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Rosetta
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#include <basic/database/open.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>#include <basic/options/option.hh>#include <basic/options/option_macros.hh>#include <basic/options/util.hh>#include <basic/Tracer.hh>#include <core/chemical/AtomType.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/util.hh>#include <core/chemical/VariantType.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/symmetry/SymDof.hh>#include <core/conformation/symmetry/SymmData.hh>#include <core/conformation/symmetry/SymmetricConformation.hh>#include <core/conformation/symmetry/SymmetryInfo.hh>#include <core/conformation/symmetry/util.hh>#include <core/conformation/symmetry/VirtualCoordinate.hh>#include <devel/init.hh>#include <core/import_pose/import_pose.hh>#include <core/id/NamedAtomID.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/io/silent/ScoreFileSilentStruct.hh>#include <core/io/silent/SilentFileData.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/MoveMap.hh>#include <core/pack/dunbrack/DunbrackRotamer.fwd.hh>#include <core/pack/dunbrack/RotamerLibrary.hh>#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>#include <core/pack/optimizeH.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/make_symmetric_task.hh>#include <core/pose/annotated_sequence.hh>#include <core/pose/Pose.hh>#include <core/pose/util.hh>#include <core/pose/symmetry/util.hh>#include <core/scoring/constraints/AmbiguousConstraint.hh>#include <core/scoring/constraints/AngleConstraint.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/constraints/DihedralConstraint.hh>#include <core/scoring/func/HarmonicFunc.hh>#include <core/scoring/func/CircularHarmonicFunc.hh>#include <core/scoring/constraints/MultiConstraint.hh>#include <core/scoring/constraints/util.hh>#include <core/scoring/func/XYZ_Func.hh>#include <core/scoring/dssp/Dssp.hh>#include <core/scoring/electron_density/util.hh>#include <core/scoring/Energies.hh>#include <core/scoring/packing/compute_holes_score.hh>#include <core/scoring/packstat/compute_sasa.hh>#include <core/scoring/rms_util.hh>#include <core/scoring/sasa.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/symmetry/SymmetricScoreFunction.hh>#include <core/util/SwitchResidueTypeSet.hh>#include <numeric/model_quality/rms.hh>#include <numeric/random/random.hh>#include <numeric/xyz.functions.hh>#include <numeric/xyz.io.hh>#include <ObjexxFCL/FArray2D.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <protocols/simple_moves/FragmentMover.hh>#include <protocols/electron_density/util.hh>#include <protocols/flxbb/FlxbbDesign.hh>#include <protocols/relax/FastRelax.hh>#include <protocols/jobdist/standard_mains.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/Mover.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/RepeatMover.hh>#include <protocols/rigid/RigidBodyMover.hh>#include <protocols/symmetry/SetupForSymmetryMover.hh>#include <protocols/minimization_packing/symmetry/SymMinMover.hh>#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/symmetry/SymDockingInitialPerturbation.hh>#include <protocols/symmetric_docking/SymDockingLowRes.hh>#include <protocols/viewer/viewers.hh>#include <sstream>#include <utility/io/izstream.hh>#include <utility/io/ozstream.hh>#include <utility/stream_util.hh>#include <apps/pilot/will/will_util.ihh>#include <apps/pilot/will/mynamespaces.ihh>#include <apps/pilot/will/frag_util.hh>#include <core/pack/task/operation/TaskOperations.hh>#include <core/pack/task/operation/NoRepackDisulfides.hh>#include <protocols/simple_task_operations/RestrictToInterface.hh>#include <core/pack/pack_rotamers.hh>Classes | |
| struct | DCST |
| struct | CST |
| class | SymRBMover |
| struct | ConstraintConfig |
| struct | HubDenovo |
Macros | |
| #define | ERROR_UINT 123456789ul |
Typedefs | |
| typedef utility::vector1< core::Size > | Sizes |
| typedef utility::vector1< std::string > | Strings |
| typedef utility::vector1< CST > | CSTs |
Functions | |
| void | register_options () |
| string | peek (std::istream &in) |
| template<typename T > | |
| bool | read_ignore_comments (std::istream &in, T &s) |
| string | read_ignore_comments (std::istream &in) |
| Strings | getline (std::istream &in) |
| std::ostream & | operator<< (std::ostream &out, CST const &c) |
| void * | run (void *) |
| int | main (int argc, char *argv[]) |
Variables | |
| static core::io::silent::SilentFileData | sfd |
| static basic::Tracer | TR ("hubdenovo") |
| #define ERROR_UINT 123456789ul |
| typedef utility::vector1<CST> CSTs |
| typedef utility::vector1<core::Size> Sizes |
| typedef utility::vector1<std::string> Strings |
| Strings getline | ( | std::istream & | in | ) |
References cal_vdw_radius_pool::buf, test.T008_Serialization::iss, docking::s, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.
Referenced by add_constraints(), CrystCluster::apply(), blosum_score_alignment(), calculate_hydrophobic_accessible_surface_area(), compare_text_files(), compute_intrinsic_deviation(), correlation(), protocols::surface_docking::AntibodyInfoRMLoader::create_resource(), create_starting_template(), design_test(), utility::exit_handler(), utility::file_contents(), fillPoseAndDataList(), filter_frags(), generateRankedAlignments(), get_native_pdb_names(), SequenceProfileDB::get_next_profile(), get_pair_keys_from_list(), get_sc(), get_sequence_and_secstruct_from_dssp(), get_silent_file_tags(), utility::io::getline(), utility::io::icstream::getline(), utility::io::izstream::getline(), hermann_phase_two_minimize(), apps::pilot::frankdt::import_motifs(), initialize_sequence_mask(), is_nonempty_input_silent_file(), HBondReporter::load_job_data(), load_loops_from_file(), TNM::load_normal_modes(), utility::options::OptionCollection::load_option_from_file(), utility::options::OptionCollection::load_options_from_stream(), basic::resource_manager::locator::FileListResourceLocator::locate_resource_stream(), main(), apps::pilot::frankdt::main(), mg_pdbstats_test(), motif_scan(), ConstraintConfig::parse_config_file(), parsefilelist(), polar_pdbstats_test(), processChildren(), processChildrenIntensification(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), RBSegmentRelax_test(), binder::Config::read(), read_alignment_fasta_file(), read_B_vals(), read_complex_type(), read_covalent_connections_file(), CapriTotalEnergy::read_datafile(), read_distances(), read_embeddings(), read_equivalent_position_file(), read_ERMS(), read_FileVector(), read_fold_tree_from_file(), numeric::interpolation::Histogram< X, Y >::read_from_db(), read_in_cl_data(), myspace::read_input(), VallReader::read_lines(), read_list_file(), read_list_pose_range(), read_master_pose_range(), read_membrane(), read_NACCESS_asa_file(), read_parameters(), read_patchdock_entry(), read_penalties(), read_RDC_file(), read_soft_segment_file(), ReadCAsFromPDB(), readPDBcoords(), PickSSE::readSSE(), recover_clustered_frags(), rhiju_pdbstats(), rna_backbone_rebuild_test(), run_pep_prep(), RunPepSpec(), set_secstruct_from_psipred_ss2(), setup_activity_table(), setup_capri_data(), DomainAssemblerNDocker::setup_cen_domains(), setup_rna_base_pair_constraints(), setup_secstruct(), simple_opte_test(), numeric::interpolation::spline_from_file(), numeric::interpolation::spline_from_stream(), statistics(), tf_specificity_test(), tokenize_line(), write_cluster_frags(), and zf_test().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
| std::ostream& operator<< | ( | std::ostream & | out, |
| CST const & | c | ||
| ) |
| string peek | ( | std::istream & | in | ) |
References create_a3b_hbs::i, and create_a3b_hbs::r.
Referenced by ConstraintConfig::parse_config_file(), and read_ignore_comments().
| string read_ignore_comments | ( | std::istream & | in | ) |
References cal_vdw_radius_pool::buf, peek(), docking::s, and utility_exit_with_message.
| bool read_ignore_comments | ( | std::istream & | in, |
| T & | s | ||
| ) |
References cal_vdw_radius_pool::buf, peek(), and docking::s.
Referenced by ConstraintConfig::parse_config_file().
| void register_options | ( | ) |
References NEW_OPT, and basic::options::OptionKeys::hotspot::target.
Referenced by main().
| void* run | ( | void * | ) |
References hd(), and basic::options::option.
Referenced by main().
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static |
Referenced by HubDenovo::run().
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static |
1.9.1