rna_protein_test.cc File Reference

#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/options/option.hh>
#include <core/options/after_opts.hh>
#include <core/options/option_macros.hh>
#include <core/pose/Pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/jobdist/JobDistributors.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <core/util/Tracer.hh>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>
#include <core/io/atom_tree_diffs/atom_tree_diff.hh>
#include <numeric/NumericTraits.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	rna_protein_repack_test ()
void	rna_protein_prepack_test ()
void	pack_interface (pose::Pose &pose, scoring::ScoreFunction &scorefxn, ObjexxFCL::FArray1D< bool > &interface_residue)
void	create_random_pose (pose::Pose &pose)
bool	check_protein_rna_clash (pose::Pose const &pose, ObjexxFCL::FArray1D< bool > &interface_residue)
void	rna_protein_rb_test ()
Vector	get_centroid (conformation::Residue const &rsd)
kinematics::Stub	get_base_coordinate_system (conformation::Residue const &rsd, Vector const &centroid)
void	check_contact_and_output (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &centroid_i, kinematics::Stub const &stub_i, Vector const &atom_j, Size const &n, utility::io::ozstream &base_out)
void	check_oxygen_contact_and_output (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &atom_i, Vector const &atom_j, Size const &m, Size const &n, utility::io::ozstream &oxygen_out)
void	rna_protein_pdbstats_test ()
void	juke_sam_test ()
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

check_contact_and_output()

void check_contact_and_output	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Vector const &	centroid_i,
		kinematics::Stub const &	stub_i,
		Vector const &	atom_j,
		Size const &	n,
		utility::io::ozstream &	base_out
	)

References ObjexxFCL::abs(), measure_params::dot(), ObjexxFCL::format::F(), test.T110_numeric::I, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, kmeans_adaptive_kernel_density_bb_dependent_rotlib::rho, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, x, predPRE::y, and predPRE::z.

Referenced by rna_protein_pdbstats_test().

check_oxygen_contact_and_output()

void check_oxygen_contact_and_output	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Vector const &	atom_i,
		Vector const &	atom_j,
		Size const &	m,
		Size const &	n,
		utility::io::ozstream &	oxygen_out
	)

References dist(), ObjexxFCL::format::F(), test.T110_numeric::I, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by rna_protein_pdbstats_test().

check_protein_rna_clash()

bool check_protein_rna_clash	(	pose::Pose const &	pose,
		ObjexxFCL::FArray1D< bool > &	interface_residue
	)

References ObjexxFCL::FArray1D< T >::dimension(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by rna_protein_rb_test().

create_random_pose()

void create_random_pose

(

pose::Pose &

pose

)

References create_a3b_hbs::j, option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, oop_conformations::phi, numeric::NumericTraits< T >::pi(), beta_nonlocal::pose, create_a3b_hbs::r, and numeric::random::uniform().

Referenced by rna_protein_rb_test().

get_base_coordinate_system()

kinematics::Stub get_base_coordinate_system	(	conformation::Residue const &	rsd,
		Vector const &	centroid
	)

References basic::options::OptionKeys::in::file::centroid, cols(), measure_params::cross(), x, predPRE::y, and predPRE::z.

Referenced by rna_protein_pdbstats_test().

get_centroid()

Vector get_centroid

(

conformation::Residue const &

rsd

)

References basic::options::OptionKeys::in::file::centroid, and create_a3b_hbs::i.

Referenced by rna_protein_pdbstats_test().

juke_sam_test()

void juke_sam_test

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::f, test.T220_AtomAtomPairEnergies::fa_elec, create_a3b_hbs::ii, 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, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by main().

main()

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

References argv, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), juke_sam_test(), NEW_OPT, option, rb_test(), repack_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), and basic::options::OptionKeys::dna::specificity::soft_rep.

pack_interface()

void pack_interface	(	pose::Pose &	pose,
		scoring::ScoreFunction &	scorefxn,
		ObjexxFCL::FArray1D< bool > &	interface_residue
	)

References utility::io::oc::cout, create_a3b_hbs::f, create_a3b_hbs::i, create_a3b_hbs::nres, option, beta_nonlocal::pose, oop_conformations::scorefxn, and vancomycin::task.

Referenced by rna_protein_rb_test().

rna_protein_pdbstats_test()

void rna_protein_pdbstats_test

(

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::centroids, check_contact_and_output(), check_oxygen_contact_and_output(), basic::options::OptionKeys::chemical::chemical, utility::io::ozstream::close(), utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, get_base_coordinate_system(), get_centroid(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, out::file::o(), option, lactamize::outfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, in::file::s(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

rna_protein_prepack_test()

void rna_protein_prepack_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, loops::cutpoint, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T220_AtomAtomPairEnergies::fa_elec, create_a3b_hbs::i, create_a3b_hbs::j, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, mutant_modeler::protein_residues, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by main().

rna_protein_rb_test()

void rna_protein_rb_test

(

)

References check_protein_rna_clash(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_random_pose(), pyrosetta::create_score_function, basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::f, test.T220_AtomAtomPairEnergies::fa_elec, create_a3b_hbs::i, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, create_a3b_hbs::nres, local::nstruct, out::nstruct(), option, pack_interface(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, average_rmsds::rmsd, in::file::s(), oop_conformations::scorefxn, legacy_score_vs_rmsd::scores, basic::options::OptionKeys::frags::scoring::scoring, out::file::silent(), basic::options::OptionKeys::dna::specificity::soft_rep, and tag.

Referenced by main().

rna_protein_repack_test()

void rna_protein_repack_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T220_AtomAtomPairEnergies::fa_elec, create_a3b_hbs::i, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by main().