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Rosetta
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#include <protocols/frags/VallData.hh>#include <protocols/frags/TorsionFragment.hh>#include <core/scoring/dna/setup.hh>#include <core/scoring/dna/base_geometry.hh>#include <core/scoring/dna/BasePartner.hh>#include <core/scoring/GenBornPotential.hh>#include <core/scoring/LREnergyContainer.hh>#include <core/scoring/methods/Methods.hh>#include <protocols/simple_moves/BackboneMover.hh>#include <protocols/minimization_packing/MinMover.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/Mover.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/OutputMovers.hh>#include <protocols/rigid/RigidBodyMover.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/minimization_packing/PackRotamersMover.hh>#include <protocols/minimization_packing/RotamerTrialsMover.hh>#include <protocols/moves/RepeatMover.hh>#include <protocols/loops/ccd_closure.hh>#include <protocols/loops/loops_main.hh>#include <protocols/viewer/viewers.hh>#include <core/types.hh>#include <core/scoring/sasa.hh>#include <core/id/SequenceMapping.hh>#include <core/chemical/AtomTypeSet.hh>#include <core/chemical/MMAtomTypeSet.hh>#include <core/chemical/AA.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueMatcher.hh>#include <core/pack/rotamer_set/RotamerCouplings.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ResidueTypeSelector.hh>#include <core/conformation/ResidueFactory.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/ChemicalManager.hh>#include <core/scoring/etable/Etable.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/Ramachandran.hh>#include <core/pack/dunbrack/RotamerLibrary.hh>#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>#include <core/scoring/hbonds/HBondSet.hh>#include <core/scoring/hbonds/hbonds.hh>#include <core/scoring/etable/count_pair/CountPairFunction.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/TaskOperation.hh>#include <core/kinematics/FoldTree.hh>#include <protocols/viewer//visualize.hh>#include <core/kinematics/MoveMap.hh>#include <core/kinematics/util.hh>#include <core/id/AtomID_Map.hh>#include <core/mm/MMTorsionLibrary.hh>#include <core/mm/MMTorsionLibrary.fwd.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <core/pose/Pose.hh>#include <core/pose/util.hh>#include <core/pose/PDBPoseMap.hh>#include <core/pose/PDBInfo.hh>#include <basic/options/util.hh>#include <basic/basic.hh>#include <basic/database/open.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <utility/vector1.hh>#include <numeric/xyzVector.hh>#include <numeric/random/random.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <core/scoring/constraints/DihedralConstraint.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/func/HarmonicFunc.hh>#include <core/scoring/func/PeriodicFunc.hh>#include <core/scoring/constraints/DOF_Constraint.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/ConstraintIO.hh>#include <core/fragment/picking/FragmentLibraryManager.hh>#include <core/fragment/picking/vall/VallLibrarian.hh>#include <core/fragment/picking/vall/gen/LengthGen.hh>#include <core/fragment/picking/vall/scores/VallFragmentScore.hh>#include <cstdlib>#include <fstream>#include <iostream>#include <string>#include <basic/Tracer.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/pep_spec.OptionKeys.gen.hh>#include <basic/options/keys/constraints.OptionKeys.gen.hh>#include <core/import_pose/import_pose.hh>Functions | |
| Size | get_n_pep_nbrs (pose::Pose const &pose, vector1< bool > const is_pep, Real const cutoff_cg) |
| void | dump_efactor_pdb (pose::Pose &pose, core::scoring::ScoreFunctionOP const scorefxn, std::string const &tag) |
| bool | has_clash (pose::Pose &pose, vector1< bool > is_checked, scoring::ScoreFunctionOP const &scorefxn, Real const clash_threshold) |
| void | normalize_res_freqs (vector1< Real > &res_freqs, Size n) |
| void | minimize_ref_weights (vector1< Real > &ref_weights, vector1< Real > res_freqs, vector1< Real > ideal_res_freqs, Real stepsize) |
| void | print_res_freqs (vector1< Real > res_freqs, vector1< Real > ideal_res_freqs, std::string res_freqs_file_name_str) |
| void | print_scorefxn (ScoreFunctionOP scorefxn, vector1< Real > ref_weights, std::string wts_file_name_str) |
| Size | aa2index (chemical::AA aa) |
| void | RunPepSpec () |
| int | main (int argc, char *argv[]) |
| Size aa2index | ( | chemical::AA | aa | ) |
References aa, enumerate_junctions::default, and ObjexxFCL::index().
Referenced by RunPepSpec().
| void dump_efactor_pdb | ( | pose::Pose & | pose, |
| core::scoring::ScoreFunctionOP const | scorefxn, | ||
| std::string const & | tag | ||
| ) |
References val2thr::atom, predPRE::chain, chains, ObjexxFCL::format::F(), lactamize::filename, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::nres, basic::options::option, erraser_single_res_analysis::out, basic::options::OptionKeys::out::file::output_virtual, beta_nonlocal::pose, oop_conformations::scorefxn, and tag.
Referenced by RunPepSpec().
| Size get_n_pep_nbrs | ( | pose::Pose const & | pose, |
| vector1< bool > const | is_pep, | ||
| Real const | cutoff_cg | ||
| ) |
| bool has_clash | ( | pose::Pose & | pose, |
| vector1< bool > | is_checked, | ||
| scoring::ScoreFunctionOP const & | scorefxn, | ||
| Real const | clash_threshold | ||
| ) |
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, test.T009_Exceptions::e, basic::init(), and RunPepSpec().
| void minimize_ref_weights | ( | vector1< Real > & | ref_weights, |
| vector1< Real > | res_freqs, | ||
| vector1< Real > | ideal_res_freqs, | ||
| Real | stepsize | ||
| ) |
References ObjexxFCL::abs(), and create_a3b_hbs::i.
Referenced by RunPepSpec().
References create_a3b_hbs::i, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.
Referenced by RunPepSpec().
| void print_res_freqs | ( | vector1< Real > | res_freqs, |
| vector1< Real > | ideal_res_freqs, | ||
| std::string | res_freqs_file_name_str | ||
| ) |
References ObjexxFCL::abs(), create_a3b_hbs::i, erraser_single_res_analysis::out, and ObjexxFCL::string_of().
Referenced by RunPepSpec().
| void print_scorefxn | ( | ScoreFunctionOP | scorefxn, |
| vector1< Real > | ref_weights, | ||
| std::string | wts_file_name_str | ||
| ) |
References create_a3b_hbs::ii, erraser_single_res_analysis::out, and oop_conformations::scorefxn.
Referenced by RunPepSpec().
| void RunPepSpec | ( | ) |
References aa2index(), utility::io::oc::cout, pyrosetta::create_score_function, dump_efactor_pdb(), create_a3b_hbs::f, getline(), create_a3b_hbs::i, make_sequence_change(), minimize_ref_weights(), normalize_res_freqs(), out::file::o(), option, demo.D010_Pose_structure::pdb_filename, bur_nodon_tyr::pdb_list, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), basic::options::OptionKeys::pepspec::pep_chain, pep_end(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, print_res_freqs(), print_scorefxn(), numeric::random::rg(), oop_conformations::scorefxn, ObjexxFCL::string_of(), numeric::random::RandomGenerator::uniform(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.
Referenced by main().
1.9.1