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Rosetta
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#include <core/scoring/rms_util.hh>#include <core/types.hh>#include <core/chemical/AA.hh>#include <core/conformation/Residue.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/conformation/ResidueFactory.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/util.hh>#include <core/chemical/ChemicalManager.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/methods/EnergyMethodOptions.hh>#include <core/chemical/rna/util.hh>#include <core/scoring/rna/RNA_CentroidInfo.hh>#include <core/scoring/rna/RNA_ScoringInfo.hh>#include <core/scoring/Energies.hh>#include <core/sequence/util.hh>#include <core/sequence/Sequence.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/tree/Atom.hh>#include <core/id/AtomID_Map.hh>#include <core/id/AtomID_Map.Pose.hh>#include <core/id/AtomID.hh>#include <core/id/NamedAtomID.hh>#include <core/id/DOF_ID.hh>#include <core/kinematics/AtomTree.hh>#include <core/kinematics/Jump.hh>#include <core/kinematics/MoveMap.hh>#include <core/io/silent/RNA_SilentStruct.hh>#include <core/io/silent/BinarySilentStruct.hh>#include <core/io/silent/SilentFileData.hh>#include <core/pack/pack_rotamers.hh>#include <core/pack/rotamer_trials.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pose/Pose.hh>#include <core/options/option.hh>#include <core/options/after_opts.hh>#include <core/options/util.hh>#include <core/options/option_macros.hh>#include <protocols/viewer/viewers.hh>#include <protocols/stepwise/modeler/util.hh>#include <protocols/stepwise/StepWiseLegacyClusterer.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <utility/vector1.hh>#include <utility/io/ozstream.hh>#include <utility/io/izstream.hh>#include <utility/file/file_sys_util.hh>#include <numeric/xyzVector.hh>#include <numeric/xyzMatrix.hh>#include <numeric/conversions.hh>#include <numeric/xyz.functions.hh>#include <numeric/angle.functions.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <fstream>#include <iostream>#include <string>#include <core/util/Tracer.hh>#include <core/options/keys/out.OptionKeys.gen.hh>#include <core/options/keys/score.OptionKeys.gen.hh>#include <core/options/keys/in.OptionKeys.gen.hh>#include <core/options/keys/cluster.OptionKeys.gen.hh>Typedefs | |
| typedef numeric::xyzMatrix< Real > | Matrix |
Functions | |
| void | setup_heavy_atoms (pose::Pose const &pose, utility::vector1< Vector > &pose_atoms, utility::vector1< Size > const &subset_res) |
| bool | check_contact (Vector const &translation, utility::vector1< Vector > const &moving_atoms, utility::vector1< Vector > const &partner_atoms) |
| bool | check_steric_overlap (Vector const &translation, utility::vector1< Vector > const &moving_atoms, utility::vector1< Vector > const &partner_atoms) |
| void | search_translations (pose::Pose &pose, pose::Pose const &pose_to_translate, utility::vector1< Size > const &moving_res, utility::vector1< Size > const &partner_res, Size &count, Size &positive_Z_count, Real &best_energy, Real &Z, core::io::silent::SilentFileDataOP sfd=0) |
| void | define_states_test () |
| void | turner_rules_test () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
| typedef numeric::xyzMatrix< Real > Matrix |
| bool check_contact | ( | Vector const & | translation, |
| utility::vector1< Vector > const & | moving_atoms, | ||
| utility::vector1< Vector > const & | partner_atoms | ||
| ) |
References DIST_CUTOFF, create_a3b_hbs::i, create_a3b_hbs::j, option, and basic::options::OptionKeys::rigid::translation.
Referenced by search_translations().
| bool check_steric_overlap | ( | Vector const & | translation, |
| utility::vector1< Vector > const & | moving_atoms, | ||
| utility::vector1< Vector > const & | partner_atoms | ||
| ) |
References DIST_CUTOFF, create_a3b_hbs::i, create_a3b_hbs::j, option, and basic::options::OptionKeys::rigid::translation.
Referenced by search_translations().
| void define_states_test | ( | ) |
References compute_difference::alpha, basic::options::OptionKeys::sample_around::alpha_increment, basic::options::OptionKeys::corrections::beta, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, count, utility::io::oc::cout, numeric::conversions::degrees(), create_a3b_hbs::f, loops::gamma, basic::options::OptionKeys::sample_around::gamma_increment, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::stepwise::protein::n_sample, out::nstruct(), basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, numeric::conversions::radians(), basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::full_model::rna::rna, pyrosetta.bindings.pose::rotate(), basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::frags::scoring::scoring, search_translations(), sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), beta_nonlocal::translate, and basic::options::OptionKeys::inout::dbms::user.
Referenced by my_main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
| void* my_main | ( | void * | ) |
References define_states_test(), and utility::options::OptionKeys::options::exit.
Referenced by main().
| void search_translations | ( | pose::Pose & | pose, |
| pose::Pose const & | pose_to_translate, | ||
| utility::vector1< Size > const & | moving_res, | ||
| utility::vector1< Size > const & | partner_res, | ||
| Size & | count, | ||
| Size & | positive_Z_count, | ||
| Real & | best_energy, | ||
| Real & | Z, | ||
| core::io::silent::SilentFileDataOP | sfd = 0 |
||
| ) |
References basic::options::OptionKeys::corrections::beta, check_contact(), check_steric_overlap(), count, oop_conformations::energy, pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, ObjexxFCL::lead_zero_string_of(), numeric::xyzVector< T >::length_squared(), option, beta_nonlocal::pose, docking::s, basic::options::OptionKeys::ddg::score_cutoff, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_heavy_atoms(), sfd, basic::options::OptionKeys::in::file::silent, tag, local::temperature, beta_nonlocal::translate, and basic::options::OptionKeys::rigid::translation.
Referenced by define_states_test().
| void setup_heavy_atoms | ( | pose::Pose const & | pose, |
| utility::vector1< Vector > & | pose_atoms, | ||
| utility::vector1< Size > const & | subset_res | ||
| ) |
References create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.
Referenced by search_translations().
| void turner_rules_test | ( | ) |
1.9.1