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Rosetta
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#include <devel/dna/protocols.hh>#include <devel/dna/util.hh>#include <protocols/loops/loops_main.hh>#include <protocols/loops/Loops.hh>#include <protocols/frags/TorsionFragment.hh>#include <utility/excn/Exceptions.hh>#include <protocols/viewer/viewers.hh>#include <protocols/minimization_packing/PackRotamersMover.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/minimization_packing/MinMover.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/rigid_body_moves.hh>#include <core/scoring/LREnergyContainer.hh>#include <core/scoring/dna/setup.hh>#include <core/scoring/dna/base_geometry.hh>#include <core/scoring/dna/BasePartner.hh>#include <core/scoring/dna/DNA_BasePotential.hh>#include <core/pack/dunbrack/RotamerLibrary.hh>#include <core/scoring/func/Func.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/CoordinateConstraint.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/etable/Etable.hh>#include <core/scoring/AtomVDW.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/rms_util.hh>#include <core/scoring/hbonds/hbonds.hh>#include <core/scoring/hbonds/HBondSet.hh>#include <core/energy_methods/FA_ElecEnergy.hh>#include <core/scoring/etable/count_pair/CountPairAll.hh>#include <core/scoring/etable/count_pair/CountPairFunction.hh>#include <core/scoring/etable/count_pair/CountPairFactory.hh>#include <core/types.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ResidueTypeSelector.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/AtomTypeSet.hh>#include <core/chemical/MMAtomTypeSet.hh>#include <core/chemical/AA.hh>#include <core/conformation/util.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueMatcher.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/rotamer_set/RotamerCouplings.hh>#include <core/pack/rotamer_set/WaterPackingInfo.hh>#include <core/kinematics/FoldTree.hh>#include <protocols/viewer/visualize.hh>#include <core/kinematics/MoveMap.hh>#include <core/id/AtomID_Map.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <core/pose/Pose.hh>#include <basic/options/util.hh>#include <basic/prof.hh>#include <basic/basic.hh>#include <core/id/SequenceMapping.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <utility/vector1.hh>#include <numeric/xyzVector.hh>#include <numeric/xyzMatrix.hh>#include <numeric/xyz.functions.hh>#include <numeric/random/random.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <fstream>#include <iostream>#include <string>#include <set>#include <cstdlib>#include <sstream>#include <math.h>#include <basic/Tracer.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/dna.OptionKeys.gen.hh>#include <basic/options/keys/loops.OptionKeys.gen.hh>#include <basic/options/keys/phil.OptionKeys.gen.hh>#include <core/import_pose/import_pose.hh>#include <core/pose/util.hh>#include <core/util/SwitchResidueTypeSet.hh>Functions | |
| void | kono_sarai_stats () |
| std::string | atom_line (std::string const &atom_name, std::string const &rsd_name, Vector const &xyz, int &counter) |
| void | kono_sarai_zscore () |
| void | loop_modeling_test () |
| void | loop_rebuilding_test () |
| void | dna_dr_test () |
| void | dna_dr_loop_test () |
| void * | my_main (void *) |
Variables | |
| static basic::Tracer | tt ("demo.phil.dna_dr_test", basic::t_info) |
| std::string atom_line | ( | std::string const & | atom_name, |
| std::string const & | rsd_name, | ||
| Vector const & | xyz, | ||
| int & | counter | ||
| ) |
| void dna_dr_loop_test | ( | ) |
References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, pyrosetta::create_score_function, loops::cutpoint, basic::Error(), utility::exit(), create_a3b_hbs::f, usec::frag_size, basic::options::OptionKeys::frags::frag_sizes, basic::options::OptionKeys::frags::frags, create_a3b_hbs::ii, create_a3b_hbs::j, create_a3b_hbs::k, ObjexxFCL::lead_zero_string_of(), demo.D080_Loop_modeling::loop_begin, pivot_selection::loop_end, kic_runner::loop_file, basic::options::OptionKeys::cluster::loops, out::nstruct(), option, drrafter_rna::output_tag, kic_runner::pdb, beta_nonlocal::pose, ObjexxFCL::pow(), basic::prof_reset(), basic::prof_show(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), ObjexxFCL::string_of(), and orn_macrocycle::wt.
Referenced by my_main().
| void dna_dr_test | ( | ) |
References beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and tt.
Referenced by my_main().
| void kono_sarai_stats | ( | ) |
References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, measure_params::dot(), ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, basic::options::OptionKeys::cm::nn, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, enumerate_junctions::q, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), x, xx, predPRE::y, yy, predPRE::z, and test.T110_numeric::zz.
Referenced by my_main().
| void kono_sarai_zscore | ( | ) |
References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, measure_params::dot(), ObjexxFCL::format::F(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::cm::nn, erraser_single_res_analysis::out, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, enumerate_junctions::q, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), x, xx, predPRE::y, yy, predPRE::z, and test.T110_numeric::zz.
Referenced by my_main().
| void loop_modeling_test | ( | ) |
References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, numeric::xyzVector< T >::distance(), basic::options::OptionKeys::matdes::dock::dump_pdb, test.T009_Exceptions::e, usec::frag_size, basic::options::OptionKeys::frags::frag_sizes, basic::options::OptionKeys::frags::frags, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, demo.D080_Loop_modeling::loop_begin, basic::options::OptionKeys::cluster::loops, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, offset, option, kic_runner::pdb, make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), and utility_exit_with_message.
| void loop_rebuilding_test | ( | ) |
References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::Error(), utility::exit(), usec::frag_size, basic::options::OptionKeys::frags::frag_sizes, basic::options::OptionKeys::frags::frags, kic_runner::loop_file, basic::options::OptionKeys::cluster::loops, option, kic_runner::pdb, beta_nonlocal::pose, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::start_file().
| void* my_main | ( | void * | ) |
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static |
Referenced by dna_dr_test().
1.9.1