coarse_rna_test.cc File Reference

#include <core/chemical/AA.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/rna/RNA_CentroidInfo.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/scoring/rna/RNA_FilteredBaseBaseInfo.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/types.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/util.hh>
#include <basic/options/option_macros.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <protocols/idealize/idealize.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/loops/Loop.hh>
#include <numeric/kinematic_closure/bridgeObjects.hh>
#include <numeric/kinematic_closure/kinematic_closure_helpers.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.hh>
#include <protocols/coarse_rna/MultipleDomainMover.hh>
#include <protocols/rna/denovo/libraries/RNA_ChunkLibrary.hh>
#include <core/io/rna/RNA_DataReader.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/denovo/secstruct/RNA_SecStructInfo.hh>
#include <protocols/rna/denovo/setup/RNA_DeNovoPoseInitializer.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/coarse_rna/CoarseRNA_DeNovoProtocol.hh>
#include <protocols/coarse_rna/CoarseRNA_LoopCloser.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/exit.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/random/random.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/Tracer.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	coarse_frag_test ()
void	pdb_stats (pose::Pose const &pose, utility::vector1< protocols::stepwise::modeler::rna::PuckerState > const &pucker_states)
void	vdw_stats (pose::Pose const &pose)
void	icoor_test ()
void	convert_to_coarse_test ()
void	output_minipose_coords_test ()
void	pdbstats_test ()
void	create_bp_jump_database_test ()
void	general_initialize (pose::Pose &pose, pose::PoseOP &native_pose, protocols::rna::denovo::RNA_DeNovoPoseInitializerOP &rna_structure_parameters_, protocols::coarse_rna::CoarseRNA_LoopCloserOP &rna_loop_closer_, protocols::rna::denovo::RNA_ChunkLibraryOP &rna_chunk_library_, core::pose::toolbox::AtomLevelDomainMapOP &atom_level_domain_map_)
void	coarse_rb_test ()
void	output_angles (core::pose::Pose const &pose)
void	get_ideal_angle_sets (utility::vector1< utility::vector1< Real > > &angle_sets, utility::vector1< utility::vector1< core::id::AtomID > > const &angle_ids, utility::vector1< Real > angle_set)
void	get_angle_sets (pose::Pose const &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map, utility::vector1< utility::vector1< Real > > &angle_sets, utility::vector1< utility::vector1< core::id::AtomID > > &angle_ids, bool const sample_angles_)
void	apply_angle_set (pose::Pose &pose, utility::vector1< utility::vector1< core::id::AtomID > > const &angle_ids, utility::vector1< Real > const &angle_set)
void	output_torsions (pose::Pose const &coarse_pose, Size const &i, utility::io::ozstream &out1)
void	pdb_little_motif_test ()
void	get_base_pair_coordinate_system (pose::Pose const &pose, Size const res1, Size const res2, Vector &centroid, Matrix &M)
void	reorient_to_base_pair_coordinate_system (pose::Pose &pose, Size const res1, Size const res2)
Matrix	cycle (Matrix const &M0)
void	determine_delx_dely_delz_alpha_beta_gamma (pose::Pose const &pose, Size const bp1_partner1, Size const bp1_partner2, Size const bp2_partner1, Size const bp2_partner2, utility::io::ozstream &out, bool const cycle_xyz_to_yzx=false)
void	tar_motif_test ()
void	mismatch_test ()
void	modeler_map_test ()
void	coarse_close_loop_test ()
void	coarse_to_full_test ()
void	coarse_rna_denovo_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

apply_angle_set()

void apply_angle_set	(	pose::Pose &	pose,
		utility::vector1< utility::vector1< core::id::AtomID > > const &	angle_ids,
		utility::vector1< Real > const &	angle_set
	)

References utility::io::oc::cout, create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by modeler_map_test().

coarse_close_loop_test()

void coarse_close_loop_test

(

)

References basic::options::OptionKeys::chemical::chemical, create_a3b_hbs::f, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::remodel::vdw.

Referenced by my_main().

coarse_frag_test()

void coarse_frag_test

(

)

References basic::options::OptionKeys::chemical::chemical, in::file::fasta(), create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, natoms(), offset, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, and ObjexxFCL::string_of().

Referenced by my_main().

coarse_rb_test()

void coarse_rb_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::cycles, basic::options::OptionKeys::rna::denovo::denovo, general_initialize(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::native_pose, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

coarse_rna_denovo_test()

void coarse_rna_denovo_test

(

)

References basic::options::OptionKeys::chemical::chemical, close_loops(), basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::cycles, basic::options::OptionKeys::motifs::data_file, basic::options::OptionKeys::magnesium::montecarlo::dump, in::file::fasta(), basic::options::OptionKeys::in::file::input_res, in::file::native(), docking::native_pose, out::nstruct(), option, basic::options::OptionKeys::flexPepDocking::params_file, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::silent(), out::file::silent(), basic::options::OptionKeys::rna::denovo::staged_constraints, local::temperature, basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by my_main().

coarse_to_full_test()

void coarse_to_full_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_a3b_hbs::i, create_a3b_hbs::j, natoms(), out::file::o(), option, lactamize::outfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::inout::dbms::user, y1, y2, basic::options::OptionKeys::motifs::z1, and basic::options::OptionKeys::motifs::z2.

Referenced by my_main().

convert_to_coarse_test()

void convert_to_coarse_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

create_bp_jump_database_test()

void create_bp_jump_database_test

(

)

References basic::options::OptionKeys::recces::base_pair::base_pair, utility::io::ozstream::close(), utility::io::oc::cout, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, out::file::o(), option, lactamize::outfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

cycle()

Matrix cycle

(

Matrix const &

M0

)

References create_a3b_hbs::k.

Referenced by GlycomutagenesisProtocol::apply(), DockGlycansProtocol::apply(), determine_delx_dely_delz_alpha_beta_gamma(), double_helix_test(), helix_ST(), main(), MC_run(), basic::database::safely_read_from_database(), and write_weights_to_db().

determine_delx_dely_delz_alpha_beta_gamma()

void determine_delx_dely_delz_alpha_beta_gamma	(	pose::Pose const &	pose,
		Size const	bp1_partner1,
		Size const	bp1_partner2,
		Size const	bp2_partner1,
		Size const	bp2_partner2,
		utility::io::ozstream &	out,
		bool const	cycle_xyz_to_yzx = false
	)

References compute_difference::alpha, basic::options::OptionKeys::corrections::beta, cycle(), loops::gamma, get_base_pair_coordinate_system(), and beta_nonlocal::pose.

Referenced by tar_motif_test().

general_initialize()

void general_initialize	(	pose::Pose &	pose,
		pose::PoseOP &	native_pose,
		protocols::rna::denovo::RNA_DeNovoPoseInitializerOP &	rna_structure_parameters_,
		protocols::coarse_rna::CoarseRNA_LoopCloserOP &	rna_loop_closer_,
		protocols::rna::denovo::RNA_ChunkLibraryOP &	rna_chunk_library_,
		core::pose::toolbox::AtomLevelDomainMapOP &	atom_level_domain_map_
	)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, in::file::fasta(), basic::database::full_name(), basic::options::OptionKeys::in::file::input_res, in::file::native(), docking::native_pose, option, basic::options::OptionKeys::flexPepDocking::params_file, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by coarse_rb_test(), and modeler_map_test().

get_angle_sets()

void get_angle_sets	(	pose::Pose const &	pose,
		core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map,
		utility::vector1< utility::vector1< Real > > &	angle_sets,
		utility::vector1< utility::vector1< core::id::AtomID > > &	angle_ids,
		bool const	sample_angles_
	)

References utility::io::oc::cout, get_ideal_angle_sets(), create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by modeler_map_test().

get_base_pair_coordinate_system()

void get_base_pair_coordinate_system	(	pose::Pose const &	pose,
		Size const	res1,
		Size const	res2,
		Vector &	centroid,
		Matrix &	M
	)

References basic::options::OptionKeys::in::file::centroid, basic::options::OptionKeys::chemical::chemical, measure_params::cross(), create_a3b_hbs::k, beta_nonlocal::pose, erraser_analysis::res1, erraser_analysis::res2, x, predPRE::y, and predPRE::z.

Referenced by determine_delx_dely_delz_alpha_beta_gamma(), and reorient_to_base_pair_coordinate_system().

get_ideal_angle_sets()

void get_ideal_angle_sets	(	utility::vector1< utility::vector1< Real > > &	angle_sets,
		utility::vector1< utility::vector1< core::id::AtomID > > const &	angle_ids,
		utility::vector1< Real >	angle_set
	)

References numeric::conversions::radians().

Referenced by get_angle_sets().

icoor_test()

void icoor_test

(

)

References basic::options::OptionKeys::chemical::chemical, and beta_nonlocal::pose.

Referenced by main(), and my_main().

main()

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

References argv, centroid_stats::bin_width(), close_loops(), convert(), basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::cycles, basic::options::OptionKeys::motifs::data_file, basic::options::OptionKeys::magnesium::montecarlo::dump, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), basic::options::OptionKeys::in::file::input_res, basic::options::OptionKeys::rna::denovo::db::jump_database, my_main(), NEW_OPT, basic::options::OptionKeys::flexPepDocking::params_file, rb_test(), basic::options::OptionKeys::rna::denovo::staged_constraints, local::temperature, and viewer_main().

mismatch_test()

void mismatch_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, lactamize::filename, create_a3b_hbs::i, create_a3b_hbs::k, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, pdbslice(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, reorient_to_base_pair_coordinate_system(), basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

modeler_map_test()

void modeler_map_test

(

)

References apply_angle_set(), a3b_test::bin_size, centroid_stats::bin_width(), basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, general_initialize(), get_angle_sets(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::k, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::native_pose, option, output_angles(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, docking::s, basic::options::OptionKeys::full_model::sample_res, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, out::file::silent(), ObjexxFCL::string_of(), tag, utility_exit_with_message, and basic::options::OptionKeys::remodel::vdw.

Referenced by my_main().

my_main()

void* my_main

(

void *

)

References coarse_close_loop_test(), coarse_frag_test(), coarse_rb_test(), coarse_rna_denovo_test(), coarse_to_full_test(), convert(), convert_to_coarse_test(), create_bp_jump_database_test(), utility::options::OptionKeys::options::exit, icoor_test(), basic::options::OptionKeys::rna::denovo::db::jump_database, mismatch_test(), modeler_map_test(), option, output_minipose_coords_test(), pdb_little_motif_test(), pdbstats_test(), rb_test(), and tar_motif_test().

Referenced by main().

output_angles()

void output_angles

(

core::pose::Pose const &

pose

)

References numeric::angle_radians(), utility::io::oc::cout, numeric::conversions::degrees(), create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by modeler_map_test().

output_minipose_coords_test()

void output_minipose_coords_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, ObjexxFCL::format::F(), figure_out_secstruct(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, and secstruct().

Referenced by my_main().

output_torsions()

void output_torsions	(	pose::Pose const &	coarse_pose,
		Size const &	i,
		utility::io::ozstream &	out1
	)

References numeric::conversions::degrees(), and create_a3b_hbs::i.

Referenced by pdb_little_motif_test().

pdb_little_motif_test()

void pdb_little_motif_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::ozstream::close(), utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::i, option, erraser_single_res_analysis::out, output_torsions(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

pdb_stats()

void pdb_stats	(	pose::Pose const &	pose,
		utility::vector1< protocols::stepwise::modeler::rna::PuckerState > const &	pucker_states
	)

References numeric::angle_radians(), utility::io::ozstream::close(), numeric::conversions::degrees(), numeric::dihedral_degrees(), oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, and basic::options::OptionKeys::full_model::rna::rna.

Referenced by pdbstats_test().

pdbstats_test()

void pdbstats_test

(

)

References basic::options::OptionKeys::chemical::chemical, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, pdb_stats(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, docking::s, and vdw_stats().

Referenced by my_main().

reorient_to_base_pair_coordinate_system()

void reorient_to_base_pair_coordinate_system	(	pose::Pose &	pose,
		Size const	res1,
		Size const	res2
	)

References basic::options::OptionKeys::in::file::centroid, get_base_pair_coordinate_system(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), beta_nonlocal::pose, erraser_analysis::res1, erraser_analysis::res2, and numeric::xyzMatrix< T >::transposed().

Referenced by mismatch_test(), and tar_motif_test().

tar_motif_test()

void tar_motif_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::ozstream::close(), utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, determine_delx_dely_delz_alpha_beta_gamma(), lactamize::filename, create_a3b_hbs::i, create_a3b_hbs::k, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, lactamize::outfile, pdbslice(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, reorient_to_base_pair_coordinate_system(), in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

vdw_stats()

void vdw_stats

(

pose::Pose const &

pose

)

References utility::io::ozstream::close(), dist(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by pdbstats_test().