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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/scoring/hbonds/HBondSet.hh>#include <core/scoring/hbonds/hbonds.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/conformation/ResidueFactory.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/util.hh>#include <core/chemical/ChemicalManager.hh>#include <core/conformation/Conformation.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/AtomTree.hh>#include <core/kinematics/Jump.hh>#include <core/kinematics/MoveMap.hh>#include <core/kinematics/RT.hh>#include <core/id/AtomID_Map.hh>#include <core/id/AtomID.hh>#include <core/id/NamedAtomID.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 <protocols/viewer/viewers.hh>#include <protocols/stepwise/modeler/StepWiseModeler.hh>#include <protocols/stepwise/modeler/options/StepWiseModelerOptions.hh>#include <protocols/stepwise/modeler/align/StepWiseLegacyClustererSilentBased.hh>#include <protocols/stepwise/legacy/modeler/protein/StepWiseProteinPoseSetup.hh>#include <protocols/stepwise/legacy/modeler/protein/util.hh>#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>#include <protocols/stepwise/modeler/protein/util.hh>#include <protocols/stepwise/modeler/protein/InputStreamWithResidueInfo.hh>#include <protocols/stepwise/modeler/file_util.hh>#include <protocols/stepwise/modeler/util.hh>#include <protocols/stepwise/modeler/rna/util.hh>#include <protocols/stepwise/sampler/NoOpStepWiseSampler.hh>#include <protocols/stepwise/sampler/protein/util.hh>#include <protocols/cluster/cluster.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 <basic/options/option.hh>#include <basic/options/after_opts.hh>#include <basic/options/util.hh>#include <basic/options/option_macros.hh>#include <core/pose/Pose.hh>#include <core/import_pose/import_pose.hh>#include <core/pose/util.hh>#include <core/pose/datacache/CacheableDataType.hh>#include <core/pose/Pose.fwd.hh>#include <core/import_pose/pose_stream/ExtendedPoseInputStream.hh>#include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>#include <basic/datacache/BasicDataCache.hh>#include <basic/datacache/CacheableString.hh>#include <basic/basic.hh>#include <basic/database/open.hh>#include <devel/init.hh>#include <core/io/pdb/pose_io.hh>#include <utility/vector1.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 <fstream>#include <iostream>#include <basic/Tracer.hh>#include <basic/options/keys/full_model.OptionKeys.gen.hh>#include <basic/options/keys/chemical.OptionKeys.gen.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/stepwise.OptionKeys.gen.hh>#include <basic/options/keys/score.OptionKeys.gen.hh>#include <basic/options/keys/cluster.OptionKeys.gen.hh>#include <basic/options/keys/edensity.OptionKeys.gen.hh>Go to the source code of this file.
Typedefs | |
| typedef numeric::xyzMatrix< Real > | Matrix |
Functions | |
| static THREAD_LOCAL basic::Tracer | TR ("swa_protein_main") |
| void | initialize_native_pose (core::pose::PoseOP &native_pose, core::chemical::ResidueTypeSetCAP &rsd_set) |
| void | rebuild_test () |
| void | cluster_outfile_test () |
| void | calc_rms_test () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
| typedef numeric::xyzMatrix< Real > Matrix |
Definition at line 142 of file swa_protein_main.cc.
| void calc_rms_test | ( | ) |
Definition at line 370 of file swa_protein_main.cc.
References app.surface_docking.surface_docking::input, ContactMap::native, test.Workshop7test::native_pose, option, options, app.surface_docking.surface_docking::pose, basic::options::silent, and utility::options::OptionKeys::options::user.
Referenced by my_main().
| void cluster_outfile_test | ( | ) |
Definition at line 327 of file swa_protein_main.cc.
References local::nstruct, option, options, basic::options::silent, and utility::options::OptionKeys::options::user.
Referenced by my_main().
| void initialize_native_pose | ( | core::pose::PoseOP & | native_pose, |
| core::chemical::ResidueTypeSetCAP & | rsd_set | ||
| ) |
Definition at line 298 of file swa_protein_main.cc.
References yaml::dump(), ContactMap::native, option, options, app.surface_docking.surface_docking::pose, utility::options::OptionKeys::options::user, and utility_exit_with_message.
Referenced by rebuild_test().
Definition at line 437 of file swa_protein_main.cc.
References numeric::model_quality::calc_rms(), cluster_test(), utility::io::oc::cout, test.G100_Functions_Input::cst_file, yaml::dump(), utility::options::OptionKeys::options::exit, devel::init(), loops_kic::min_type, utility::excn::EXCN_Base::msg(), my_main(), NEW_OPT, option, and options.
| void* my_main | ( | void * | ) |
Definition at line 411 of file swa_protein_main.cc.
References numeric::model_quality::calc_rms(), calc_rms_test(), cluster_outfile_test(), cluster_test(), utility::options::OptionKeys::options::exit, option, options, rebuild_test(), and utility_exit_with_message.
Referenced by main().
| void rebuild_test | ( | ) |
Definition at line 188 of file swa_protein_main.cc.
References app.surface_docking.surface_docking::constraints, test.G100_Functions_Input::cst_file, yaml::dump(), initialize_native_pose(), test.Workshop7test::native_pose, option, options, loops::pack, app.surface_docking.surface_docking::pose, runtime_assert, PyMOL_demo::scorefxn, basic::options::silent, utility::options::OptionKeys::options::user, and test.T200_Scoring::weights.
Referenced by my_main().
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static |
1.8.7