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Rosetta
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test centroid rot model More...
#include <core/chemical/AA.hh>#include <core/chemical/ResidueType.fwd.hh>#include <core/chemical/ResidueTypeSet.fwd.hh>#include <core/chemical/ChemicalManager.hh>#include <core/conformation/Residue.hh>#include <devel/init.hh>#include <core/types.hh>#include <core/id/AtomID.hh>#include <core/id/DOF_ID.hh>#include <core/kinematics/MoveMap.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/dssp/Dssp.hh>#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/task/operation/TaskOperations.hh>#include <core/pose/Pose.hh>#include <core/pose/extra_pose_info_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/run.OptionKeys.gen.hh>#include <basic/options/keys/relax.OptionKeys.gen.hh>#include <basic/options/keys/abinitio.OptionKeys.gen.hh>#include <basic/options/keys/evaluation.OptionKeys.gen.hh>#include <basic/options/option_macros.hh>#include <basic/Tracer.hh>#include <numeric/random/random.hh>#include <utility/vector1.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/CartesianMinimizer.hh>#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>#include <protocols/minimization_packing/PackRotamersMover.hh>#include <protocols/viewer/viewers.hh>#include <protocols/moves/Mover.fwd.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/moves/RepeatMover.hh>#include <core/fragment/FragSet.fwd.hh>#include <core/fragment/FragmentIO.hh>#include <protocols/simple_moves/GunnCost.hh>#include <protocols/simple_moves/FragmentMover.fwd.hh>#include <protocols/simple_moves/SmoothFragmentMover.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/TrialMover.fwd.hh>#include <protocols/simple_moves/BBGaussianMover.hh>#include <utility/tools/make_vector1.hh>#include <protocols/docking/util.hh>#include <protocols/docking/types.hh>#include <protocols/rigid/RigidBodyMover.hh>#include <protocols/jd2/Job.hh>#include <protocols/jd2/JobDistributor.hh>#include <string>#include <fstream>#include <core/optimization/MinimizerOptions.hh>#include <core/kinematics/FoldTree.hh>Classes | |
| class | OutputCenrotIntCoord |
| class | ClearPoseHeader |
| class | RepackCenrotMover |
| class | CenRotSidechainMover |
| class | CenRotCanonicalMover |
| class | CenRotRBRelaxMover |
| class | CenRotDockingMover |
| class | SmoothFragRepackMover |
| class | RescoreCenrot |
| class | RepackMinCenrotMover |
| class | MinCenrotMover |
| class | CenRotRelaxMover |
Typedefs | |
| using | RepackCenrotMoverOP = utility::pointer::shared_ptr< RepackCenrotMover > |
| using | RepackMinCenrotMoverOP = utility::pointer::shared_ptr< RepackMinCenrotMover > |
| using | CenRotRelaxMoverOP = utility::pointer::shared_ptr< CenRotRelaxMover > |
| using | SmoothFragRepackMoverOP = utility::pointer::shared_ptr< SmoothFragRepackMover > |
| using | CenRotDockingMoverOP = utility::pointer::shared_ptr< CenRotDockingMover > |
| using | CenRotRBRelaxMoverOP = utility::pointer::shared_ptr< CenRotRBRelaxMover > |
| using | RescoreCenrotOP = utility::pointer::shared_ptr< RescoreCenrot > |
| using | MinCenrotMoverOP = utility::pointer::shared_ptr< MinCenrotMover > |
| using | CenRotCanonicalMoverOP = utility::pointer::shared_ptr< CenRotCanonicalMover > |
Functions | |
| void * | my_main (void *) |
| OPT_1GRP_KEY (Boolean, min, cenrot) int main(int argc | |
| NEW_OPT (switch_to_centroid, "switch the fa pdb to the old centroid", false) | |
| NEW_OPT (output_cenrot_intcoord, "output the internal coordinate, for building lib", false) | |
| NEW_OPT (output_bestrot_err, "output the distance between the native rot and best fitted one", false) | |
| NEW_OPT (input_cenrot_pdb, "input centroid pdbs for scoring", false) | |
| NEW_OPT (output_cenrot_pdb, "output centroid pdbs for building database", false) | |
| NEW_OPT (output_cenrot_score, "score the centroid pdbs", "cenrot_score.out") | |
| NEW_OPT (output_cenrot_dir, "dir for output centroid pdbs", ".") | |
| NEW_OPT (output_cenrot_prefix, "prefix for pdbs", "idealized_") | |
| NEW_OPT (repack_cenrot, "repack the centroid rotamer model", false) | |
| NEW_OPT (repack_bfactor_cutoff, "count repack side-chain with Bfactor lower than default 100", 100.0) | |
| NEW_OPT (repack_buried_cutoff, "count repack side-chain with buried cutoff", 0) | |
| NEW_OPT (repack_ncycle, "how many times to repack", 1) | |
| NEW_OPT (cenrot_score, "cenrot score weight file", "test.wts") | |
| NEW_OPT (cenrot_canonical, "relax the centroid rotamer model, bbg+sc", false) | |
| NEW_OPT (canonical_recover, "recover_low at the end of canonical mover", false) | |
| NEW_OPT (canonical_sc_prob, "sampling probability of sidechain", 0.8) | |
| NEW_OPT (docking_cenrot, "docking", false) | |
| NEW_OPT (docking_skip_repack, "docking without repack", false) | |
| NEW_OPT (rbrelax_cenrot, "rbrelax_cenrot", false) | |
| NEW_OPT (keep_silent_header, "keep old scoring lines in silent file", false) | |
| NEW_OPT (relax_cenrot, "relax the centroid rotamer model", false) | |
| NEW_OPT (frag_repack, "frag insertion and repack", false) | |
| NEW_OPT (opt_after_relax, "opt after relax", false) | |
| NEW_OPT (repack_min, "repack+min", false) | |
| NEW_OPT (relax_bb, "repack backbone", false) | |
| NEW_OPT (repack_vdw_scale, "repack using scaled vdw", 1.0) | |
| NEW_OPT (relax_temp, "temp", 1.0) | |
| NEW_OPT (relax_step_per_cycle, "step", 100) | |
| NEW_OPT (relax_cycle_number, "cycle", 1) | |
| NEW_OPT (min::cenrot, "add min mover alone", false) | |
| NEW_OPT (min::debug, "debug derivs?", false) | |
| NEW_OPT (min::cartesian, "cartesian minimization?", false) | |
| catch (utility::excn::Exception const &e) | |
Variables | |
| static basic::Tracer | TR ("pilot.wendao.cenrotjd2") |
| utility::vector1< core::Size > | nrecovery (20) |
| utility::vector1< core::Size > | n_total (20) |
| char * | argv [] |
| try | |
| return | |
test centroid rot model
| using CenRotCanonicalMoverOP = utility::pointer::shared_ptr<CenRotCanonicalMover> |
| using CenRotDockingMoverOP = utility::pointer::shared_ptr<CenRotDockingMover> |
| using CenRotRBRelaxMoverOP = utility::pointer::shared_ptr<CenRotRBRelaxMover> |
| using CenRotRelaxMoverOP = utility::pointer::shared_ptr<CenRotRelaxMover> |
| using MinCenrotMoverOP = utility::pointer::shared_ptr<MinCenrotMover> |
| typedef utility::pointer::shared_ptr< RepackCenrotMover > RepackCenrotMoverOP |
| using RepackMinCenrotMoverOP = utility::pointer::shared_ptr<RepackMinCenrotMover> |
| using RescoreCenrotOP = utility::pointer::shared_ptr<RescoreCenrot> |
| using SmoothFragRepackMoverOP = utility::pointer::shared_ptr<SmoothFragRepackMover> |
| catch | ( | utility::excn::Exception const & | e | ) |
References test.T009_Exceptions::e.
| void* my_main | ( | void * | ) |
References basic::options::OptionKeys::corrections::score::cenrot, basic::Tracer::Debug, pyrosetta.distributed.io::get_score_function(), in::file::native(), docking::native_pose, option, pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::abinitio::relax, basic::options::OptionKeys::casp::repack, rescore(), basic::options::OptionKeys::in::file::residue_type_set, beta_nonlocal::score_fxn, TR, and basic::options::OptionKeys::inout::dbms::user.
| NEW_OPT | ( | canonical_recover | , |
| "recover_low at the end of canonical mover" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | canonical_sc_prob | , |
| "sampling probability of sidechain" | , | ||
| 0. | 8 | ||
| ) |
| NEW_OPT | ( | cenrot_canonical | , |
| "relax the centroid rotamer | model, | ||
| bbg+sc" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | cenrot_score | , |
| "cenrot score weight file" | , | ||
| "test.wts" | |||
| ) |
| NEW_OPT | ( | docking_cenrot | , |
| "docking" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | docking_skip_repack | , |
| "docking without repack" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | frag_repack | , |
| "frag insertion and repack" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | keep_silent_header | , |
| "keep old scoring lines in silent file" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | min::cartesian | , |
| "cartesian minimization?" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | min::cenrot | , |
| "add min mover alone" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | min::debug | , |
| "debug derivs?" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | opt_after_relax | , |
| "opt after relax" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | output_bestrot_err | , |
| "output the distance between the native rot and best fitted one" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | output_cenrot_intcoord | , |
| "output the internal | coordinate, | ||
| for building lib" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | output_cenrot_score | , |
| "score the centroid pdbs" | , | ||
| "cenrot_score.out" | |||
| ) |
| NEW_OPT | ( | rbrelax_cenrot | , |
| "rbrelax_cenrot" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | relax_bb | , |
| "repack backbone" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | relax_cenrot | , |
| "relax the centroid rotamer model" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | relax_cycle_number | , |
| "cycle" | , | ||
| 1 | |||
| ) |
| NEW_OPT | ( | relax_step_per_cycle | , |
| "step" | , | ||
| 100 | |||
| ) |
| NEW_OPT | ( | relax_temp | , |
| "temp" | , | ||
| 1. | 0 | ||
| ) |
| NEW_OPT | ( | repack_bfactor_cutoff | , |
| "count repack side-chain with Bfactor lower than default 100" | , | ||
| 100. | 0 | ||
| ) |
| NEW_OPT | ( | repack_cenrot | , |
| "repack the centroid rotamer model" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | repack_min | , |
| "repack+min" | , | ||
| false | |||
| ) |
| NEW_OPT | ( | repack_ncycle | , |
| "how many times to repack" | , | ||
| 1 | |||
| ) |
| NEW_OPT | ( | repack_vdw_scale | , |
| "repack using scaled vdw" | , | ||
| 1. | 0 | ||
| ) |
| NEW_OPT | ( | switch_to_centroid | , |
| "switch the fa pdb to the old centroid" | , | ||
| false | |||
| ) |
| OPT_1GRP_KEY | ( | Boolean | , |
| min | , | ||
| cenrot | |||
| ) |
| char* argv[] |
Referenced by devel_main(), apps::pilot::KicSandbox::KicSandbox(), utility::options::OptionCollection::load(), main(), apps::pilot::frankdt::main(), main2(), my_main(), not_main(), protocols_main(), and sicdock_thread_num().
| utility::vector1<core::Size> n_total(20) | ( | 20 | ) |
Referenced by measure_sequence_recovery().
| utility::vector1<core::Size> nrecovery(20) | ( | 20 | ) |
| return |
Referenced by enumerate_junctions.Design::attach_valid(), add_xyz_to_pose::collect_xyz(), self-test::execute(), update_ui_project::execute(), build::execute(), enumerate_junctions::generate_starting_round_structures(), enumerate_junctions::get_all_dhrs(), enumerate_junctions::get_all_junctions(), enumerate_junctions.Design::get_current_c_term(), enumerate_junctions.Design::get_current_c_term_dhr(), enumerate_junctions.Design::get_current_n_term(), enumerate_junctions.Design::get_current_n_term_dhr(), build::get_defines(), add_xyz_to_pose::get_dist(), enumerate_junctions.Design::get_informative_name(), enumerate_junctions::get_single_junction(), enumerate_junctions::get_terminal_pdb(), enumerate_junctions.Design::length(), enumerate_junctions.Design::number_of_components(), enumerate_junctions.Design::output_string(), enumerate_junctions.Design::output_valid(), CloudArchiveManagerWrapper::read_batch(), add_xyz_to_pose::select_area(), enumerate_junctions.Junction::to_component(), enumerate_junctions.DHR::to_component(), and enumerate_junctions.Component::to_string().
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static |
| try |
1.9.1