stepwise_test.cc File Reference

#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/scoring/dunbrack/DunbrackRotamer.hh>
#include <core/scoring/Energies.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomICoor.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Ramachandran.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/viewer/viewers.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID_Map.Pose.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/AtomTree.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 <protocols/stepwise/StepWiseLegacyClusterer.hh>
#include <protocols/stepwise/protein/StepWiseProteinFilterer.hh>
#include <protocols/stepwise/protein/StepWiseProteinPoseMinimizer.hh>
#include <protocols/stepwise/protein/StepWiseProteinPoseSetup.hh>
#include <protocols/stepwise/protein/StepWiseProteinScreener.hh>
#include <protocols/stepwise/protein/util.hh>
#include <protocols/stepwise/protein/StepWiseProteinConnectionSampler.hh>
#include <protocols/stepwise/protein/MainChainTorsionSet.hh>
#include <protocols/cluster/cluster.hh>
#include <protocols/minimization_packing/GreenPacker.hh>
#include <protocols/minimization_packing/GreenPacker.fwd.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/optimizeH.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/util.hh>
#include <core/options/option_macros.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/io/pose_stream/PoseInputStream.hh>
#include <core/io/pose_stream/PoseInputStream.fwd.hh>
#include <core/io/pose_stream/PDBPoseInputStream.hh>
#include <core/io/pose_stream/SilentFilePoseInputStream.hh>
#include <core/util/datacache/BasicDataCache.hh>
#include <core/util/datacache/CacheableString.hh>
#include <core/util/basic.hh>
#include <core/io/database/open.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/etable/count_pair/CountPairFunction.hh>
#include <core/scoring/etable/count_pair/CountPairFactory.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/conversions.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/angle.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <protocols/jobdist/JobDistributors.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <deque>
#include <vector>
#include <core/util/Tracer.hh>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>
#include <core/options/keys/score.OptionKeys.gen.hh>
#include <core/options/keys/cluster.OptionKeys.gen.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	pdbslice (core::pose::Pose &pose, Size const &start_res, Size const &end_res)
void	sample_rama_test ()
void	minimizer_test ()
void	repack_test ()
Real	get_sidechain_rmsd (pose::Pose const &pose, pose::Pose const &start_pose, Size const &n)
void	sample_trp_test ()
void	add_chi_tags (core::pose::Pose &pose, core::pose::Pose const &native_pose, Size const n_trp, Size const n_tyr)
void	sample_trp_tyr_test ()
std::string	get_file_name (std::string const &silent_file, std::string const &tag)
void	rebuild_test ()
void	cluster_outfile_test_OLD ()
void	peptide_plane_test ()
void	peptide_plane_test_OLD ()
void	cluster_outfile_test ()
void	score12_plot_test ()
void	eval_lj (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const &d2, Real &fa_atr_score, Real &fa_rep_score, scoring::etable::Etable const &etable)
Real	get_lj_atom_score (core::id::AtomID const atom_id, core::pose::Pose const &pose, scoring::etable::Etable const &etable)
void	color_by_lj_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

add_chi_tags()

void add_chi_tags	(	core::pose::Pose &	pose,
		core::pose::Pose const &	native_pose,
		Size const	n_trp,
		Size const	n_tyr
	)

References docking::native_pose, and beta_nonlocal::pose.

Referenced by sample_trp_tyr_test().

cluster_outfile_test()

void cluster_outfile_test

(

)

References basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, out::nstruct(), option, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::cluster::score_diff_cut, in::file::silent(), out::file::silent(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

cluster_outfile_test_OLD()

void cluster_outfile_test_OLD

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::cluster::cluster, gaussian-sampling::input, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::cluster::remove_singletons, docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), tag, and basic::options::OptionKeys::inout::dbms::user.

color_by_lj_test()

void color_by_lj_test

(

)

References basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, get_lj_atom_score(), create_a3b_hbs::i, gaussian-sampling::input, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, create_a3b_hbs::pdb_info, beta_nonlocal::pose, in::file::s(), basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::recces::thermal_sampling::sample_residues, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, in::file::silent(), ObjexxFCL::string_of(), in::file::tags(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

eval_lj()

void eval_lj	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const &	d2,
		Real &	fa_atr_score,
		Real &	fa_rep_score,
		scoring::etable::Etable const &	etable
	)

References ObjexxFCL::FArray3D< T >::index(), and test.G201_Module_Structure::l1.

Referenced by get_lj_atom_score().

get_file_name()

std::string get_file_name	(	std::string const &	silent_file,
		std::string const &	tag
	)

References make_symmdef_file_denovo::pos, and tag.

Referenced by rebuild_test().

get_lj_atom_score()

Real get_lj_atom_score	(	core::id::AtomID const	atom_id,
		core::pose::Pose const &	pose,
		scoring::etable::Etable const &	etable
	)

References eval_lj(), create_a3b_hbs::i, create_a3b_hbs::j, numeric::xyzVector< T >::length_squared(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, numeric::xyzVector< T >::normalized(), beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and create_a3b_hbs::score.

Referenced by color_by_lj_test().

get_sidechain_rmsd()

Real get_sidechain_rmsd	(	pose::Pose const &	pose,
		pose::Pose const &	start_pose,
		Size const &	n
	)

References count, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.

Referenced by sample_trp_test().

main()

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

References argv, basic::options::OptionKeys::stepwise::protein::centroid_output, basic::options::OptionKeys::stepwise::protein::centroid_score_diff_cut, basic::options::OptionKeys::stepwise::rna::centroid_screen, basic::options::OptionKeys::stepwise::protein::centroid_weights, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, cluster_test(), basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, test.T009_Exceptions::e, indel::end_res, utility::options::OptionKeys::options::exit, basic::options::OptionKeys::stepwise::protein::filter_native_big_bins, basic::options::OptionKeys::in::file::fullatom, basic::options::OptionKeys::stepwise::protein::ghost_loops, basic::init(), basic::options::OptionKeys::dna::design::minimize, minimize_test(), my_main(), basic::options::OptionKeys::stepwise::protein::n_sample, NEW_OPT, basic::options::OptionKeys::stepwise::protein::nstruct_centroid, basic::options::OptionKeys::score::pack_weights, rebuild(), basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::cluster::score_diff_cut, indel::start_res, and viewer_main().

minimizer_test()

void minimizer_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, basic::options::OptionKeys::matdes::dock::dump_pdb, utility::options::OptionKeys::options::exit, gaussian-sampling::input, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), basic::options::OptionKeys::optimization::optimization, option, options, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::stepwise::protein::protein, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), tag_from_pose(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

my_main()

void* my_main

(

void *

)

References cluster_outfile_test(), cluster_test(), color_by_lj_test(), utility::options::OptionKeys::options::exit, minimize_test(), minimizer_test(), option, peptide_plane_test_OLD(), rebuild(), rebuild_test(), basic::options::OptionKeys::casp::repack, repack_test(), sample_rama_test(), sample_trp_test(), sample_trp_tyr_test(), and score12_plot_test().

Referenced by main().

pdbslice()

void pdbslice	(	core::pose::Pose &	pose,
		Size const &	start_res,
		Size const &	end_res
	)

References basic::options::OptionKeys::chemical::chemical, indel::end_res, create_a3b_hbs::i, beta_nonlocal::pose, and indel::start_res.

Referenced by calc_rms_test(), calculate_helical_parameters_helper(), generate_combined_model(), mismatch_test(), parse_pathway_test(), sample_rama_test(), stepwise_template_test(), tar_motif_test(), and write_base_pair_step_to_silent_struct().

peptide_plane_test()

void peptide_plane_test

(

)

References basic::options::OptionKeys::hotspot::angle, numeric::angle_radians(), basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, gaussian-sampling::input, option, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), tag_from_pose(), and numeric::conversions::to_degrees().

peptide_plane_test_OLD()

void peptide_plane_test_OLD

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, beta_nonlocal::pose, residue, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

rebuild_test()

void rebuild_test

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, in::file::fasta(), get_file_name(), in::file::native(), docking::native_pose, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::stepwise::protein::protein, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), in::file::tags(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

repack_test()

void repack_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::optimization::optimization, option, basic::options::OptionKeys::score::pack_weights, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, and vancomycin::task.

Referenced by my_main().

sample_rama_test()

void sample_rama_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, indel::end_res, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, docking::native_pose, option, pdbslice(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::stepwise::protein::protein, basic::options::OptionKeys::remodel::rama, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, out::file::silent(), indel::start_res, tag, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

sample_trp_test()

void sample_trp_test

(

)

References basic::options::OptionKeys::chemical::chemical, count, pyrosetta::create_score_function, get_sidechain_rmsd(), create_a3b_hbs::i, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::stepwise::protein::n_sample, in::file::native(), basic::options::OptionKeys::optimization::optimization, option, basic::options::OptionKeys::score::pack_weights, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::packing::prevent_repacking, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, out::file::silent(), tag, and vancomycin::task.

Referenced by my_main().

sample_trp_tyr_test()

void sample_trp_tyr_test

(

)

References add_chi_tags(), basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::stepwise::protein::n_sample, docking::native_pose, basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, tag, and vancomycin::task.

Referenced by my_main().

score12_plot_test()

void score12_plot_test

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::cluster::cluster, count, utility::io::oc::cout, lactamize::filename, create_a3b_hbs::i, ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::stepwise::protein::n_sample, option, oop_conformations::phi, beta_nonlocal::pose, oop_conformations::psi, docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, challenge::ss, and tag.

Referenced by my_main().