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Rosetta
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Rosetta
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#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/chemical/AtomType.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueMatcher.hh>#include <core/conformation/ResidueFactory.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.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 <core/io/pdb/pose_io.hh>#include <core/pose/util.hh>#include <core/pose/util.tmpl.hh>#include <core/pose/annotated_sequence.hh>#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>#include <core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh>#include <core/import_pose/import_pose.hh>#include <basic/options/option.hh>#include <basic/options/keys/chemical.OptionKeys.gen.hh>#include <basic/options/keys/score.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 <core/pose/Pose.hh>#include <core/pose/PDBInfo.hh>#include <core/pose/rna/util.hh>#include <core/chemical/rna/RNA_FittedTorsionInfo.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/constraints/util.hh>#include <core/scoring/rms_util.tmpl.hh>#include <core/pack/pack_rotamers.hh>#include <core/pack/rotamer_trials.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <utility/vector1.hh>#include <utility/io/ozstream.hh>#include <utility/io/izstream.hh>#include <utility/file/file_sys_util.hh>#include <utility/excn/Exceptions.hh>#include <numeric/xyzVector.hh>#include <numeric/conversions.hh>#include <protocols/viewer/viewers.hh>#include <protocols/farna/movers/RNA_Minimizer.hh>#include <protocols/farna/options/RNA_MinimizerOptions.hh>#include <protocols/farna/util.hh>#include <protocols/stepwise/modeler/output_util.hh>#include <protocols/stepwise/modeler/rna/util.hh>#include <protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh>#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>#include <protocols/stepwise/legacy/modeler/rna/util.hh>#include <protocols/farna/movers/RNA_LoopCloser.hh>#include <protocols/farna/movers/RNA_LoopCloser.fwd.hh>#include <core/pose/rna/RNA_BaseDoubletClasses.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <core/io/silent/BinarySilentStruct.hh>#include <fstream>#include <iostream>#include <sstream>#include <string>#include <algorithm>#include <cctype>#include <iomanip>#include <map>#include <cstdlib>#include <ctime>#include <list>#include <stdio.h>#include <math.h>Go to the source code of this file.
Typedefs | |
| typedef numeric::xyzMatrix< Real > | Matrix |
Functions | |
| static THREAD_LOCAL basic::Tracer | TR ("swa_rna_util") |
| core::scoring::ScoreFunctionOP | create_scorefxn () |
| void | align_pose_general (core::pose::Pose const &static_pose, std::string const &static_tag, core::pose::Pose &moving_pose, std::string const &moving_tag, utility::vector1< std::pair< Size, Size > > const &alignment_res_pair_list, bool const base_only) |
| Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh. More... | |
| core::Real | check_alignment_RMSD_cutoff (core::pose::Pose const &static_pose, std::string const &static_tag, core::pose::Pose &moving_pose, std::string const &moving_tag, utility::vector1< std::pair< Size, Size > > const &alignment_res_pair_list, bool const base_only, core::Real const alignment_RMSD_cutoff) |
| Real | full_length_rmsd_over_reside_list_general (pose::Pose const &pose_one, pose::Pose const &pose_two, utility::vector1< std::pair< Size, Size > > const &rmsd_res_pair_list, bool const verbose, bool const ignore_virtual_atom) |
| Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh. More... | |
| void | align_pdbs () |
| void | calculate_pairwise_RMSD () |
| void | import_and_dump_pdb () |
| void | o2prime_packer () |
| void | mutate_residue (pose::Pose &pose, Size const seq_num, std::string const &res_name) |
| void | mutate_residues_wrapper () |
| void | slice_ellipsoid_envelope () |
| void | slice_sample_res_and_surrounding () |
| void | pdb_to_silent_file () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
| typedef numeric::xyzMatrix< Real > Matrix |
Definition at line 134 of file swa_rna_util.cc.
| void align_pdbs | ( | ) |
Definition at line 450 of file swa_rna_util.cc.
References align_pose_general(), check_alignment_RMSD_cutoff(), utility::io::oc::cout, test.T200_Scoring::ii, ContactMap::native, option, app.surface_docking.surface_docking::pose, app.pyrosetta_toolkit.modules.SQLPDB::s, basic::options::silent, TR(), utility::options::OptionKeys::options::user, and utility_exit_with_message.
Referenced by my_main().
| void align_pose_general | ( | core::pose::Pose const & | static_pose, |
| std::string const & | static_tag, | ||
| core::pose::Pose & | moving_pose, | ||
| std::string const & | moving_tag, | ||
| utility::vector1< std::pair< Size, Size > > const & | alignment_res_pair_list, | ||
| bool const | base_only | ||
| ) |
Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh.
Definition at line 202 of file swa_rna_util.cc.
References utility::io::oc::cout, TR(), and utility_exit_with_message.
Referenced by align_pdbs(), and calculate_pairwise_RMSD().
| void calculate_pairwise_RMSD | ( | ) |
Definition at line 571 of file swa_rna_util.cc.
References align_pose_general(), check_alignment_RMSD_cutoff(), utility::io::oc::cout, yaml::dump(), full_length_rmsd_over_reside_list_general(), test.T200_Scoring::ii, ContactMap::native, test.Workshop7test::native_pose, option, app.surface_docking.surface_docking::pose, app.pyrosetta_toolkit.modules.SQLPDB::s, basic::options::silent, ObjexxFCL::string_of(), TR(), utility::options::OptionKeys::options::user, and utility_exit_with_message.
Referenced by my_main().
| core::Real check_alignment_RMSD_cutoff | ( | core::pose::Pose const & | static_pose, |
| std::string const & | static_tag, | ||
| core::pose::Pose & | moving_pose, | ||
| std::string const & | moving_tag, | ||
| utility::vector1< std::pair< Size, Size > > const & | alignment_res_pair_list, | ||
| bool const | base_only, | ||
| core::Real const | alignment_RMSD_cutoff | ||
| ) |
Definition at line 269 of file swa_rna_util.cc.
References utility::io::oc::cout, app.pyrosetta_toolkit.modules.tools.analysis::rmsd(), and utility_exit_with_message.
Referenced by align_pdbs(), and calculate_pairwise_RMSD().
| core::scoring::ScoreFunctionOP create_scorefxn | ( | ) |
Definition at line 163 of file swa_rna_util.cc.
References utility::io::oc::cout, option, PyMOL_demo::scorefxn, utility::options::OptionKeys::options::user, utility_exit_with_message, and test.T200_Scoring::weights.
Referenced by o2prime_packer(), post_rebuild_bulge_assembly(), rna_sample_virtual_sugar(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), and swa_rna_sample().
| Real full_length_rmsd_over_reside_list_general | ( | pose::Pose const & | pose_one, |
| pose::Pose const & | pose_two, | ||
| utility::vector1< std::pair< Size, Size > > const & | rmsd_res_pair_list, | ||
| bool const | verbose, | ||
| bool const | ignore_virtual_atom | ||
| ) |
Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh.
Definition at line 318 of file swa_rna_util.cc.
References utility::io::oc::cout, max(), app.pyrosetta_toolkit.modules.tools.analysis::rmsd(), ObjexxFCL::string_of(), TR(), and utility_exit_with_message.
Referenced by calculate_pairwise_RMSD().
| void import_and_dump_pdb | ( | ) |
Definition at line 694 of file swa_rna_util.cc.
References utility::file::file_exists(), option, app.surface_docking.surface_docking::pose, app.pyrosetta_toolkit.modules.SQLPDB::s, utility::options::OptionKeys::options::user, and utility_exit_with_message.
Referenced by my_main().
Definition at line 1453 of file swa_rna_util.cc.
References utility::io::oc::cout, yaml::dump(), basic::init(), utility::excn::EXCN_Base::msg(), my_main(), and NEW_OPT.
| void mutate_residue | ( | pose::Pose & | pose, |
| Size const | seq_num, | ||
| std::string const & | res_name | ||
| ) |
Definition at line 789 of file swa_rna_util.cc.
References utility::io::oc::cout, app.surface_docking.surface_docking::pose, and app.surface_docking.surface_docking::start_pose.
Referenced by mutate_residues_wrapper().
| void mutate_residues_wrapper | ( | ) |
Definition at line 822 of file swa_rna_util.cc.
References app.surface_docking.surface_docking::constraints, utility::io::oc::cout, mutate_residue(), name, option, app.surface_docking.surface_docking::pose, app.pyrosetta_toolkit.modules.SQLPDB::s, and basic::options::silent.
Referenced by my_main().
| void* my_main | ( | void * | ) |
Definition at line 1413 of file swa_rna_util.cc.
References align_pdbs(), calculate_pairwise_RMSD(), utility::io::oc::cout, utility::options::OptionKeys::options::exit, import_and_dump_pdb(), mutate_residues_wrapper(), o2prime_packer(), option, pdb_to_silent_file(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), and utility_exit_with_message.
Referenced by main().
| void o2prime_packer | ( | ) |
Definition at line 728 of file swa_rna_util.cc.
References utility::io::oc::cout, create_scorefxn(), option, app.surface_docking.surface_docking::pose, app.pyrosetta_toolkit.modules.SQLPDB::s, and PyMOL_demo::scorefxn.
Referenced by my_main().
| void pdb_to_silent_file | ( | ) |
Definition at line 1307 of file swa_rna_util.cc.
References utility::io::oc::cout, test.T200_Scoring::ii, option, app.surface_docking.surface_docking::pose, app.pyrosetta_toolkit.modules.SQLPDB::s, basic::options::silent, tag, utility::options::OptionKeys::options::user, and utility_exit_with_message.
Referenced by my_main().
| void slice_ellipsoid_envelope | ( | ) |
Definition at line 863 of file swa_rna_util.cc.
References numeric::xyzMatrix< typename >::cols(), utility::io::oc::cout, create_scorefxn(), numeric::kinematic_closure::cross(), test.T200_Scoring::ii, numeric::inverse(), make_symmdef_file_denovo::length, numeric::xyzVector< typename >::normalize(), option, app.surface_docking.surface_docking::pose, numeric::rotation_matrix(), app.pyrosetta_toolkit.modules.SQLPDB::s, PyMOL_demo::scorefxn, basic::options::silent, ObjexxFCL::string_of(), app.surface_docking.surface_docking::time_start, TR(), utility::options::OptionKeys::options::user, utility_exit_with_message, numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().
Referenced by my_main().
| void slice_sample_res_and_surrounding | ( | ) |
Definition at line 1122 of file swa_rna_util.cc.
References utility::io::oc::cout, create_scorefxn(), test.T200_Scoring::ii, make_symmdef_file_denovo::length, option, app.surface_docking.surface_docking::pose, app.pyrosetta_toolkit.modules.SQLPDB::s, PyMOL_demo::scorefxn, basic::options::silent, ObjexxFCL::string_of(), app.surface_docking.surface_docking::time_start, TR(), utility::options::OptionKeys::options::user, and utility_exit_with_message.
Referenced by my_main().
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