dna_design_test.cc File Reference

#include <protocols/dna/RestrictDesignToProteinDNAInterface.hh>
#include <protocols/viewer/viewers.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <utility/excn/Exceptions.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <numeric/random/random_permutation.hh>
#include <ObjexxFCL/format.hh>
#include <fstream>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>

Functions
void	rescale_phosphate_charges (Real const scale_factor)
vector1< Real >	get_boltzmann_probabilities (vector1< Real > const &E, Real const KT)
void	design_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tt ("demo.phil.dna_design_test", basic::t_info)

Function Documentation

design_test()

void design_test

(

)

References aa, ObjexxFCL::abs(), contacts(), utility::io::oc::cout, data, revert_app::design, basic::options::OptionKeys::dna::specificity::design_DNA, execute::dry_run, ObjexxFCL::format::F(), lactamize::filename, create_a3b_hbs::first, amino_acids::frequency, get_boltzmann_probabilities(), getline(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, extract_by_sidechain_sasa_score::l, line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::dna::specificity::nloop, create_a3b_hbs::nres, basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::dna::specificity::only_repack, option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), basic::prof_show(), numeric::random::random_permutation(), basic::options::OptionKeys::casp::repack, rescale_phosphate_charges(), reverse(), numeric::random::rg(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), tag, vancomycin::task, tt, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

get_boltzmann_probabilities()

vector1< Real > get_boltzmann_probabilities	(	vector1< Real > const &	E,
		Real const	KT
	)

References ObjexxFCL::format::E(), create_a3b_hbs::i, utility::min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, P, and spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob.

Referenced by design_test().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), and viewer_main().

my_main()

void* my_main

(

void *

)

References design_test(), and utility::options::OptionKeys::options::exit.

Referenced by main().

rescale_phosphate_charges()

void rescale_phosphate_charges

(

Real const

scale_factor

)

References atoms, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, and tt.

Referenced by design_test().

Variable Documentation

tt

basic::Tracer tt("demo.phil.dna_design_test", basic::t_info) ( "demo.phil.dna_design_test"  , basic::t_info    )

static

Referenced by design_test(), and rescale_phosphate_charges().