_torsions (core::pose::Pose &mod_pose, core::pose::Pose const &template_pose)
core::scoring::ScoreFunctionOP	protocols::stepwise::modeler::rna::rescale_scorefxn (core::scoring::ScoreFunctionOP const &starting_scorefxn, Real const scaling_factor)
void	protocols::stepwise::modeler::rna::show_scorefxn_weight_lines (core::scoring::ScoreFunctionOP const &scorefxn, std::string const title)
void	protocols::stepwise::modeler::rna::choose_random_if_unspecified_nucleotide (char &newrestype)
bool	protocols::stepwise::modeler::rna::mutate_res_if_allowed (pose::Pose &pose, Size const mutate_res, Real const mutation_frequency)
std::string	protocols::stepwise::modeler::rna::create_tag (std::string const &prestring, Size const i)
std::string	protocols::stepwise::modeler::rna::create_torsion_value_string (core::Real const &torsion_value)
std::string	protocols::stepwise::modeler::rna::create_rotamer_string (core::pose::Pose const &pose, Size const moving_res, bool const is_prepend)
std::string	protocols::stepwise::modeler::rna::create_rotamer_string (core::pose::Pose const &pose, Size const moving_res, Size const reference_res)
void	protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap (pose::Pose &pose, Size const five_prime_res, Size const three_prime_res, Size const gap_size)
void	protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint (pose::Pose &pose, Size const five_prime_res)
void	protocols::stepwise::modeler::rna::get_possible_O3prime_C5prime_distance_range (Size const gap_size_, Distance &min_dist, Distance &max_dist)
void	protocols::stepwise::modeler::rna::remove_all_virtual_phosphates (core::pose::Pose &pose)
utility::vector1< Size >	protocols::stepwise::modeler::rna::just_rna (utility::vector1< Size > const &res_list, pose::Pose const &pose)
void	protocols::stepwise::modeler::rna::figure_out_moving_rna_chain_breaks (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res, utility::vector1< Size > &rna_cutpoints_closed, utility::vector1< Size > &rna_five_prime_chain_breaks, utility::vector1< Size > &rna_three_prime_chain_breaks, utility::vector1< Size > &rna_chain_break_gap_sizes)
void	protocols::stepwise::modeler::rna::virtualize_free_rna_moieties (pose::Pose &pose)
bool	protocols::stepwise::modeler::rna::just_modeling_RNA (std::string const &sequence)

Detailed Description

Util functions for Stepwise Assembly RNA.

Author

Parin Sripakdeevong

Function Documentation

static thread_local basic::Tracer TR ( "protocols.stepwise.modeler.rna.util"  )

static