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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/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/scoring/constraints/CoordinateConstraint.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/constraints/ConstraintIO.hh>#include <core/scoring/func/HarmonicFunc.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/modeler/util.hh>#include <protocols/stepwise/protein/util.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/datacache/CacheableDataType.hh>#include <core/pose/Pose.fwd.hh>#include <core/io/pose_stream/ExtendedPoseInputStream.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/datacache/BasicDataCache.hh>#include <core/util/datacache/CacheableString.hh>#include <core/util/basic.hh>#include <core/io/database/open.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 | |
| core::io::pose_stream::PoseInputStreamOP | setup_pose_input_stream (utility::vector1< std::string > const &option_s1, utility::vector1< std::string > const &option_silent1, utility::vector1< std::string > const &option_tags1) |
| void | parse_pathway_test () |
| void | stepwise_template_test () |
| void | cluster_outfile_test () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
| typedef numeric::xyzMatrix< Real > Matrix |
| void cluster_outfile_test | ( | ) |
References basic::options::OptionKeys::cluster::auto_tune, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, out::nstruct(), option, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::cluster::score_diff_cut, in::file::silent(), out::file::silent(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by my_main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References basic::options::OptionKeys::stepwise::align_pdb, argv, basic::options::OptionKeys::cluster::auto_tune, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, cluster_test(), 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::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* my_main | ( | void * | ) |
References cluster_outfile_test(), cluster_test(), utility::options::OptionKeys::options::exit, option, parse_pathway_test(), and stepwise_template_test().
Referenced by main().
| void parse_pathway_test | ( | ) |
References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, basic::options::OptionKeys::optimization::optimization, option, options, pdbslice(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, out::file::silent(), ObjexxFCL::string_of(), tag, and basic::options::OptionKeys::inout::dbms::user.
Referenced by my_main().
| core::io::pose_stream::PoseInputStreamOP setup_pose_input_stream | ( | utility::vector1< std::string > const & | option_s1, |
| utility::vector1< std::string > const & | option_silent1, | ||
| utility::vector1< std::string > const & | option_tags1 | ||
| ) |
Referenced by stepwise_template_test().
| void stepwise_template_test | ( | ) |
References basic::options::OptionKeys::stepwise::align_pdb, align_pose(), basic::options::OptionKeys::chemical::chemical, constraint_set_slice(), basic::options::OptionKeys::constraints::constraints, count, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, in::file::fasta(), create_a3b_hbs::i, basic::options::OptionKeys::stepwise::input_res1, basic::options::OptionKeys::stepwise::input_res2, ObjexxFCL::lead_zero_string_of(), beta_nonlocal::mm, in::file::native(), docking::native_pose, basic::options::OptionKeys::optimization::optimization, option, options, basic::options::OptionKeys::score::pack_weights, pdbslice(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::stepwise::protein::protein, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::frags::scoring::scoring, setup_pose_input_stream(), basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::OptionKeys::stepwise::silent1, basic::options::OptionKeys::stepwise::silent2, basic::options::OptionKeys::stepwise::slice_res1, basic::options::OptionKeys::stepwise::slice_res2, superimpose_pose(), basic::options::OptionKeys::stepwise::tags1, basic::options::OptionKeys::stepwise::tags2, vancomycin::task, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::full_model::working_res.
Referenced by my_main().
1.9.1