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Rosetta
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test centroid rot model More...
#include <core/chemical/AA.hh>#include <core/chemical/Atom.hh>#include <core/chemical/ResidueType.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ChemicalManager.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/util.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/io/silent/SilentFileData.hh>#include <core/io/silent/SilentStructFactory.hh>#include <core/types.hh>#include <core/id/AtomID.hh>#include <core/id/DOF_ID.hh>#include <core/kinematics/MoveMap.hh>#include <core/pose/PDBInfo.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/Energies.hh>#include <core/scoring/rms_util.hh>#include <core/scoring/TenANeighborGraph.hh>#include <core/pack/dunbrack/RotamerLibrary.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/task/operation/TaskOperations.hh>#include <core/pose/Pose.hh>#include <core/pose/util.hh>#include <core/import_pose/import_pose.hh>#include <core/pack/dunbrack/cenrot/SingleResidueCenrotLibrary.hh>#include <basic/options/option.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/score.OptionKeys.gen.hh>#include <basic/options/option_macros.hh>#include <basic/Tracer.hh>#include <numeric/random/random.hh>#include <numeric/constants.hh>#include <utility/vector1.hh>#include <utility/fixedsizearray1.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/CartesianMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <core/optimization/Minimizer.hh>#include <protocols/minimization_packing/MinMover.hh>#include <core/scoring/dssp/Dssp.hh>#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>#include <protocols/minimization_packing/PackRotamersMover.hh>#include <protocols/viewer/viewers.hh>#include <protocols/moves/PyMOLMover.hh>#include <protocols/moves/Mover.fwd.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/moves/RepeatMover.hh>#include <protocols/simple_moves/BBGaussianMover.hh>#include <sstream>#include <iostream>#include <string>#include <fstream>#include <map>Functions | |
| void * | my_main (void *) |
| void | fit_centroid_to_the_best_rot (core::pose::Pose &pose, utility::vector1< Size > &rotlist) |
| void | process_the_pose (core::pose::PoseOP &native_pose, core::pose::Pose &p, std::string const &tag) |
| void | relax_cenrot_pose (core::pose::PoseOP &native_pose, core::pose::Pose &p, std::string const &tag) |
| void | rescore_pose (core::scoring::ScoreFunctionOP score_fxn, core::pose::PoseOP &native_pose, core::pose::Pose &p, std::string const &tag) |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("pilot.wendao.cenrot") |
| std::map< std::string, Real > | masslst |
| utility::vector1< core::Size > | nrecovery (20) |
| utility::vector1< core::Size > | n_total (20) |
test centroid rot model
| void fit_centroid_to_the_best_rot | ( | core::pose::Pose & | pose, |
| utility::vector1< Size > & | rotlist | ||
| ) |
References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, create_a3b_hbs::i, option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, PHI, THETA, and TR.
Referenced by process_the_pose().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, basic::init(), masslst, my_main(), NEW_OPT, and viewer_main().
| void* my_main | ( | void * | ) |
References aa, pyrosetta.io::create_score_function, end, basic::options::OptionKeys::optE::fixed, create_a3b_hbs::i, subloop_histogram::iterator, in::file::l(), n_total, in::file::native(), docking::native_pose, nrecovery, option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), process_the_pose(), relax_cenrot_pose(), rescore_pose(), beta_nonlocal::score_fxn, in::file::silent(), subloop_histogram::size, tag, docking::to_centroid, TR, and basic::options::OptionKeys::inout::dbms::user.
Referenced by main().
| void process_the_pose | ( | core::pose::PoseOP & | native_pose, |
| core::pose::Pose & | p, | ||
| std::string const & | tag | ||
| ) |
References pyrosetta.io::create_score_function, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, test.T009_Exceptions::e, fit_centroid_to_the_best_rot(), create_a3b_hbs::i, oop_conformations::length, beta_nonlocal::mm, n_total, docking::native_pose, nrecovery, option, test.G203_Module_SQLPDB::outdir, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, PHI, create_a3b_hbs::r, rescore_pose(), beta_nonlocal::score_fxn, tag, vancomycin::task, THETA, TR, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::remodel::vdw, and basic::options::OptionKeys::in::file::xyz.
Referenced by my_main().
| void relax_cenrot_pose | ( | core::pose::PoseOP & | native_pose, |
| core::pose::Pose & | p, | ||
| std::string const & | tag | ||
| ) |
References pyrosetta.io::create_score_function, test.T009_Exceptions::e, basic::Tracer::flush(), create_a3b_hbs::i, test.T400_Refinement::minmover, basic::options::OptionKeys::MonteCarlo::MonteCarlo, option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, basic::options::OptionKeys::run::run, vancomycin::task, TR, and gaussian-sampling::trial.
Referenced by my_main().
| void rescore_pose | ( | core::scoring::ScoreFunctionOP | score_fxn, |
| core::pose::PoseOP & | native_pose, | ||
| core::pose::Pose & | p, | ||
| std::string const & | tag | ||
| ) |
References basic::options::OptionKeys::in::file::dssp, docking::native_pose, option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, average_rmsds::rmsd, sfd, challenge::ss, and tag.
Referenced by my_main(), and process_the_pose().
| utility::vector1<core::Size> n_total(20) | ( | 20 | ) |
Referenced by my_main(), and process_the_pose().
| utility::vector1<core::Size> nrecovery(20) | ( | 20 | ) |
Referenced by my_main(), and process_the_pose().
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static |
Referenced by fit_centroid_to_the_best_rot(), my_main(), process_the_pose(), and relax_cenrot_pose().
1.9.1