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Rosetta
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#include <core/types.hh>#include <core/chemical/AA.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/scoring/Energies.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/pack/pack_rotamers.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/task/operation/TaskOperation.hh>#include <core/kinematics/MoveMap.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <core/pose/Pose.hh>#include <basic/options/util.hh>#include <basic/options/after_opts.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <utility/excn/Exceptions.hh>#include <numeric/xyzVector.hh>#include <numeric/random/random.hh>#include <core/pack/task/ResfileReader.hh>#include <fstream>#include <iostream>#include <sstream>#include <ios>#include <utility/io/izstream.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/FArray2D.hh>#include <cstdlib>#include <string>#include <basic/Tracer.hh>#include <basic/options/keys/ddg.OptionKeys.gen.hh>#include <core/import_pose/import_pose.hh>Typedefs | |
| typedef std::vector< double > | ddGs |
Functions | |
| double | sum (ddGs &scores_to_sum) |
| double | average (utility::vector1< double > &scores_to_average) |
| int | store_energies (ObjexxFCL::FArray2D< double > &two_d_e_arrays, scoring::ScoreFunction &s, pose::Pose &p, int next_index, int size_to_expect) |
| int | average_score_components (ObjexxFCL::FArray2D< double > &scores_to_average, utility::vector1< double > &averaged_scores) |
| int | main (int argc, char *argv[]) |
| double average | ( | utility::vector1< double > & | scores_to_average | ) |
References create_a3b_hbs::i, and sum().
Referenced by main().
| int average_score_components | ( | ObjexxFCL::FArray2D< double > & | scores_to_average, |
| utility::vector1< double > & | averaged_scores | ||
| ) |
References create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::FArray2D< T >::l1(), ObjexxFCL::FArray2D< T >::l2(), ObjexxFCL::FArray2D< T >::u1(), and ObjexxFCL::FArray2D< T >::u2().
Referenced by main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References job_manager::app, argv, average(), average_score_components(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::ddg::debug_output, basic::options::OptionKeys::ddg::dump_pdbs, test.T009_Exceptions::e, utility::exit(), ObjexxFCL::format::F(), lactamize::filename, header(), create_a3b_hbs::i, basic::options::OptionKeys::in::in, basic::init(), autocorrelation::iterations, create_a3b_hbs::j, create_a3b_hbs::k, line, demo.D090_Ala_scan::mutant_aa, local::num_iterations, basic::options::OptionKeys::out::file::o, option, erraser_single_res_analysis::out, output_pdb(), parse_resfile(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, enumerate_junctions::q, create_a3b_hbs::r, predPRE::resnum, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), store_energies(), sum(), vancomycin::task, and basic::options::OptionKeys::ddg::weight_file.
| int store_energies | ( | ObjexxFCL::FArray2D< double > & | two_d_e_arrays, |
| scoring::ScoreFunction & | s, | ||
| pose::Pose & | p, | ||
| int | next_index, | ||
| int | size_to_expect | ||
| ) |
References ObjexxFCL::FArray2D< T >::dimension(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and docking::s.
Referenced by main().
References create_a3b_hbs::i.
1.9.1