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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/Energies.hh>#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/chemical/VariantType.hh>#include <core/chemical/util.hh>#include <core/chemical/ChemicalManager.hh>#include <core/sequence/util.hh>#include <core/sequence/Sequence.hh>#include <core/sequence/Sequence.fwd.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/Ramachandran.hh>#include <protocols/rna/denovo/util.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 <protocols/stepwise/StepWiseLegacyClusterer.hh>#include <protocols/loops/Loop.hh>#include <protocols/loops/ccd_closure.hh>#include <protocols/loops/CCDLoopClosureMover.hh>#include <numeric/kinematic_closure/bridgeObjects.hh>#include <numeric/kinematic_closure/kinematic_closure_helpers.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/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 <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 | |
| void | extend_loop (pose::Pose &pose, utility::vector1< Size > const &loop_residues) |
| void | read_native_pose (pose::PoseOP &native_pose, core::chemical::ResidueTypeSetCAP &rsd_set) |
| void | setup_pose_with_loop (pose::Pose &pose, utility::vector1< Size > const &loop_residues, protocols::loops::Loop &loop) |
| void | ccd_loop_close (pose::Pose &pose, utility::vector1< Size > const &loop_residues, protocols::loops::Loop const &loop) |
| void | output_chainTORS (utility::vector1< core::Real > const &dt_ang, utility::vector1< core::Real > const &db_ang, utility::vector1< core::Real > const &db_len) |
| void | fill_chainTORS_info (pose::Pose const &pose, utility::vector1< utility::vector1< Real > > &atoms, utility::vector1< Real > &dt_ang, utility::vector1< Real > &db_ang, utility::vector1< Real > &db_len, Size const &start_res_, Size const &end_res_, bool const verbose=true) |
| void | KIC_loop_close (pose::Pose &pose, protocols::loops::Loop const &loop, utility::vector1< pose::PoseOP > &pose_list, bool const verbose=false) |
| void | loop_closure_test () |
| void | output_to_silent (Size const count, pose::Pose const &pose, Size const nsol, Size const &sample_residue, utility::vector1< Size > const &loop_residues, pose::PoseOP &native_pose, core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file_out) |
| void | modeler_closure_test () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
| typedef numeric::xyzMatrix< Real > Matrix |
| void ccd_loop_close | ( | pose::Pose & | pose, |
| utility::vector1< Size > const & | loop_residues, | ||
| protocols::loops::Loop const & | loop | ||
| ) |
| void extend_loop | ( | pose::Pose & | pose, |
| utility::vector1< Size > const & | loop_residues | ||
| ) |
References create_a3b_hbs::i, basic::options::OptionKeys::recces::thermal_sampling::loop_residues, make_symmdef_file_denovo::pos, and beta_nonlocal::pose.
Referenced by loop_closure_test(), main(), and modeler_closure_test().
| void fill_chainTORS_info | ( | pose::Pose const & | pose, |
| utility::vector1< utility::vector1< Real > > & | atoms, | ||
| utility::vector1< Real > & | dt_ang, | ||
| utility::vector1< Real > & | db_ang, | ||
| utility::vector1< Real > & | db_len, | ||
| Size const & | start_res_, | ||
| Size const & | end_res_, | ||
| bool const | verbose = true |
||
| ) |
| void KIC_loop_close | ( | pose::Pose & | pose, |
| protocols::loops::Loop const & | loop, | ||
| utility::vector1< pose::PoseOP > & | pose_list, | ||
| bool const | verbose = false |
||
| ) |
References atoms, numeric::kinematic_closure::bridgeObjects(), utility::io::oc::cout, fill_chainTORS_info(), create_a3b_hbs::i, internal_coordinates::loop, loops_kic::middle_offset, basic::options::OptionKeys::AnchoredDesign::filters::omega, output_chainTORS(), oop_conformations::phi, run_backbone::pivots, beta_nonlocal::pose, oop_conformations::psi, res, predPRE::resnum, ObjexxFCL::string_of(), and basic::options::OptionKeys::sc::verbose.
Referenced by loop_closure_test(), and modeler_closure_test().
| void loop_closure_test | ( | ) |
References ccd_loop_close(), basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, extend_loop(), KIC_loop_close(), internal_coordinates::loop, basic::options::OptionKeys::recces::thermal_sampling::loop_residues, docking::native_pose, basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, read_native_pose(), in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, setup_pose_with_loop(), and basic::options::OptionKeys::in::file::silent.
Referenced by my_main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, basic::options::OptionKeys::cluster::auto_tune, centroid_stats::bin_width(), basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), basic::options::OptionKeys::stepwise::input_res1, basic::options::OptionKeys::stepwise::input_res2, my_main(), NEW_OPT, basic::options::OptionKeys::score::pack_weights, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::cluster::score_diff_cut, basic::options::OptionKeys::stepwise::silent1, basic::options::OptionKeys::stepwise::silent2, basic::options::OptionKeys::stepwise::slice_res1, basic::options::OptionKeys::stepwise::slice_res2, basic::options::OptionKeys::stepwise::tags1, basic::options::OptionKeys::stepwise::tags2, and viewer_main().
| void modeler_closure_test | ( | ) |
References a3b_test::bin_size, centroid_stats::bin_width(), basic::options::OptionKeys::full_model::calc_rms_res, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, basic::options::OptionKeys::constraints::constraints, count, utility::io::oc::cout, extend_loop(), create_a3b_hbs::i, create_a3b_hbs::j, KIC_loop_close(), internal_coordinates::loop, basic::options::OptionKeys::recces::thermal_sampling::loop_residues, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::native_pose, out::nstruct(), basic::options::OptionKeys::optimization::optimization, option, output_to_silent(), oop_conformations::phi, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::psi, basic::options::OptionKeys::cluster::radius, read_native_pose(), in::file::s(), basic::options::OptionKeys::full_model::sample_res, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_pose_with_loop(), basic::options::OptionKeys::in::file::silent, out::file::silent(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by my_main().
| void* my_main | ( | void * | ) |
References utility::options::OptionKeys::options::exit, loop_closure_test(), modeler_closure_test(), and option.
Referenced by main().
| void output_chainTORS | ( | utility::vector1< core::Real > const & | dt_ang, |
| utility::vector1< core::Real > const & | db_ang, | ||
| utility::vector1< core::Real > const & | db_len | ||
| ) |
References utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, and create_a3b_hbs::j.
Referenced by fill_chainTORS_info(), and KIC_loop_close().
| void output_to_silent | ( | Size const | count, |
| pose::Pose const & | pose, | ||
| Size const | nsol, | ||
| Size const & | sample_residue, | ||
| utility::vector1< Size > const & | loop_residues, | ||
| pose::PoseOP & | native_pose, | ||
| core::io::silent::SilentFileData & | silent_file_data, | ||
| std::string const & | silent_file_out | ||
| ) |
References count, create_a3b_hbs::k, ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::recces::thermal_sampling::loop_residues, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, docking::native_pose, beta_nonlocal::pose, docking::s, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, ObjexxFCL::string_of(), and tag.
Referenced by modeler_closure_test().
| void read_native_pose | ( | pose::PoseOP & | native_pose, |
| core::chemical::ResidueTypeSetCAP & | rsd_set | ||
| ) |
References in::file::native(), docking::native_pose, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::inout::dbms::user.
Referenced by loop_closure_test(), and modeler_closure_test().
| void setup_pose_with_loop | ( | pose::Pose & | pose, |
| utility::vector1< Size > const & | loop_residues, | ||
| protocols::loops::Loop & | loop | ||
| ) |
References basic::options::OptionKeys::chemical::chemical, loops::cutpoint, create_a3b_hbs::f, create_a3b_hbs::i, internal_coordinates::loop, basic::options::OptionKeys::recces::thermal_sampling::loop_residues, option, beta_nonlocal::pose, and basic::options::OptionKeys::inout::dbms::user.
Referenced by loop_closure_test(), and modeler_closure_test().
1.9.1