parin_test.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <utility/excn/Exceptions.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/util.hh>
#include <core/pose/init_id_map.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/rms_util.tmpl.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 <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <protocols/idealize/idealize.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/stepwise/sampling/rna/util.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/denovo/RNA_BasePairClassifier.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_ResidueInfo.hh>
#include <protocols/stepwise/sampling/rna/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/StepWiseLegacyClusterer.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_RotamerGeneratorWrapper.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_RotamerGeneratorWrapper.fwd.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_BaseSugarRotamer.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_BaseSugarRotamer.fwd.hh>
#include <protocols/rna/denovo/RNA_LoopCloser.hh>
#include <protocols/rna/denovo/RNA_LoopCloser.fwd.hh>
#include <core/scoring/rna/RNA_BaseDoubletClasses.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <algorithm>
#include <cctype>
#include <iomanip>
#include <map>
#include <cstdlib>
#include <ctime>
#include <list>
#include <stdio.h>
#include <math.h>

Classes
class	Combine_Tags_Info

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
	OPT_KEY (Boolean, idl_close_chainbreaks) OPT_KEY(Real
atom_pair_constraint_weight	OPT_KEY (Real, coordinate_constraint_weight) core
void	multiple_variant_type_test ()
void	align_pdbs_function (pose::Pose const static_pose, utility::vector1< pose_data_struct2 > &moving_pose_data_list, utility::vector1< std::string > const &alignment_res_pair_list, Real const alignment_RMSD_cutoff)
utility::vector1< pose_data_struct2 >	convert_silent_file_to_pose_data_list (std::string const silent_file)
void	copy_virtual_variant_type (pose::Pose &full_pose, pose::Pose const &start_pose_with_variant, utility::vector1< core::Size > const &input_res_map)
void	copy_DOFS_local (pose::Pose &pose, pose::Pose const start_pose, utility::vector1< core::Size > const &input_res)
void	hermann_phase_two_minimize ()
void	hermann_phase_two ()
void	journal_club_syn_chi ()
void	calculate_theoretical_RNA_length ()
void	calculate_theoretical_RNA_length_with_bond_angle_dependence ()
void	extract_hydrogen_bonds_statistic ()
void	test_function ()
void	get_pose_energy_breakdown ()
void	minimize_pdb ()
std::string	hack_create_torsion_value_string (core::Real const &torsion_value)
std::string	hack_create_rotamer_string (core::pose::Pose const &pose, bool const is_prepend, Size const moving_res)
bool	is_new_cluster_center_rotamer (pose::Pose const &pose, pose::Pose &cluster_center_pose, Size const rotamer_count, Size const sample_res, bool const is_prepend, Real const cluster_rmsd, utility::vector1< utility::vector1< Torsion_Info > > const &cluster_center_rotamer_list)
void	get_residue_xyz_list (pose::Pose const &pose, Size const sample_res, bool const is_prepend, utility::vector1< numeric::xyzVector< Real > > &xyz_list)
bool	is_new_cluster_center_xyz (pose::Pose const &pose, Size const rotamer_count, Size const sample_res, bool const is_prepend, Real const cluster_rmsd, utility::vector1< utility::vector1< numeric::xyzVector< Real > > > &cluster_center_xyz_list)
bool	is_cluster_member (utility::vector1< numeric::xyzVector< Real > > const &cluster_center_xyzs, utility::vector1< numeric::xyzVector< Real > > const &curr_xyz_list, Real const CUTOFF_sum_square_deviation)
bool	is_new_cluster_center_second_stage (pose::Pose const &pose, Size const rotamer_count, Size const sample_res, bool const is_prepend, Real const cluster_rmsd, Real const large_cluster_rmsd, utility::vector1< utility::vector1< Size > > &large_to_small_cluster_center_map_list, utility::vector1< utility::vector1< numeric::xyzVector< Real > > > &small_cluster_center_xyz_list, utility::vector1< utility::vector1< numeric::xyzVector< Real > > > const &large_cluster_center_xyz_list)
bool	is_bonded_neighbor_atoms_at_phosphate_interface (std::string const &atom_name_1, Size const seq_num_1, std::string const &atom_name_2, Size const seq_num_2)
void	setup_VDW_rep_atom_map_list (pose::Pose const &pose, utility::vector1< std::pair< std::pair< Size, Size >, utility::vector1< std::pair< Size, Size > > > > &VDW_rep_atom_map_list)
bool	pass_VDW_replusion_screen_fast (pose::Pose const &pose, Real const VDW_overlap_dist_cutoff, Size const num_atom_VDW_clash_cutoff, utility::vector1< std::pair< std::pair< Size, Size >, utility::vector1< std::pair< Size, Size > > > > const &VDW_rep_atom_map_list)
bool	pass_VDW_replusion_screen_slow (pose::Pose const &pose, Real const VDW_overlap_dist_cutoff, Size const num_atom_VDW_clash_cutoff)
void	cluster_rotamers (bool const second_stage, bool const optimize_screening, Real const cluster_rmsd, Real const large_cluster_rmsd, utility::vector1< utility::vector1< numeric::xyzVector< Real > > > const &input_cluster_center_xyz_list, utility::vector1< utility::vector1< numeric::xyzVector< Real > > > &cluster_center_xyz_list)
void	cluster_rotamers_wrapper ()
void	rna_idealize_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

align_pdbs_function()

void align_pdbs_function	(	pose::Pose const	static_pose,
		utility::vector1< pose_data_struct2 > &	moving_pose_data_list,
		utility::vector1< std::string > const &	alignment_res_pair_list,
		Real const	alignment_RMSD_cutoff
	)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::ii, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, output_pdb(), beta_nonlocal::pose, average_rmsds::rmsd, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, superimpose_pose(), utility_exit_with_message, and basic::options::OptionKeys::sc::verbose.

Referenced by hermann_phase_two().

calculate_theoretical_RNA_length()

void calculate_theoretical_RNA_length

(

)

References docking::a2, docking::b2, a3b_test::bin_size, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, build_jacobian::distance, indel::end_res, oop_conformations::length, local::max_angle, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, and indel::start_res.

Referenced by my_main().

calculate_theoretical_RNA_length_with_bond_angle_dependence()

void calculate_theoretical_RNA_length_with_bond_angle_dependence

(

)

References docking::a3, docking::b3, a3b_test::bin_size, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, measure_params::dot(), vector::dot_product(), indel::end_res, basic::options::OptionKeys::optE::fixed, basic::options::OptionKeys::ufv::left, oop_conformations::length, local::max_angle, numeric::xyzVector< T >::normalize(), lactamize::outfile, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::mp::visualize::spacing, indel::start_res, and basic::options::OptionKeys::motifs::z2.

cluster_rotamers()

void cluster_rotamers	(	bool const	second_stage,
		bool const	optimize_screening,
		Real const	cluster_rmsd,
		Real const	large_cluster_rmsd,
		utility::vector1< utility::vector1< numeric::xyzVector< Real > > > const &	input_cluster_center_xyz_list,
		utility::vector1< utility::vector1< numeric::xyzVector< Real > > > &	cluster_center_xyz_list
	)

References a3b_test::bin_size, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::in::file::fold_tree, hack_create_rotamer_string(), is_new_cluster_center_rotamer(), is_new_cluster_center_second_stage(), is_new_cluster_center_xyz(), ObjexxFCL::lead_zero_string_of(), option, pass_VDW_replusion_screen_fast(), pass_VDW_replusion_screen_slow(), beta_nonlocal::pose, docking::s, basic::options::OptionKeys::full_model::sample_res, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, setup_VDW_rep_atom_map_list(), basic::options::OptionKeys::in::file::silent, tag, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by cluster_rotamers_wrapper().

cluster_rotamers_wrapper()

void cluster_rotamers_wrapper

(

)

References cluster_rotamers(), option, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

convert_silent_file_to_pose_data_list()

utility::vector1< pose_data_struct2 > convert_silent_file_to_pose_data_list

(

std::string const

silent_file

)

References basic::options::OptionKeys::chemical::chemical, beta_nonlocal::pose, create_a3b_hbs::score, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, tag, and utility_exit_with_message.

Referenced by hermann_phase_two(), and hermann_phase_two_minimize().

copy_DOFS_local()

void copy_DOFS_local	(	pose::Pose &	pose,
		pose::Pose const	start_pose,
		utility::vector1< core::Size > const &	input_res
	)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::in::file::input_res, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.

Referenced by hermann_phase_two_minimize().

copy_virtual_variant_type()

void copy_virtual_variant_type	(	pose::Pose &	full_pose,
		pose::Pose const &	start_pose_with_variant,
		utility::vector1< core::Size > const &	input_res_map
	)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and utility_exit_with_message.

Referenced by hermann_phase_two_minimize().

extract_hydrogen_bonds_statistic()

void extract_hydrogen_bonds_statistic

(

)

References utility_exit_with_message.

Referenced by my_main().

get_pose_energy_breakdown()

void get_pose_energy_breakdown

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_scorefxn(), basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), in::file::tags(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

get_residue_xyz_list()

void get_residue_xyz_list	(	pose::Pose const &	pose,
		Size const	sample_res,
		bool const	is_prepend,
		utility::vector1< numeric::xyzVector< Real > > &	xyz_list
	)

References utility::io::oc::cout, beta_nonlocal::pose, basic::options::OptionKeys::full_model::sample_res, and utility_exit_with_message.

Referenced by is_new_cluster_center_second_stage(), and is_new_cluster_center_xyz().

hack_create_rotamer_string()

std::string hack_create_rotamer_string	(	core::pose::Pose const &	pose,
		bool const	is_prepend,
		Size const	moving_res
	)

References hack_create_torsion_value_string(), and beta_nonlocal::pose.

Referenced by cluster_rotamers().

hack_create_torsion_value_string()

std::string hack_create_torsion_value_string

(

core::Real const &

torsion_value

)

References ObjexxFCL::abs(), ObjexxFCL::lead_zero_string_of(), and numeric::principal_angle_degrees().

Referenced by hack_create_rotamer_string().

hermann_phase_two()

void hermann_phase_two

(

)

References align_pdbs_function(), basic::options::OptionKeys::chemical::chemical, convert_silent_file_to_pose_data_list(), utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::ii, basic::options::OptionKeys::ufv::left, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), option, lactamize::outfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::sc::verbose.

Referenced by my_main().

hermann_phase_two_minimize()

void hermann_phase_two_minimize

(

)

References align_poses(), basic::options::OptionKeys::chemical::chemical, Combine_Tags_Info::combine_score, basic::options::OptionKeys::constraints::constraints, convert_silent_file_to_pose_data_list(), copy_DOFS_local(), copy_virtual_variant_type(), utility::io::oc::cout, create_scorefxn(), basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::matdes::dock::dump_pdb, in::file::fasta(), basic::options::OptionKeys::in::file::fold_tree, getline(), create_a3b_hbs::i, create_a3b_hbs::ii, Combine_Tags_Info::lower_tag, basic::options::OptionKeys::in::file::minimize_res, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), basic::options::OptionKeys::stepwise::rna::native_alignment_res, docking::native_pose, basic::options::OptionKeys::stepwise::rna::native_virtual_res, basic::options::OptionKeys::optimization::optimization, option, options, Combine_Tags_Info::overlap_rmsd, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::stepwise::rna::rmsd_res, basic::options::OptionKeys::full_model::rna::rna, docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), basic::options::OptionKeys::rna::erraser::skip_minimize, ObjexxFCL::string_of(), rna_decompose::total_res, TR, Combine_Tags_Info::upper_tag, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::sc::verbose.

Referenced by my_main().

is_bonded_neighbor_atoms_at_phosphate_interface()

bool is_bonded_neighbor_atoms_at_phosphate_interface	(	std::string const &	atom_name_1,
		Size const	seq_num_1,
		std::string const &	atom_name_2,
		Size const	seq_num_2
	)

Referenced by pass_VDW_replusion_screen_slow(), and setup_VDW_rep_atom_map_list().

is_cluster_member()

bool is_cluster_member	(	utility::vector1< numeric::xyzVector< Real > > const &	cluster_center_xyzs,
		utility::vector1< numeric::xyzVector< Real > > const &	curr_xyz_list,
		Real const	CUTOFF_sum_square_deviation
	)

References utility::io::oc::cout, and utility_exit_with_message.

Referenced by is_new_cluster_center_second_stage().

is_new_cluster_center_rotamer()

bool is_new_cluster_center_rotamer	(	pose::Pose const &	pose,
		pose::Pose &	cluster_center_pose,
		Size const	rotamer_count,
		Size const	sample_res,
		bool const	is_prepend,
		Real const	cluster_rmsd,
		utility::vector1< utility::vector1< Torsion_Info > > const &	cluster_center_rotamer_list
	)

References utility::io::oc::cout, beta_nonlocal::pose, average_rmsds::rmsd, basic::options::OptionKeys::full_model::sample_res, and basic::options::OptionKeys::sc::verbose.

Referenced by cluster_rotamers().

is_new_cluster_center_second_stage()

bool is_new_cluster_center_second_stage	(	pose::Pose const &	pose,
		Size const	rotamer_count,
		Size const	sample_res,
		bool const	is_prepend,
		Real const	cluster_rmsd,
		Real const	large_cluster_rmsd,
		utility::vector1< utility::vector1< Size > > &	large_to_small_cluster_center_map_list,
		utility::vector1< utility::vector1< numeric::xyzVector< Real > > > &	small_cluster_center_xyz_list,
		utility::vector1< utility::vector1< numeric::xyzVector< Real > > > const &	large_cluster_center_xyz_list
	)

References utility::io::oc::cout, get_residue_xyz_list(), is_cluster_member(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, basic::options::OptionKeys::full_model::sample_res, and utility_exit_with_message.

Referenced by cluster_rotamers().

is_new_cluster_center_xyz()

bool is_new_cluster_center_xyz	(	pose::Pose const &	pose,
		Size const	rotamer_count,
		Size const	sample_res,
		bool const	is_prepend,
		Real const	cluster_rmsd,
		utility::vector1< utility::vector1< numeric::xyzVector< Real > > > &	cluster_center_xyz_list
	)

References utility::io::oc::cout, get_residue_xyz_list(), beta_nonlocal::pose, basic::options::OptionKeys::full_model::sample_res, subloop_histogram::size, utility_exit_with_message, and basic::options::OptionKeys::sc::verbose.

Referenced by cluster_rotamers().

journal_club_syn_chi()

void journal_club_syn_chi

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::matdes::dock::dump_pdb, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::magnesium::montecarlo::dump, test.T009_Exceptions::e, basic::options::OptionKeys::dna::specificity::fast, basic::init(), basic::options::OptionKeys::in::file::input_res, basic::options::OptionKeys::in::file::minimize_res, my_main(), basic::options::OptionKeys::stepwise::rna::native_alignment_res, basic::options::OptionKeys::stepwise::rna::native_virtual_res, NEW_OPT, basic::options::OptionKeys::stepwise::rna::rmsd_res, basic::options::OptionKeys::full_model::sample_res, viewer_main(), and basic::options::OptionKeys::full_model::virtual_res.

minimize_pdb()

void minimize_pdb

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_scorefxn(), basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::in::file::fold_tree, get_tag_from_pdb_filename(), create_a3b_hbs::ii, basic::options::OptionKeys::in::file::minimize_res, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, basic::options::OptionKeys::optimization::optimization, option, options, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, ObjexxFCL::string_of(), TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

multiple_variant_type_test()

void multiple_variant_type_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and TR.

Referenced by my_main().

my_main()

void* my_main

(

void *

)

References calculate_theoretical_RNA_length(), cluster_rotamers_wrapper(), utility::io::oc::cout, utility::options::OptionKeys::options::exit, extract_hydrogen_bonds_statistic(), get_pose_energy_breakdown(), hermann_phase_two(), hermann_phase_two_minimize(), journal_club_syn_chi(), minimize_pdb(), multiple_variant_type_test(), option, rna_idealize_test(), and test_function().

Referenced by main().

OPT_KEY() [1/2]

OPT_KEY	(	Boolean	,
		idl_close_chainbreaks
	)

OPT_KEY() [2/2]

atom_pair_constraint_weight OPT_KEY	(	Real	,
		coordinate_constraint_weight
	)

References utility::io::oc::cout, pyrosetta::create_score_function, option, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::score::weights.

pass_VDW_replusion_screen_fast()

bool pass_VDW_replusion_screen_fast	(	pose::Pose const &	pose,
		Real const	VDW_overlap_dist_cutoff,
		Size const	num_atom_VDW_clash_cutoff,
		utility::vector1< std::pair< std::pair< Size, Size >, utility::vector1< std::pair< Size, Size > > > > const &	VDW_rep_atom_map_list
	)

References utility::io::oc::cout, create_a3b_hbs::ii, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, and basic::options::OptionKeys::sc::verbose.

Referenced by cluster_rotamers().

pass_VDW_replusion_screen_slow()

bool pass_VDW_replusion_screen_slow	(	pose::Pose const &	pose,
		Real const	VDW_overlap_dist_cutoff,
		Size const	num_atom_VDW_clash_cutoff
	)

References utility::io::oc::cout, is_bonded_neighbor_atoms_at_phosphate_interface(), oop_conformations::length, beta_nonlocal::pose, utility_exit_with_message, and basic::options::OptionKeys::sc::verbose.

Referenced by cluster_rotamers().

rna_idealize_test()

void rna_idealize_test

(

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

setup_VDW_rep_atom_map_list()

void setup_VDW_rep_atom_map_list	(	pose::Pose const &	pose,
		utility::vector1< std::pair< std::pair< Size, Size >, utility::vector1< std::pair< Size, Size > > > > &	VDW_rep_atom_map_list
	)

References utility::io::oc::cout, is_bonded_neighbor_atoms_at_phosphate_interface(), beta_nonlocal::pose, and utility_exit_with_message.

Referenced by cluster_rotamers().

test_function()

void test_function

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, docking::s, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().