test1.cc File Reference

Some simple examples of how to use basic functionality + some DNA functionality. More...

#include <devel/init.hh>
#include <protocols/frags/VallData.hh>
#include <protocols/frags/TorsionFragment.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/OutputMovers.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/loops/loop_closure/ccd/CCDLoopClosureMover.hh>
#include <protocols/loops/loop_closure/ccd/RamaCheck.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/viewer/visualize.hh>
#include <core/id/AtomID_Map.hh>
#include <core/types.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/chemical/AtomType.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/base_geometry.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/GenBornPotential.hh>
#include <core/scoring/LREnergyContainer.hh>
#include <core/scoring/methods/Methods.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueProperties.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/sequence/DerivedSequenceMapping.hh>
#include <core/sequence/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/init_id_map.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/pack/rtmin.hh>
#include <core/pack/min_pack.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibrary.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/options/util.hh>
#include <basic/prof.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/basic.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/phil.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/random/init_random_generator.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <numeric/conversions.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/pack/task/ResidueLevelTask.hh>

Functions
std::ostream &	operator<< (std::ostream &out, Vector const &v)
void	read_list_file (std::string const &filename, utility::vector1< std::string > &l)
void	setup_atom_number (pose::Pose const &pose, id::AtomID_Map< int > &atom_number)
void	show_rasmol_hbonds (scoring::hbonds::HBondSet const &hbond_set, id::AtomID_Map< int > const &atom_number, std::ostream &out)
void	dump_hbond_pdb (pose::Pose &pose, std::string const &filename)
void	show_intrachain_energies (pose::Pose &pose, scoring::ScoreFunction const &scorefxn)
void	test_dunbrack_io ()
void	test_gb ()
void	test_rama ()
void	test_scorefxn_io ()
void	simple_rotamer_test ()
void	set_fullatom_flag_test ()
void	delete_test ()
void	simple_loop_modeling_test ()
void *	simple_loop_modeling_test_wrapper (void *)
void	dna_deriv_test_old ()
void	dna_deriv_test ()
void	dna_io_test ()
void	old_simple_conformation_test ()
void	simple_centroid_test ()
void	simple_frag_test ()
void	dna_design_test_old (pose::Pose &pose)
void	dna_coupled_rotamer_design_test ()
void	dna_design_test ()
void	simple_dna_test ()
void	simple_copy_test ()
void	simple_hbond_test ()
void	atom_tree_torsion_test ()
void	fa_scorefxn_test ()
void	rotamer_trials_test ()
	STOP REMOVING FUNCTIONS FROM TEST1. More...
void	pack_rotamers_test ()
void	small_min_test ()
void	rb_test ()
void	ccd_test ()
void	sasa_test ()
void	simple_benchmark ()
void	mm_pack_test ()
void	start_file_test ()
void	ss_test ()
void	backrub_min_test ()
void	bk_test ()
void	bk_test2 ()
void	ligrot_test ()
void	proclose_test ()
void	set_stub_transform_test ()
void	lk_ball_wtd_deriv_test ()
void	atom_types_test ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tt ("demo.phil.test1", basic::t_trace)

Detailed Description

Some simple examples of how to use basic functionality + some DNA functionality.

Author

Phil Bradley (pbrad.nosp@m.ley@.nosp@m.fhcrc.nosp@m..org)

Function Documentation

atom_tree_torsion_test()

void atom_tree_torsion_test

(

)

References ObjexxFCL::abs(), basic::options::OptionKeys::matdes::dock::dump_pdb, test.T009_Exceptions::e, create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, offset, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::r, and basic::subtract_degree_angles().

Referenced by simple_benchmark().

atom_types_test()

void atom_types_test

(

)

References utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, and basic::options::OptionKeys::in::file::residue_type_set.

backrub_min_test()

void backrub_min_test

(

)

References val2thr::atom, utility::io::oc::cout, create_a3b_hbs::i, create_a3b_hbs::k, beta_nonlocal::mm, PHI, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, ObjexxFCL::string_of(), and utility_exit_with_message.

Referenced by main().

bk_test()

void bk_test

(

)

References utility::options::OptionKeys::options::exit, create_a3b_hbs::i, create_a3b_hbs::nres, beta_nonlocal::pose, test.T008_Serialization::pose2, and pyrosetta.distributed.io::pose_from_file.

Referenced by main().

bk_test2()

void bk_test2

(

)

References utility::io::oc::cout, utility::options::OptionKeys::options::exit, create_a3b_hbs::i, beta_nonlocal::mm, test.T008_Serialization::pose1, test.T008_Serialization::pose2, pyrosetta.distributed.io::pose_from_file, numeric::conversions::radians(), oop_conformations::scorefxn, basic::options::start_files(), and tt.

Referenced by main().

ccd_test()

void ccd_test

(

)

References loops::cutpoint, basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::f, create_a3b_hbs::i, internal_coordinates::loop, beta_nonlocal::mm, create_a3b_hbs::nres, options, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by simple_benchmark().

delete_test()

void delete_test

(

)

References utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, create_a3b_hbs::nres, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and oop_conformations::scorefxn.

Referenced by main(), and simple_benchmark().

dna_coupled_rotamer_design_test()

void dna_coupled_rotamer_design_test

(

)

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, test.T220_AtomAtomPairEnergies::fa_elec, create_a3b_hbs::i, create_a3b_hbs::ii, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, create_a3b_hbs::nres, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::remodel::rama, test.T500_Packing::rotamer_trials, runtime_assert, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, show_intrachain_energies(), and vancomycin::task.

Referenced by main(), and simple_benchmark().

dna_deriv_test()

void dna_deriv_test

(

)

References local::chain1, utility::io::oc::cout, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::frags::frags, create_a3b_hbs::j, vancomycin::min_mover, beta_nonlocal::mm, create_a3b_hbs::nres, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and tt.

Referenced by main(), and simple_benchmark().

dna_deriv_test_old()

void dna_deriv_test_old

(

)

References local::chain1, utility::io::oc::cout, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::frags::frags, create_a3b_hbs::j, beta_nonlocal::mm, create_a3b_hbs::nres, options, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), and tt.

dna_design_test()

void dna_design_test

(

)

References utility::io::oc::cout, dna_design_test_old(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::start_files().

Referenced by main().

dna_design_test_old()

void dna_design_test_old

(

pose::Pose &

pose

)

References basic::options::OptionKeys::dna::dna, create_a3b_hbs::i, create_a3b_hbs::nres, basic::options::OptionKeys::dna::specificity::params, kic_runner::pdb, beta_nonlocal::pose, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by dna_design_test().

dna_io_test()

void dna_io_test

(

)

References utility::io::oc::cout, basic::options::OptionKeys::frags::frags, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, num_chains(), kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::start_files().

dump_hbond_pdb()

void dump_hbond_pdb	(	pose::Pose &	pose,
		std::string const &	filename
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::options::OptionKeys::matdes::dock::dump_pdb, lactamize::filename, test.T200_Scoring::hbond_set, erraser_single_res_analysis::out, PHI, beta_nonlocal::pose, setup_atom_number(), show_rasmol_hbonds(), and THETA.

Referenced by simple_hbond_test().

fa_scorefxn_test()

void fa_scorefxn_test

(

)

References utility::io::oc::cout, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::remodel::rama, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by simple_benchmark().

ligrot_test()

void ligrot_test

(

)

References utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, erraser_single_res_analysis::out, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::start_files().

Referenced by main().

lk_ball_wtd_deriv_test()

void lk_ball_wtd_deriv_test

(

)

References utility::io::oc::cout, ObjexxFCL::format::F(), lactamize::filename, create_a3b_hbs::i, test.T110_numeric::I, basic::options::OptionKeys::min_pack, beta_nonlocal::mm, options, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::rot_anl::rtmin, oop_conformations::scorefxn, basic::options::start_file(), and vancomycin::task.

Referenced by main().

main()

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

References argv, backrub_min_test(), basic::options::OptionKeys::hotspot::benchmark, bk_test(), bk_test2(), delete_test(), dna_coupled_rotamer_design_test(), dna_deriv_test(), dna_design_test(), test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), ligrot_test(), lk_ball_wtd_deriv_test(), mm_pack_test(), option, pack_rotamers_test(), proclose_test(), rb_test(), set_stub_transform_test(), simple_benchmark(), simple_loop_modeling_test(), simple_loop_modeling_test_wrapper(), ss_test(), start_file_test(), test_gb(), test_scorefxn_io(), and viewer_main().

mm_pack_test()

void mm_pack_test

(

)

References utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

old_simple_conformation_test()

void old_simple_conformation_test

(

)

References basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::f, create_a3b_hbs::nres, beta_nonlocal::pose, and pyrosetta.distributed.io::pose_from_file.

operator<<()

std::ostream& operator<<	(	std::ostream &	out,
		Vector const &	v
	)

References ObjexxFCL::format::F(), erraser_single_res_analysis::out, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

pack_rotamers_test()

void pack_rotamers_test

(

)

References utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::ii, basic::options::OptionKeys::corrections::score::p_aa_pp, parse_resfile(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by main(), and simple_benchmark().

proclose_test()

void proclose_test

(

)

References utility::io::oc::cout, create_a3b_hbs::i, beta_nonlocal::mm, create_a3b_hbs::nres, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, and basic::options::start_file().

Referenced by main().

rb_test()

void rb_test

(

)

References basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::f, vancomycin::f2, beta_nonlocal::mm, create_a3b_hbs::nres, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::remodel::rama, basic::options::OptionKeys::in::file::residue_type_set, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

read_list_file()

void read_list_file	(	std::string const &	filename,
		utility::vector1< std::string > &	l
	)

References utility::io::oc::cout, data, lactamize::filename, getline(), extract_by_sidechain_sasa_score::l, line, and utility_exit_with_message.

rotamer_trials_test()

void rotamer_trials_test

(

)

STOP REMOVING FUNCTIONS FROM TEST1.

References utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, test.T500_Packing::rotamer_trials, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by simple_benchmark().

sasa_test()

void sasa_test

(

)

References utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by simple_benchmark().

set_fullatom_flag_test()

void set_fullatom_flag_test

(

)

References utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::frags::frags, create_a3b_hbs::i, create_a3b_hbs::j, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, and basic::options::OptionKeys::frags::scoring::scoring.

set_stub_transform_test()

void set_stub_transform_test

(

)

References docking::a1, docking::a2, docking::a3, docking::b1, docking::b2, docking::b3, loops::cutpoint, create_a3b_hbs::f, create_a3b_hbs::nres, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by main().

setup_atom_number()

void setup_atom_number	(	pose::Pose const &	pose,
		id::AtomID_Map< int > &	atom_number
	)

References create_a3b_hbs::i, create_a3b_hbs::j, and beta_nonlocal::pose.

Referenced by dump_hbond_pdb().

show_intrachain_energies()

void show_intrachain_energies	(	pose::Pose &	pose,
		scoring::ScoreFunction const &	scorefxn
	)

References utility::io::oc::cout, ObjexxFCL::format::F(), utility::graph::Edge::get_node(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and utility::graph::Node::upper_edge_list_end().

Referenced by dna_coupled_rotamer_design_test().

show_rasmol_hbonds()

void show_rasmol_hbonds	(	scoring::hbonds::HBondSet const &	hbond_set,
		id::AtomID_Map< int > const &	atom_number,
		std::ostream &	out
	)

References test.T200_Scoring::hbond_set, and create_a3b_hbs::i.

Referenced by dump_hbond_pdb().

simple_benchmark()

void simple_benchmark

(

)

References atom_tree_torsion_test(), ccd_test(), delete_test(), dna_coupled_rotamer_design_test(), dna_deriv_test(), fa_scorefxn_test(), basic::random::init_random_generators(), pack_rotamers_test(), rotamer_trials_test(), sasa_test(), simple_dna_test(), simple_rotamer_test(), test_rama(), and test_scorefxn_io().

Referenced by main().

simple_centroid_test()

void simple_centroid_test

(

)

References basic::options::OptionKeys::remodel::cbeta, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, env, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, pair, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, oop_conformations::scorefxn, and basic::options::OptionKeys::remodel::vdw.

simple_copy_test()

void simple_copy_test

(

)

References basic::options::OptionKeys::matdes::dock::dump_pdb, beta_nonlocal::pose, and pyrosetta.distributed.io::pose_from_file.

simple_dna_test()

void simple_dna_test

(

)

References utility::io::oc::cout, create_a3b_hbs::ii, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::remodel::rama, test.T500_Packing::rotamer_trials, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by simple_benchmark().

simple_frag_test()

void simple_frag_test

(

)

References basic::options::OptionKeys::matdes::dock::dump_pdb, usec::frag_size, basic::options::OptionKeys::frags::frags, create_a3b_hbs::i, create_a3b_hbs::nres, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::vall, and basic::options::OptionKeys::loops::vall_file.

simple_hbond_test()

void simple_hbond_test

(

)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, dump_hbond_pdb(), basic::options::OptionKeys::matdes::dock::dump_pdb, vancomycin::min_mover, PHI, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, and THETA.

simple_loop_modeling_test()

void simple_loop_modeling_test

(

)

References basic::options::OptionKeys::remodel::cbeta, utility::io::oc::cout, loops::cutpoint, basic::options::OptionKeys::matdes::dock::dump_pdb, ObjexxFCL::format::E(), env, create_a3b_hbs::f, usec::frag_size, basic::options::OptionKeys::frags::frags, create_a3b_hbs::i, create_a3b_hbs::ii, init_omega(), init_phi(), init_psi(), create_a3b_hbs::k, mc, beta_nonlocal::mm, basic::options::OptionKeys::ddg::nfrags, basic::options::OptionKeys::cm::nn, create_a3b_hbs::nres, option, pair, kic_runner::pdb, make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::prof_reset(), basic::prof_show(), numeric::random::rg(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, subloop_histogram::size, basic::options::start_file(), tt, numeric::random::uniform(), numeric::random::RandomGenerator::uniform(), basic::options::OptionKeys::in::file::vall, basic::options::OptionKeys::loops::vall_file, and basic::options::OptionKeys::remodel::vdw.

Referenced by main(), and simple_loop_modeling_test_wrapper().

simple_loop_modeling_test_wrapper()

void* simple_loop_modeling_test_wrapper

(

void *

)

References simple_loop_modeling_test().

Referenced by main().

simple_rotamer_test()

void simple_rotamer_test

(

)

References basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::i, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and rot.

Referenced by simple_benchmark().

small_min_test()

void small_min_test

(

)

References basic::options::OptionKeys::matdes::dock::dump_pdb, mc, vancomycin::min_mover, beta_nonlocal::mm, basic::options::OptionKeys::MonteCarlo::MonteCarlo, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::dna::specificity::nloop, basic::options::OptionKeys::mp::quickrelax::nmoves, local::nstruct, basic::options::OptionKeys::out::file::o, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::remodel::rama, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, test.Workshop5test::small_mover, basic::options::start_file(), ObjexxFCL::string_of(), and vancomycin::task.

ss_test()

void ss_test

(

)

References utility::io::oc::cout, create_a3b_hbs::ii, predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::remodel::rsigma, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, basic::options::OptionKeys::remodel::ss_pair, and basic::options::start_files().

Referenced by main().

start_file_test()

void start_file_test

(

)

References utility::io::oc::cout, create_a3b_hbs::i, basic::options::start_file(), and basic::options::start_files().

Referenced by main().

test_dunbrack_io()

void test_dunbrack_io

(

)

References create_a3b_hbs::i, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::frags::scoring::scoring.

test_gb()

void test_gb

(

)

References utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T200_Scoring::emap, utility::options::OptionKeys::options::exit, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), and vancomycin::task.

Referenced by main().

test_rama()

void test_rama

(

)

References utility::io::oc::cout, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::remodel::rama, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by simple_benchmark().

test_scorefxn_io()

void test_scorefxn_io

(

)

References utility::io::oc::cout, pyrosetta::create_score_function, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::trRosetta::scorefxn2, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main(), and simple_benchmark().

Variable Documentation

tt

basic::Tracer tt("demo.phil.test1", basic::t_trace) ( "demo.phil.test1"  , basic::t_trace    )

static

Referenced by bk_test2(), dna_deriv_test(), dna_deriv_test_old(), and simple_loop_modeling_test().