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Rosetta
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#include <core/scoring/rms_util.hh>#include <core/scoring/rms_util.tmpl.hh>#include <core/scoring/dunbrack/SingleResidueDunbrackLibrary.hh>#include <core/scoring/dunbrack/DunbrackRotamer.hh>#include <core/scoring/Energies.hh>#include <core/types.hh>#include <core/chemical/AA.hh>#include <core/chemical/AtomICoor.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/chemical/VariantType.hh>#include <core/chemical/util.hh>#include <core/chemical/ChemicalManager.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <protocols/viewer/viewers.hh>#include <core/kinematics/FoldTree.hh>#include <core/id/AtomID_Map.hh>#include <core/id/AtomID_Map.Pose.hh>#include <core/id/AtomID.hh>#include <core/id/DOF_ID.hh>#include <core/kinematics/AtomTree.hh>#include <core/kinematics/Jump.hh>#include <core/kinematics/MoveMap.hh>#include <protocols/moves/Mover.hh>#include <protocols/moves/Mover.fwd.hh>#include <protocols/rigid/RigidBodyMover.hh>#include <protocols/stepwise/StepWiseLegacyClusterer.hh>#include <protocols/stepwise/StepWiseProteinPoseSetup.hh>#include <protocols/stepwise/StepWisePoseSampleGenerator.hh>#include <protocols/stepwise/StepWiseDoNothingSampleGenerator.hh>#include <protocols/stepwise/InputStreamWithResidueInfo.hh>#include <protocols/stepwise/protein/StepWiseProteinMainChainSampleGenerator.hh>#include <protocols/stepwise/protein/StepWiseProteinPoseSetup.hh>#include <protocols/stepwise/protein/StepWiseProteinScreener.hh>#include <protocols/stepwise/protein/util.hh>#include <protocols/stepwise/protein/StepWiseProteinConnectionSampler.hh>#include <protocols/stepwise/protein/StepWiseProteinPacker.hh>#include <protocols/stepwise/protein/MainChainTorsionSet.hh>#include <protocols/cluster/cluster.hh>#include <protocols/minimization_packing/GreenPacker.hh>#include <protocols/minimization_packing/GreenPacker.fwd.hh>#include <core/io/silent/ProteinSilentStruct.hh>#include <core/io/silent/BinarySilentStruct.hh>#include <core/io/silent/SilentFileData.hh>#include <core/pack/pack_rotamers.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/task/operation/TaskOperations.hh>#include <core/pack/optimizeH.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <core/options/option.hh>#include <core/options/after_opts.hh>#include <core/options/util.hh>#include <core/options/option_macros.hh>#include <core/pose/Pose.hh>#include <core/pose/util.hh>#include <core/pose/PDBInfo.hh>#include <core/pose/datacache/CacheableDataType.hh>#include <core/pose/Pose.fwd.hh>#include <core/io/pose_stream/PoseInputStream.hh>#include <core/io/pose_stream/PoseInputStream.fwd.hh>#include <core/io/pose_stream/PDBPoseInputStream.hh>#include <core/io/pose_stream/SilentFilePoseInputStream.hh>#include <core/util/basic.hh>#include <core/io/database/open.hh>#include <utility/tools/make_vector1.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <utility/vector1.hh>#include <utility/io/ozstream.hh>#include <numeric/xyzVector.hh>#include <numeric/conversions.hh>#include <numeric/random/random.hh>#include <numeric/xyz.functions.hh>#include <numeric/angle.functions.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <ObjexxFCL/FArray1D.hh>#include <protocols/jobdist/JobDistributors.hh>#include <protocols/jobdist/Jobs.hh>#include <protocols/jobdist/standard_mains.hh>#include <fstream>#include <iostream>#include <string>#include <deque>#include <vector>#include <core/util/Tracer.hh>#include <core/options/keys/out.OptionKeys.gen.hh>#include <core/options/keys/in.OptionKeys.gen.hh>#include <core/options/keys/score.OptionKeys.gen.hh>#include <core/options/keys/cluster.OptionKeys.gen.hh>Typedefs | |
| typedef numeric::xyzMatrix< Real > | Matrix |
Functions | |
| Real | sidechain_sample (pose::Pose &pose, utility::vector1< Real > const &temperatures, utility::vector1< Real > &deltaG_diff_tot, Real &min_delta_score_tot, bool ignore_current_sidechain) |
| void | output_stuff (Real const start_score, Real const min_delta_score_tot, utility::vector1< Real > const &temperatures, utility::vector1< Real > const &deltaG_diff_tot, std::ostream &out) |
| void | entropy_calculate_test () |
| void | each_aa_test () |
| void | output_connect (std::ostream &out, Size const &count_child, Real const &best_rmsd, Size const &count_parent, Real const build_direction) |
| void | setup_atom_id_map (std::map< id::AtomID, id::AtomID > &atom_id_map, pose::Pose const &pose_child, pose::Pose const &pose_parent, int const build_direction) |
| void | find_close_parents (pose::Pose const &pose_child, Size const count_child, utility::vector1< pose::PoseOP > &pose_parent_list, int const build_direction, std::ostream &out, Size &total_connect, Real &best_rmsd, Size &best_count, int &best_parent) |
| void | fill_pose_list (utility::vector1< pose::PoseOP > &pose_list, core::io::pose_stream::PoseInputStreamOP input_parent, core::chemical::ResidueTypeSetCAP rsd_set) |
| void | connectivity_test () |
| Vector | get_xyz (pose::Pose const &pose, Size const i) |
| void | output_distance_matrix (pose::Pose const &pose, std::ostream &out) |
| void | dist_matrix_test () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
| typedef numeric::xyzMatrix< Real > Matrix |
| void connectivity_test | ( | ) |
References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, fill_pose_list(), find_close_parents(), out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, output_connect(), beta_nonlocal::pose, basic::options::OptionKeys::in::file::silent, in::file::silent(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by my_main().
| void dist_matrix_test | ( | ) |
References basic::options::OptionKeys::chemical::chemical, gaussian-sampling::input, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, output_distance_matrix(), beta_nonlocal::pose, basic::options::OptionKeys::in::file::silent, and in::file::silent().
Referenced by my_main().
| void each_aa_test | ( | ) |
References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::full_model::cutpoint_closed, create_a3b_hbs::i, create_a3b_hbs::j, numeric::log(), utility::tools::make_vector1(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, erraser_single_res_analysis::out, lactamize::outfile, output_stuff(), beta_nonlocal::pose, basic::options::OptionKeys::stepwise::protein::protein, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, sidechain_sample(), and basic::options::OptionKeys::in::file::silent.
Referenced by my_main().
| void entropy_calculate_test | ( | ) |
References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_a3b_hbs::i, gaussian-sampling::input, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, output_stuff(), beta_nonlocal::pose, in::file::s(), sidechain_sample(), basic::options::OptionKeys::in::file::silent, in::file::silent(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by my_main().
| void fill_pose_list | ( | utility::vector1< pose::PoseOP > & | pose_list, |
| core::io::pose_stream::PoseInputStreamOP | input_parent, | ||
| core::chemical::ResidueTypeSetCAP | rsd_set | ||
| ) |
References beta_nonlocal::pose.
Referenced by connectivity_test().
| void find_close_parents | ( | pose::Pose const & | pose_child, |
| Size const | count_child, | ||
| utility::vector1< pose::PoseOP > & | pose_parent_list, | ||
| int const | build_direction, | ||
| std::ostream & | out, | ||
| Size & | total_connect, | ||
| Real & | best_rmsd, | ||
| Size & | best_count, | ||
| int & | best_parent | ||
| ) |
References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, output_connect(), beta_nonlocal::pose, basic::options::OptionKeys::cluster::radius, average_rmsds::rmsd, basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, basic::options::OptionKeys::frags::scoring::scoring, setup_atom_id_map(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by connectivity_test().
| Vector get_xyz | ( | pose::Pose const & | pose, |
| Size const | i | ||
| ) |
References create_a3b_hbs::i, and beta_nonlocal::pose.
Referenced by output_distance_matrix().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), my_main(), NEW_OPT, and viewer_main().
| void* my_main | ( | void * | ) |
References connectivity_test(), dist_matrix_test(), each_aa_test(), entropy_calculate_test(), utility::options::OptionKeys::options::exit, and option.
Referenced by main().
| void output_connect | ( | std::ostream & | out, |
| Size const & | count_child, | ||
| Real const & | best_rmsd, | ||
| Size const & | count_parent, | ||
| Real const | build_direction | ||
| ) |
Referenced by connectivity_test(), and find_close_parents().
| void output_distance_matrix | ( | pose::Pose const & | pose, |
| std::ostream & | out | ||
| ) |
References get_xyz(), create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, and beta_nonlocal::pose.
Referenced by dist_matrix_test().
| void output_stuff | ( | Real const | start_score, |
| Real const | min_delta_score_tot, | ||
| utility::vector1< Real > const & | temperatures, | ||
| utility::vector1< Real > const & | deltaG_diff_tot, | ||
| std::ostream & | out | ||
| ) |
References create_a3b_hbs::i.
Referenced by each_aa_test(), and entropy_calculate_test().
| void setup_atom_id_map | ( | std::map< id::AtomID, id::AtomID > & | atom_id_map, |
| pose::Pose const & | pose_child, | ||
| pose::Pose const & | pose_parent, | ||
| int const | build_direction | ||
| ) |
| Real sidechain_sample | ( | pose::Pose & | pose, |
| utility::vector1< Real > const & | temperatures, | ||
| utility::vector1< Real > & | deltaG_diff_tot, | ||
| Real & | min_delta_score_tot, | ||
| bool | ignore_current_sidechain | ||
| ) |
References basic::options::OptionKeys::chemical::chemical, create_a3b_hbs::i, numeric::log(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, numeric::principal_angle_degrees(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, and local::temperature.
Referenced by each_aa_test(), and entropy_calculate_test().
1.9.1