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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/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/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/chemical/ResidueType.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/variant_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/DihedralConstraint.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/FadeFunc.hh>
#include <core/scoring/func/CircularSplineFunc.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.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 <utility/file/file_sys_util.hh>
#include <iostream>
#include <fstream>
#include <sstream>
#include <ObjexxFCL/format.hh>
#include <set>
#include <ctime>
#include <map>
#include <cstdio>
#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 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< core::Sizeprotocols::stepwise::modeler::rna::apply_full_to_sub_mapping (utility::vector1< core::Size > const &res_vector, utility::vector1< core::Size > const &is_working_res, std::map< core::Size, core::Size > const &full_to_sub)
 
utility::vector1< core::Sizeprotocols::stepwise::modeler::rna::apply_full_to_sub_mapping (utility::vector1< core::Size > const &res_vector, working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
utility::vector1< core::Sizeprotocols::stepwise::modeler::rna::apply_sub_to_full_mapping (utility::vector1< core::Size > const &working_res_vector, working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
void protocols::stepwise::modeler::rna::ensure_valid_full_seq_num (core::Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
 
bool protocols::stepwise::modeler::rna::check_is_working_res (core::Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
 
core::Size protocols::stepwise::modeler::rna::check_validity_and_get_working_res (core::Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
 
std::map< core::Size, core::Sizeprotocols::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 const &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, core::Size const res_num_1, core::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, core::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, core::Size const base_res_1, core::Size const base_res_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
 
id::AtomID_Map< id::AtomIDprotocols::stepwise::modeler::rna::create_alignment_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)
 
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::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, core::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< core::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 (core::Size const &suite_num_1, core::Size const &suite_num_2, pose::Pose const &pose1, pose::Pose const &pose2)
 
Real protocols::stepwise::modeler::rna::atom_square_deviation (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, core::Size const &atomno_1, core::Size const &atomno_2, bool verbose)
 
void protocols::stepwise::modeler::rna::base_atoms_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, core::Size const &moving_res_1, core::Size const &moving_res_2, core::Size &atom_count, Real &sum_sd, bool verbose, bool const )
 
void protocols::stepwise::modeler::rna::phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, core::Size const &moving_res_1, core::Size const &moving_res_2, core::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, core::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, core::Size const &moving_res_1, core::Size const &moving_res_2, core::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, core::Size const &moving_res_1, core::Size const &moving_res_2, core::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, core::Size const total_residue)
 
utility::vector1< core::Sizeprotocols::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, core::Size const cutpoint)
 
void protocols::stepwise::modeler::rna::remove_chain_break_variants (core::pose::Pose &pose, core::Size const &cutpoint)
 
utility::vector1< boolprotocols::stepwise::modeler::rna::get_partition_definition_floating_base (pose::Pose const &pose, core::Size const &moving_res)
 
Size protocols::stepwise::modeler::rna::get_anchor_res (core::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, core::Size const five_prime_res)
 
void protocols::stepwise::modeler::rna::print_atom_info (pose::Pose const &pose, core::Size const seq_num, std::string const &pose_name)
 
void protocols::stepwise::modeler::rna::print_individual_atom_info (core::conformation::Residue const &rsd, core::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)
 
utility::vector1< std::string > protocols::stepwise::modeler::rna::possible_rts (utility::tools::make_vector1("RAD","RGU","RCY","URA","OMA","OMC","OMG","OMU","PSU","H2U","PUR","1MA","NPU","8OG","6MG","5IU","5FC","5FU"))
 
std::string protocols::stepwise::modeler::rna::choose_randomly_from_allowed_at_position (core::pose::Pose const &, core::Size const )
 
bool protocols::stepwise::modeler::rna::mutate_res_if_allowed (pose::Pose &pose, core::Size const mutate_res, Real const mutation_frequency)
 
std::string protocols::stepwise::modeler::rna::create_tag (std::string const &prestring, core::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, core::Size const moving_res, bool const is_prepend)
 
std::string protocols::stepwise::modeler::rna::create_rotamer_string (core::pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res)
 
void protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap (pose::Pose &pose, core::Size const five_prime_res, core::Size const three_prime_res, core::Size const gap_size)
 
void protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint (pose::Pose &pose, core::Size const five_prime_res)
 
void protocols::stepwise::modeler::rna::get_possible_O3prime_C5prime_distance_range (core::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< core::Sizeprotocols::stepwise::modeler::rna::just_rna (utility::vector1< core::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< core::Size > const &moving_partition_res, utility::vector1< core::Size > &rna_cutpoints_closed, utility::vector1< core::Size > &rna_five_prime_chain_breaks, utility::vector1< core::Size > &rna_three_prime_chain_breaks, utility::vector1< core::Size > &rna_chain_break_gap_sizes)
 

Detailed Description

Util functions for Stepwise Assembly RNA.

Author
Parin Sripakdeevong

Function Documentation

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