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Rosetta
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Rosetta
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#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetupFromCommandLine.hh>#include <protocols/stepwise/modeler/StepWiseModeler.hh>#include <core/types.hh>#include <core/chemical/AA.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/util.hh>#include <core/chemical/ChemicalManager.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/ResidueMatcher.hh>#include <core/conformation/Conformation.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>#include <core/chemical/rna/util.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/EnergyGraph.hh>#include <core/scoring/Energies.hh>#include <core/scoring/EnergyMap.hh>#include <core/scoring/EnergyMap.fwd.hh>#include <core/scoring/rms_util.hh>#include <core/scoring/func/CharmmPeriodicFunc.hh>#include <core/scoring/constraints/DihedralConstraint.hh>#include <core/sequence/util.hh>#include <core/sequence/Sequence.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/tree/Atom.hh>#include <core/kinematics/MoveMap.hh>#include <core/id/AtomID_Map.hh>#include <core/id/AtomID.hh>#include <core/id/DOF_ID.hh>#include <core/init/init.hh>#include <utility/file/file_sys_util.hh>#include <basic/options/option.hh>#include <basic/options/keys/chemical.OptionKeys.gen.hh>#include <basic/options/keys/cluster.OptionKeys.gen.hh>#include <basic/options/keys/stepwise.OptionKeys.gen.hh>#include <basic/options/keys/rna.OptionKeys.gen.hh>#include <basic/options/keys/score.OptionKeys.gen.hh>#include <basic/options/keys/edensity.OptionKeys.gen.hh>#include <basic/options/keys/full_model.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/OptionKeys.hh>#include <basic/options/option_macros.hh>#include <basic/Tracer.hh>#include <protocols/idealize/idealize.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <core/pose/Pose.hh>#include <core/pose/PDBInfo.hh>#include <utility/vector1.hh>#include <utility/io/ozstream.hh>#include <utility/io/izstream.hh>#include <utility/excn/Exceptions.hh>#include <numeric/xyzVector.hh>#include <numeric/conversions.hh>#include <core/pose/MiniPose.hh>#include <core/pose/util.hh>#include <core/pose/copydofs/util.hh>#include <core/pose/rna/util.hh>#include <core/io/pdb/pose_io.hh>#include <core/io/silent/SilentStruct.hh>#include <core/io/silent/SilentFileData.hh>#include <core/io/silent/util.hh>#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>#include <core/import_pose/import_pose.hh>#include <protocols/viewer/viewers.hh>#include <protocols/farna/util.hh>#include <protocols/farna/movers/RNA_LoopCloser.hh>#include <protocols/stepwise/modeler/rna/StepWiseRNA_OutputData.hh>#include <protocols/stepwise/modeler/rna/StepWiseRNA_CombineLongLoopFilterer.hh>#include <protocols/stepwise/modeler/rna/StepWiseRNA_CombineLongLoopFilterer.fwd.hh>#include <protocols/stepwise/modeler/rna/sugar/VirtualSugarSamplerFromStringList.hh>#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Minimizer.hh>#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetup.fwd.hh>#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetup.hh>#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.hh>#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.hh>#include <protocols/stepwise/modeler/rna/checker/RNA_VDW_BinChecker.hh>#include <protocols/stepwise/modeler/rna/checker/RNA_BaseCentroidChecker.hh>#include <protocols/stepwise/modeler/util.hh>#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>#include <protocols/stepwise/legacy/modeler/rna/util.hh>#include <ObjexxFCL/string.functions.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/FArray1D.hh>#include <ObjexxFCL/FArray2D.hh>#include <fstream>#include <iostream>#include <sstream>#include <string>#include <algorithm>#include <cctype>#include <iomanip>#include <map>#include <cstdlib>#include <ctime>#include <unistd.h>#include <libgen.h>#include <list>#include <stdio.h>#include <math.h>Go to the source code of this file.
Macros | |
| #define | GetCurrentDir getcwd |
Typedefs | |
| typedef numeric::xyzMatrix< Real > | Matrix |
Functions | |
| static THREAD_LOCAL basic::Tracer | TR ("swa_rna_main") |
| void | swa_rna_sample () |
| void | swa_rna_cluster () |
| void | rna_sample_virtual_sugar () |
| void | filter_combine_long_loop () |
| void | post_rebuild_bulge_assembly () |
| Oct 22, 2011. More... | |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
Definition in file swa_rna_main.cc.
| #define GetCurrentDir getcwd |
Definition at line 132 of file swa_rna_main.cc.
| typedef numeric::xyzMatrix< Real > Matrix |
Definition at line 151 of file swa_rna_main.cc.
| void filter_combine_long_loop | ( | ) |
Definition at line 481 of file swa_rna_main.cc.
References utility::io::oc::cout, utility::file::file_exists(), option, clean_pdb_keep_ligand::outfile, app.surface_docking.surface_docking::pose, runtime_assert, basic::options::silent, and utility::options::OptionKeys::options::user.
Referenced by my_main().
Definition at line 820 of file swa_rna_main.cc.
References utility::io::oc::cout, basic::init(), utility::excn::EXCN_Base::msg(), my_main(), NEW_OPT, option, and options.
| void* my_main | ( | void * | ) |
Definition at line 780 of file swa_rna_main.cc.
References utility::io::oc::cout, utility::options::OptionKeys::options::exit, filter_combine_long_loop(), option, options, post_rebuild_bulge_assembly(), rna_sample_virtual_sugar(), swa_rna_cluster(), swa_rna_sample(), and utility_exit_with_message.
Referenced by main().
| void post_rebuild_bulge_assembly | ( | ) |
Oct 22, 2011.
Definition at line 552 of file swa_rna_main.cc.
References ObjexxFCL::abs(), utility::io::oc::cout, create_scorefxn(), yaml::dump(), app.delta_score_per_mutation::mm, option, options, app.surface_docking.surface_docking::pose, runtime_assert, PyMOL_demo::scorefxn, basic::options::silent, amino_acids::size, app.surface_docking.surface_docking::start_pose, ObjexxFCL::string_of(), TR(), utility::options::OptionKeys::options::user, and utility_exit_with_message.
Referenced by my_main().
| void rna_sample_virtual_sugar | ( | ) |
Definition at line 424 of file swa_rna_main.cc.
References create_scorefxn(), option, app.surface_docking.surface_docking::pose, runtime_assert, PyMOL_demo::scorefxn, basic::options::silent, TR(), and utility::options::OptionKeys::options::user.
Referenced by my_main().
| void swa_rna_cluster | ( | ) |
Definition at line 276 of file swa_rna_main.cc.
References utility::io::oc::cout, yaml::dump(), utility::file::file_exists(), option, clean_pdb_keep_ligand::outfile, runtime_assert, basic::options::silent, ObjexxFCL::string_of(), TR(), utility::options::OptionKeys::options::user, and utility_exit_with_message.
Referenced by my_main().
| void swa_rna_sample | ( | ) |
Definition at line 195 of file swa_rna_main.cc.
References basic::Tracer::Blue, create_scorefxn(), ContactMap::native, test.Workshop7test::native_pose, local::nstruct, option, app.surface_docking.surface_docking::pose, basic::Tracer::Reset, PyMOL_demo::scorefxn, basic::options::silent, app.surface_docking.surface_docking::start_pose, TR(), and utility::options::OptionKeys::options::user.
Referenced by my_main().
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static |
Referenced by post_rebuild_bulge_assembly(), rna_sample_virtual_sugar(), swa_rna_cluster(), and swa_rna_sample().
1.8.7