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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/fragment/Frame.hh>#include <core/fragment/FrameList.hh>#include <core/fragment/FragSet.hh>#include <core/fragment/ConstantLengthFragSet.hh>#include <core/fragment/FragmentIO.hh>#include <core/fragment/util.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/StepWiseFilterer.hh>#include <protocols/stepwise/StepWiseLegacyClusterer.hh>#include <protocols/stepwise/StepWisePoseMinimizer.hh>#include <protocols/stepwise/StepWiseProteinPoseSetup.hh>#include <protocols/stepwise/modeler/util.hh>#include <protocols/stepwise/StepWiseResidueSampler.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/io/silent/SilentFileData.fwd.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/PoseInputStream.hh>#include <core/io/pose_stream/PoseInputStream.fwd.hh>#include <core/io/pose_stream/SilentFilePoseInputStream.hh>#include <core/io/pose_stream/PDBPoseInputStream.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 <ObjexxFCL/format/formatted.o.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>#include <core/options/keys/abinitio.OptionKeys.gen.hh>#include <core/options/keys/frags.OptionKeys.gen.hh>Typedefs | |
| typedef numeric::xyzMatrix< Real > | Matrix |
| typedef std::map< std::string, core::pose::PoseOP > | PoseList |
Functions | |
| void | output_centroid_silent_struct (core::pose::Pose const &pose, core::pose::PoseCOP const &native_pose_op, core::io::silent::SilentFileDataOP &sfd, std::string const &tag, std::string const &parent_tag, std::string const silent_file="") |
| Size | figure_out_nested_positions (std::string const &inside_sequence, std::string const &desired_sequence, Size const min_start_res=0) |
| void | slice_pdb (core::pose::Pose &pose, Size const &start_res, Size const &end_res) |
| void | slice_sequence (std::string &sequence, Size const &start_res, Size const &end_res) |
| core::scoring::constraints::ConstraintSetOP | constraint_set_slice (core::scoring::constraints::ConstraintSetOP &cst_set, Size const &min_res, Size const &max_res) |
| void | apply_all_frags (pose::Pose &pose, pose::PoseOP &native_pose, Size const &insert_pos, std::string const &parent_tag, Real const &score_cut, Real &score_min, Size &count, core::io::silent::SilentFileDataOP &sfd, core::fragment::ConstantLengthFragSetOP &fragset, core::scoring::ScoreFunctionOP &scorefxn) |
| Size | setup_pose (pose::Pose &pose, pose::Pose const &start_pose, std::string const &desired_sequence, Size const min_start_res=0) |
| void | rebuild_centroid_test () |
| void | cluster_outfile_test () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
| typedef numeric::xyzMatrix< Real > Matrix |
| typedef std::map< std::string, core::pose::PoseOP > PoseList |
| void apply_all_frags | ( | pose::Pose & | pose, |
| pose::PoseOP & | native_pose, | ||
| Size const & | insert_pos, | ||
| std::string const & | parent_tag, | ||
| Real const & | score_cut, | ||
| Real & | score_min, | ||
| Size & | count, | ||
| core::io::silent::SilentFileDataOP & | sfd, | ||
| core::fragment::ConstantLengthFragSetOP & | fragset, | ||
| core::scoring::ScoreFunctionOP & | scorefxn | ||
| ) |
References count, utility::io::oc::cout, test.Workshop4test::fragset, numeric::kinematic_closure::frame(), score_vs_rmsd::frames, docking::native_pose, output_centroid_silent_struct(), beta_nonlocal::pose, enumerate_junctions::q, create_a3b_hbs::score, basic::options::OptionKeys::magnesium::score_cut, sfd, ObjexxFCL::string_of(), and tag.
Referenced by rebuild_centroid_test().
| void cluster_outfile_test | ( | ) |
References 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().
| core::scoring::constraints::ConstraintSetOP constraint_set_slice | ( | core::scoring::constraints::ConstraintSetOP & | cst_set, |
| Size const & | min_res, | ||
| Size const & | max_res | ||
| ) |
References utility::options::BooleanOptionKey::clone(), basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, basic::options::OptionKeys::templates::cst::cst, create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::mh::harvest::max_res, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and basic::options::OptionKeys::frags::scoring::scoring.
Referenced by rebuild_centroid_test(), and stepwise_template_test().
| Size figure_out_nested_positions | ( | std::string const & | inside_sequence, |
| std::string const & | desired_sequence, | ||
| Size const | min_start_res = 0 |
||
| ) |
References create_a3b_hbs::i.
Referenced by setup_pose().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, basic::options::OptionKeys::stepwise::rna::centroid_screen, basic::options::OptionKeys::stepwise::protein::centroid_weights, 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::mh::harvest::max_res, my_main(), NEW_OPT, basic::options::OptionKeys::cluster::score_diff_cut, and viewer_main().
| void* my_main | ( | void * | ) |
References cluster_outfile_test(), cluster_test(), utility::options::OptionKeys::options::exit, option, and rebuild_centroid_test().
Referenced by main().
| void output_centroid_silent_struct | ( | core::pose::Pose const & | pose, |
| core::pose::PoseCOP const & | native_pose_op, | ||
| core::io::silent::SilentFileDataOP & | sfd, | ||
| std::string const & | tag, | ||
| std::string const & | parent_tag, | ||
| std::string const | silent_file = "" |
||
| ) |
References beta_nonlocal::pose, average_rmsds::rmsd, docking::s, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::in::file::silent, and tag.
Referenced by apply_all_frags().
| void rebuild_centroid_test | ( | ) |
References apply_all_frags(), basic::options::OptionKeys::stepwise::protein::centroid_weights, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, 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(), in::file::frag_files(), test.Workshop4test::fragset, basic::options::OptionKeys::mh::harvest::max_res, in::file::native(), docking::native_pose, out::nstruct(), option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::cluster::radius, in::file::s(), basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::magnesium::score_cut, basic::options::OptionKeys::cluster::score_diff_cut, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_pose(), sfd, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), slice_pdb(), slice_sequence(), tag_from_pose(), in::file::tags(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by my_main().
| Size setup_pose | ( | pose::Pose & | pose, |
| pose::Pose const & | start_pose, | ||
| std::string const & | desired_sequence, | ||
| Size const | min_start_res = 0 |
||
| ) |
References count, indel::end_res, figure_out_nested_positions(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, and indel::start_res.
Referenced by rebuild_centroid_test().
| void slice_pdb | ( | core::pose::Pose & | pose, |
| Size const & | start_res, | ||
| Size const & | end_res | ||
| ) |
References basic::options::OptionKeys::chemical::chemical, indel::end_res, create_a3b_hbs::i, beta_nonlocal::pose, and indel::start_res.
Referenced by rebuild_centroid_test().
References indel::end_res, basic::options::OptionKeys::relax::sequence, and indel::start_res.
Referenced by rebuild_centroid_test().
1.9.1