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Rosetta
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Namespaces | |
| ligand | |
Functions | |
| def | T (x) |
| BooleanOptionKey const | kick_relax ("docking:kick_relax") |
| BooleanOptionKey const | docking ("docking") |
| BooleanOptionKey const | view ("docking:view") |
| BooleanOptionKey const | no_filters ("docking:no_filters") |
| StringVectorOptionKey const | design_chains ("docking:design_chains") |
| FileOptionKey const | recover_sidechains ("docking:recover_sidechains") |
| StringOptionKey const | partners ("docking:partners") |
| BooleanOptionKey const | docking_local_refine ("docking:docking_local_refine") |
| BooleanOptionKey const | low_res_protocol_only ("docking:low_res_protocol_only") |
| StringOptionKey const | docking_low_res_score ("docking:docking_low_res_score") |
| BooleanOptionKey const | randomize1 ("docking:randomize1") |
| BooleanOptionKey const | randomize2 ("docking:randomize2") |
| BooleanOptionKey const | use_ellipsoidal_randomization ("docking:use_ellipsoidal_randomization") |
| BooleanOptionKey const | spin ("docking:spin") |
| RealVectorOptionKey const | tilt ("docking:tilt") |
| StringOptionKey const | tilt1_center ("docking:tilt1_center") |
| StringOptionKey const | tilt2_center ("docking:tilt2_center") |
| RealVectorOptionKey const | dock_pert ("docking:dock_pert") |
| RealOptionKey const | uniform_trans ("docking:uniform_trans") |
| BooleanOptionKey const | center_at_interface ("docking:center_at_interface") |
| IntegerOptionKey const | dock_mcm_first_cycles ("docking:dock_mcm_first_cycles") |
| IntegerOptionKey const | dock_mcm_second_cycles ("docking:dock_mcm_second_cycles") |
| IntegerOptionKey const | docking_centroid_outer_cycles ("docking:docking_centroid_outer_cycles") |
| IntegerOptionKey const | docking_centroid_inner_cycles ("docking:docking_centroid_inner_cycles") |
| BooleanOptionKey const | dock_min ("docking:dock_min") |
| StringOptionKey const | flexible_bb_docking ("docking:flexible_bb_docking") |
| RealOptionKey const | flexible_bb_docking_interface_dist ("docking:flexible_bb_docking_interface_dist") |
| StringOptionKey const | ensemble1 ("docking:ensemble1") |
| StringOptionKey const | ensemble2 ("docking:ensemble2") |
| RealOptionKey const | dock_mcm_trans_magnitude ("docking:dock_mcm_trans_magnitude") |
| RealOptionKey const | dock_mcm_rot_magnitude ("docking:dock_mcm_rot_magnitude") |
| RealOptionKey const | minimization_threshold ("docking:minimization_threshold") |
| RealOptionKey const | temperature ("docking:temperature") |
| IntegerOptionKey const | repack_period ("docking:repack_period") |
| BooleanOptionKey const | extra_rottrial ("docking:extra_rottrial") |
| BooleanOptionKey const | dock_rtmin ("docking:dock_rtmin") |
| BooleanOptionKey const | sc_min ("docking:sc_min") |
| BooleanOptionKey const | norepack1 ("docking:norepack1") |
| BooleanOptionKey const | norepack2 ("docking:norepack2") |
| IntegerVectorOptionKey const | bb_min_res ("docking:bb_min_res") |
| IntegerVectorOptionKey const | sc_min_res ("docking:sc_min_res") |
| BooleanOptionKey const | dock_ppk ("docking:dock_ppk") |
| IntegerOptionKey const | max_repeats ("docking:max_repeats") |
| RealVectorOptionKey const | dock_lowres_filter ("docking:dock_lowres_filter") |
| RealOptionKey const | SymDock_lowres_filter ("docking:SymDock_lowres_filter") |
| IntegerVectorOptionKey const | multibody ("docking:multibody") |
| BooleanOptionKey const | ignore_default_docking_task ("docking:ignore_default_docking_task") |
| StringOptionKey const | low_patch ("docking:low_patch") |
| StringOptionKey const | high_patch ("docking:high_patch") |
| StringOptionKey const | high_min_patch ("docking:high_min_patch") |
| StringOptionKey const | pack_patch ("docking:pack_patch") |
| BooleanOptionKey const | use_legacy_protocol ("docking:use_legacy_protocol") |
| RealOptionKey const | docklowres_trans_magnitude ("docking:docklowres_trans_magnitude") |
| RealOptionKey const | docklowres_rot_magnitude ("docking:docklowres_rot_magnitude") |
| BooleanOptionKey const | enable_pymol_viewer ("docking:enable_pymol_viewer") |
| BooleanOptionKey const | SymDock_reduce_motif_dock_weights ("docking:SymDock_reduce_motif_dock_weights") |
| RealOptionKey const | SymDock_fa_rep_max ("docking:SymDock_fa_rep_max") |
| RealOptionKey const | SymDock_fa_sol_max ("docking:SymDock_fa_sol_max") |
Variables | |
| jumps = rosetta.utility.vector1_int() | |
| pose = rosetta.pose_from_file('/Users/sergey/rosie_uploads/docking/1brs.pdb') | |
| scorefxn = rosetta.get_fa_scorefxn() | |
| pymol = rosetta.PyMOL_Mover() | |
| docking_jump = jumps[1] | |
| a1 = rosetta.numeric.xyzVector_double(0,0,0) | |
| a2 = rosetta.numeric.xyzVector_double(1,0,0) | |
| a3 = rosetta.numeric.xyzVector_double(0,1,0) | |
| an = rosetta.numeric.xyzVector_double(0,0,1) | |
| b1 = rosetta.numeric.xyzVector_double(10 + 0,0,0) | |
| b2 = rosetta.numeric.xyzVector_double(10 + 1,0,0) | |
| b3 = rosetta.numeric.xyzVector_double(10 + 0,1,0) | |
| bn = rosetta.numeric.xyzVector_double(10 + 0,0,1) | |
| Q = rosetta.numeric.xyzMatrix_double() | |
| U = rosetta.numeric.xyzMatrix_double() | |
| R = U * rosetta.numeric.inverse(Q) | |
| s = b1 - R * a1 | |
| p = Pose() | |
| starting_p = Pose() | |
| dock_prot = DockingProtocol() | |
| int | dock_jump = 1 |
| scorefxn_low = create_score_function('interchain_cen') | |
| scorefxn_high = create_score_function('docking') | |
| scorefxn_high_min = create_score_function('docking','docking_min') | |
| to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover('centroid') | |
| to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover('fa_standard') | |
| recover_sidechains = protocols.simple_moves.ReturnSidechainMover(starting_p) | |
| randomize1 = RigidBodyRandomizeMover(p, dock_jump, rigid.partner_upstream) | |
| randomize2 = RigidBodyRandomizeMover(p, dock_jump, rigid.partner_downstream) | |
| dock_pert = RigidBodyPerturbMover(dock_jump, 3, 8) | |
| spin = RigidBodySpinMover( dock_jump ) | |
| slide_into_contact = protocols.docking.DockingSlideIntoContact( dock_jump ) | |
| docking_lowres = DockingLowRes( scorefxn_low, dock_jump ) | |
| docking_highres = DockingHighRes( scorefxn_high_min, dock_jump ) | |
| jd = PyJobDistributor("dock_output", 20, scorefxn_high) | |
| native_pose | |
| starting_p_centroid = Pose() | |
| IntegerVectorOptionKey const docking::bb_min_res | ( | "docking:bb_min_res" | ) |
| BooleanOptionKey const docking::center_at_interface | ( | "docking:center_at_interface" | ) |
| StringVectorOptionKey const docking::design_chains | ( | "docking:design_chains" | ) |
| RealVectorOptionKey const docking::dock_lowres_filter | ( | "docking:dock_lowres_filter" | ) |
| IntegerOptionKey const docking::dock_mcm_first_cycles | ( | "docking:dock_mcm_first_cycles" | ) |
| RealOptionKey const docking::dock_mcm_rot_magnitude | ( | "docking:dock_mcm_rot_magnitude" | ) |
| IntegerOptionKey const docking::dock_mcm_second_cycles | ( | "docking:dock_mcm_second_cycles" | ) |
| RealOptionKey const docking::dock_mcm_trans_magnitude | ( | "docking:dock_mcm_trans_magnitude" | ) |
| BooleanOptionKey const docking::dock_min | ( | "docking:dock_min" | ) |
| RealVectorOptionKey const docking::dock_pert | ( | "docking:dock_pert" | ) |
References dock_pert.
| BooleanOptionKey const docking::dock_ppk | ( | "docking:dock_ppk" | ) |
| BooleanOptionKey const docking::dock_rtmin | ( | "docking:dock_rtmin" | ) |
| BooleanOptionKey const docking::docking | ( | "docking" | ) |
| IntegerOptionKey const docking::docking_centroid_inner_cycles | ( | "docking:docking_centroid_inner_cycles" | ) |
| IntegerOptionKey const docking::docking_centroid_outer_cycles | ( | "docking:docking_centroid_outer_cycles" | ) |
| BooleanOptionKey const docking::docking_local_refine | ( | "docking:docking_local_refine" | ) |
| StringOptionKey const docking::docking_low_res_score | ( | "docking:docking_low_res_score" | ) |
| RealOptionKey const docking::docklowres_rot_magnitude | ( | "docking:docklowres_rot_magnitude" | ) |
| RealOptionKey const docking::docklowres_trans_magnitude | ( | "docking:docklowres_trans_magnitude" | ) |
| BooleanOptionKey const docking::enable_pymol_viewer | ( | "docking:enable_pymol_viewer" | ) |
| StringOptionKey const docking::ensemble1 | ( | "docking:ensemble1" | ) |
| StringOptionKey const docking::ensemble2 | ( | "docking:ensemble2" | ) |
| BooleanOptionKey const docking::extra_rottrial | ( | "docking:extra_rottrial" | ) |
| StringOptionKey const docking::flexible_bb_docking | ( | "docking:flexible_bb_docking" | ) |
| RealOptionKey const docking::flexible_bb_docking_interface_dist | ( | "docking:flexible_bb_docking_interface_dist" | ) |
| StringOptionKey const docking::high_min_patch | ( | "docking:high_min_patch" | ) |
| StringOptionKey const docking::high_patch | ( | "docking:high_patch" | ) |
| BooleanOptionKey const docking::ignore_default_docking_task | ( | "docking:ignore_default_docking_task" | ) |
| BooleanOptionKey const docking::kick_relax | ( | "docking:kick_relax" | ) |
| StringOptionKey const docking::low_patch | ( | "docking:low_patch" | ) |
| BooleanOptionKey const docking::low_res_protocol_only | ( | "docking:low_res_protocol_only" | ) |
| IntegerOptionKey const docking::max_repeats | ( | "docking:max_repeats" | ) |
| RealOptionKey const docking::minimization_threshold | ( | "docking:minimization_threshold" | ) |
| IntegerVectorOptionKey const docking::multibody | ( | "docking:multibody" | ) |
| BooleanOptionKey const docking::no_filters | ( | "docking:no_filters" | ) |
| BooleanOptionKey const docking::norepack1 | ( | "docking:norepack1" | ) |
| BooleanOptionKey const docking::norepack2 | ( | "docking:norepack2" | ) |
| StringOptionKey const docking::pack_patch | ( | "docking:pack_patch" | ) |
| StringOptionKey const docking::partners | ( | "docking:partners" | ) |
| BooleanOptionKey const docking::randomize1 | ( | "docking:randomize1" | ) |
References randomize1.
| BooleanOptionKey const docking::randomize2 | ( | "docking:randomize2" | ) |
References randomize2.
| FileOptionKey const docking::recover_sidechains | ( | "docking:recover_sidechains" | ) |
References recover_sidechains.
| IntegerOptionKey const docking::repack_period | ( | "docking:repack_period" | ) |
| BooleanOptionKey const docking::sc_min | ( | "docking:sc_min" | ) |
| IntegerVectorOptionKey const docking::sc_min_res | ( | "docking:sc_min_res" | ) |
| BooleanOptionKey const docking::spin | ( | "docking:spin" | ) |
References spin.
| RealOptionKey const docking::SymDock_fa_rep_max | ( | "docking:SymDock_fa_rep_max" | ) |
| RealOptionKey const docking::SymDock_fa_sol_max | ( | "docking:SymDock_fa_sol_max" | ) |
| RealOptionKey const docking::SymDock_lowres_filter | ( | "docking:SymDock_lowres_filter" | ) |
| BooleanOptionKey const docking::SymDock_reduce_motif_dock_weights | ( | "docking:SymDock_reduce_motif_dock_weights" | ) |
| def docking.T | ( | x | ) |
| RealOptionKey const docking::temperature | ( | "docking:temperature" | ) |
| RealVectorOptionKey const docking::tilt | ( | "docking:tilt" | ) |
| StringOptionKey const docking::tilt1_center | ( | "docking:tilt1_center" | ) |
| StringOptionKey const docking::tilt2_center | ( | "docking:tilt2_center" | ) |
| RealOptionKey const docking::uniform_trans | ( | "docking:uniform_trans" | ) |
Referenced by main().
| BooleanOptionKey const docking::use_ellipsoidal_randomization | ( | "docking:use_ellipsoidal_randomization" | ) |
| BooleanOptionKey const docking::use_legacy_protocol | ( | "docking:use_legacy_protocol" | ) |
| BooleanOptionKey const docking::view | ( | "docking:view" | ) |
| docking.a1 = rosetta.numeric.xyzVector_double(0,0,0) |
Referenced by TCDock.__dock_base__(), align_carboxyl_diiron_OLD(), angle_diff(), numeric::EulerAngles< T >.angular_distance_between(), ConstraintConfig.apply_fa_csts(), numeric::interpolation::periodic_range::full.bilinearly_interpolated(), numeric::interpolation::periodic_range::half.bilinearly_interpolated(), bind_std_forward_list(), bind_std_functional_hash(), bind_std_stl_deque(), bind_std_stl_multiset(), bind_std_stl_vector(), bind_std_unordered_map(), bind_std_unordered_set(), bind_T05_default(), check_jump(), clash(), contacts(), cyclize_pose(), dock(), enforce_atoms_coplanar(), PyCallBack_aaa_A_double_t.foo(), numeric::fourier::SO3coeffs.genWigner_ds(), get_aln(), get_coordinate_system(), get_jump(), local::HbondInfo.HbondInfo(), numeric::MathMatrix< T >.inverse_square_matrix(), main(), TCDock.min_termini_dis(), TCDock.min_termini_proj(), output_sugar_geometry_parameters(), PoseWrap.PoseWrap(), put_it_in_list(), numeric::linear_algebra.qzit(), numeric::linear_algebra.qzval(), set_stub_transform_test(), setargs(), CL.setargs(), numeric::kinematic_closure.sincos(), numeric::kinematic_closure::radians.sincos(), TCDock.termini_score(), and Arch.xform1().
| docking.a2 = rosetta.numeric.xyzVector_double(1,0,0) |
Referenced by TCDock.__dock_base__(), align_carboxyl_diiron(), align_carboxyl_diiron_OLD(), angle_diff(), numeric::EulerAngles< T >.angular_distance_between(), ConstraintConfig.apply_fa_csts(), numeric::interpolation::periodic_range::full.bilinearly_interpolated(), numeric::interpolation::periodic_range::half.bilinearly_interpolated(), bind_std_functional_hash(), bind_std_stl_multiset(), bind_std_unordered_map(), bind_std_unordered_set(), bind_T05_default(), numeric::alignment::QCPKernel< Real >.calc_rmsd_Theobald_method(), calculate_theoretical_RNA_length(), check_jump(), numeric::geometry::hashing::xyzStripeHash.clash(), clash(), numeric::geometry::hashing::xyzStripeHash.clash_amount(), numeric::geometry::hashing::xyzStripeHash.clash_check_ball(), numeric::geometry::hashing::xyzStripeHash.clash_not_resid(), numeric::geometry::hashing::xyzStripeHash.clash_raw(), contacts(), cyclize_pose(), dock(), numeric::geometry::hashing::xyzStripeHash.fill_pairs(), PyCallBack_aaa_A_double_t.foo(), numeric::fourier::SO3coeffs.genWigner_ds(), get_aln(), get_backbone_rotamers(), get_coordinate_system(), get_jump(), local::HbondInfo.HbondInfo(), numeric::MathMatrix< T >.inverse_square_matrix(), main(), TCDock.min_termini_dis(), TCDock.min_termini_proj(), numeric::geometry::hashing::xyzStripeHash.nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.nbcount(), numeric::geometry::hashing::xyzStripeHash.nbcount_raw(), output_sugar_geometry_parameters(), PoseWrap.PoseWrap(), put_it_in_list(), numeric::linear_algebra.qzit(), numeric::linear_algebra.qzval(), numeric::model_quality.rsym_eigenval(), set_stub_transform_test(), setargs(), CL.setargs(), TCDock.termini_score(), numeric::statistics.w(), and Arch.xform2().
| docking.a3 = rosetta.numeric.xyzVector_double(0,1,0) |
Referenced by align_carboxyl_diiron_OLD(), bind_T05_default(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), check_jump(), clash(), contacts(), get_aln(), get_coordinate_system(), get_jump(), local::HbondInfo.HbondInfo(), main(), output_sugar_geometry_parameters(), put_it_in_list(), numeric::linear_algebra.qzit(), numeric::model_quality.rsym_eigenval(), set_stub_transform_test(), setargs(), and CL.setargs().
| docking.an = rosetta.numeric.xyzVector_double(0,0,1) |
Referenced by numeric::linear_algebra.qzval().
| docking.b1 = rosetta.numeric.xyzVector_double(10 + 0,0,0) |
Referenced by numeric::interpolation::periodic_range::full.bilinearly_interpolated(), numeric::interpolation::periodic_range::half.bilinearly_interpolated(), check_jump(), cyclize_pose(), ObjexxFCL::FArray2D< T >.FArray2D(), ObjexxFCL::FArray3D< T >.FArray3D(), ObjexxFCL::FArray4D< T >.FArray4D(), ObjexxFCL::FArray5D< T >.FArray5D(), ObjexxFCL::FArray6D< T >.FArray6D(), numeric::fourier::SO3coeffs.genWigner_ds(), get_jump(), ObjexxFCL::KeyFArray2D< T >.KeyFArray2D(), ObjexxFCL::KeyFArray3D< T >.KeyFArray3D(), ObjexxFCL::KeyFArray4D< T >.KeyFArray4D(), ObjexxFCL::KeyFArray5D< T >.KeyFArray5D(), ObjexxFCL::KeyFArray6D< T >.KeyFArray6D(), main(), numeric::MathNTensor< T, N >.operator()(), PoseWrap.PoseWrap(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >.put_long_as_uint32(), zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >.put_long_as_uint32(), zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >.read_uint32(), and set_stub_transform_test().
| docking.b2 = rosetta.numeric.xyzVector_double(10 + 1,0,0) |
Referenced by align_carboxyl_diiron(), numeric::interpolation::periodic_range::full.bilinearly_interpolated(), numeric::interpolation::periodic_range::half.bilinearly_interpolated(), calculate_theoretical_RNA_length(), check_jump(), cyclize_pose(), ObjexxFCL::FArray2D< T >.FArray2D(), ObjexxFCL::FArray3D< T >.FArray3D(), ObjexxFCL::FArray4D< T >.FArray4D(), ObjexxFCL::FArray5D< T >.FArray5D(), ObjexxFCL::FArray6D< T >.FArray6D(), get_backbone_rotamers(), get_jump(), ObjexxFCL::KeyFArray2D< T >.KeyFArray2D(), ObjexxFCL::KeyFArray3D< T >.KeyFArray3D(), ObjexxFCL::KeyFArray4D< T >.KeyFArray4D(), ObjexxFCL::KeyFArray5D< T >.KeyFArray5D(), ObjexxFCL::KeyFArray6D< T >.KeyFArray6D(), main(), numeric::MathNTensor< T, N >.operator()(), PoseWrap.PoseWrap(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >.put_long_as_uint32(), zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >.put_long_as_uint32(), zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >.read_uint32(), and set_stub_transform_test().
| docking.b3 = rosetta.numeric.xyzVector_double(10 + 0,1,0) |
Referenced by calculate_theoretical_RNA_length_with_bond_angle_dependence(), check_jump(), ObjexxFCL::FArray3D< T >.FArray3D(), ObjexxFCL::FArray4D< T >.FArray4D(), ObjexxFCL::FArray5D< T >.FArray5D(), ObjexxFCL::FArray6D< T >.FArray6D(), get_jump(), ObjexxFCL::KeyFArray3D< T >.KeyFArray3D(), ObjexxFCL::KeyFArray4D< T >.KeyFArray4D(), ObjexxFCL::KeyFArray5D< T >.KeyFArray5D(), ObjexxFCL::KeyFArray6D< T >.KeyFArray6D(), numeric::MathNTensor< T, N >.operator()(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >.put_long_as_uint32(), zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >.put_long_as_uint32(), zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >.read_uint32(), and set_stub_transform_test().
| docking.bn = rosetta.numeric.xyzVector_double(10 + 0,0,1) |
Referenced by numeric::linear_algebra.qzval().
| docking.dock_pert = RigidBodyPerturbMover(dock_jump, 3, 8) |
Referenced by dock_pert(), and main().
| docking.dock_prot = DockingProtocol() |
| docking.docking_highres = DockingHighRes( scorefxn_high_min, dock_jump ) |
| docking.docking_jump = jumps[1] |
| docking.docking_lowres = DockingLowRes( scorefxn_low, dock_jump ) |
| docking.jd = PyJobDistributor("dock_output", 20, scorefxn_high) |
| docking.jumps = rosetta.utility.vector1_int() |
Referenced by ThisApplication.analyze_tree(), MPInterfaceStatistics.apply(), protocols::jumping::LibraryJumpSetup.create_jump_sample(), protocols::jumping::SpecificJumpSetup.create_jump_sample(), ChallengeMover.do_rigid_body_moves(), main(), make_float_sc_min_mover(), make_two_trimers(), minimize(), PoseWrap.PoseWrap(), and MinTestMover.set_foldtree_for_variable_movement().
| docking.native_pose |
Referenced by add_chi_tags(), analyze_base_pair_test(), ConstraintMinimizer.apply(), LocalRmsd.apply(), HolesTrainingDataMover.apply(), LoopHashRelax_Sampler.apply(), MinPackMinMover.apply(), HDdesignMover.apply(), ZincSiteEvaluator.apply(), compute_Irmsd.apply(), apply_all_frags(), backrub_protocol(), build_template(), byres_analysis(), calc_dihedral_rms(), ConstraintStatsMover.calc_native_stats(), calc_rms_test(), calc_rmsd_test(), calculate_helical_tail_variance(), calculate_pairwise_RMSD(), check_chi_correct(), check_quality_of_cluster_frags(), chi_stats_test(), coarse_rb_test(), coarse_rna_denovo_test(), StepWiseJobQueen.complete_larval_job_maturation(), compute_intrinsic_deviation(), compute_min_mean_rmsd_frag(), ConstraintStatsMover.ConstraintStatsMover(), distribute_jobs(), easy_loop_model_test(), easy_target_test(), erraser_monte_carlo(), myspace.evaluate_and_write(), ZincSiteEvaluator.evaluate_mutations_native(), fillPoseAndDataList(), finely_sample_base_pair_test(), general_initialize(), generate_combined_model(), get_all_1helix_docks(), get_all_2helix_docks(), get_frag_rmsd(), get_jump(), get_opte_data(), get_res_data_ss(), get_rmsd(), get_sc_bfactor(), get_sc_rmsd(), get_three_atom_sc_rmsd(), HemeReplace.HemeReplace(), hermann_phase_two_minimize(), if(), initialize_native_pose(), insert_chunk(), LocalRmsd.LocalRmsd(), loop_closure_test(), LoopBuild_main(), main(), measure_sequence_recovery(), minimize_protocol(), modeler_closure_test(), modeler_map_test(), my_main(), native_frag_CA_RMSD(), optimize_weights(), output_backbone_stats(), output_chi_stats(), output_to_silent(), pack_phosphates(), ExposedStrandMover.print_sheets_extras(), process_the_pose(), processChildren(), processChildrenIntensification(), read_native_pose(), readPoseAndData_PDB(), readPoseAndData_SILENT(), rebuild_centroid_test(), rebuild_test(), res_lvl_analysis(), rescore_pose(), rna_assemble_all_combinations_test(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_lores_score_silent_test(), rna_protein_rb_test(), rna_resample_test(), rna_stats_test(), RotamerAnalysis(), run(), DockFragmentsMover.run(), run_parallel_docking(), sample_rama_test(), sample_state_to_state(), sample_trp_tyr_test(), score_and_minimize(), score_clustered_frags(), score_loop(), score_loops(), screen_phosphates(), search_translations(), set_pose_occ_and_bfac(), setup_pose_setup_class(), simple_opte_test(), spinner_test(), stepwise_lores_test(), stepwise_monte_carlo_legacy(), stepwise_template_test(), superimpose_A_to_all(), and swa_rna_sample().
| docking.p = Pose() |
| docking.pose = rosetta.pose_from_file('/Users/sergey/rosie_uploads/docking/1brs.pdb') |
| docking.pymol = rosetta.PyMOL_Mover() |
| docking.Q = rosetta.numeric.xyzMatrix_double() |
Referenced by utility::graph.breadth_first_search_prune(), utility::graph.breadth_first_visit_prune(), numeric::kinematic_closure.chainParams(), numeric::kinematic_closure::radians.chainParams(), numeric::kinematic_closure.chainTORS(), numeric::kinematic_closure::radians.chainTORS(), numeric::kinematic_closure.chainXYZ(), numeric::kinematic_closure::radians.chainXYZ(), numeric::kinematic_closure.dixon_sturm(), CrystFFTDock.do_convolution(), evaluate_score(), numeric::linear_algebra.minimum_bounding_ellipse(), multiclass_probability(), numeric.quat2R(), numeric.R2quat(), run_trace(), numeric::kinematic_closure.test_chainParams(), numeric::kinematic_closure.test_chainTORS(), numeric::kinematic_closure.test_chainXYZ(), and traceCAs().
Referenced by apps::pilot::AlignChunkMover.align_chunk(), align_pose(), numeric.alignVectorSets(), apply_transform(), apps::pilot::AlignChunkMover.apply_transform(), binder.base_default_default_constructor_available(), binder.bind_member_functions_for_call_back(), binder.binding_template_bases(), bk_test(), numeric::kinematic_closure.build_dixon_matrices(), calculate_helical_parameters(), cxdock_design(), numeric::kinematic_closure.dixonResultant(), CrystFFTDock.do_convolution(), dock(), CrystFFTDock.dump_transformed_pdb(), euler2rot(), numeric::kinematic_closure.frame(), numeric::kinematic_closure::radians.frame(), numeric::UniformRotationSampler.get(), numeric::AxisRotationSampler.get(), get_axis_angle(), CrystFFTDock.get_clash_score_exact(), TCDock.get_cmp1(), TCDock.get_cmp2(), CrystFFTDock.get_interfaces_allatom(), get_reflection_axis(), get_rmsd(), get_rmsd_debug(), get_rotation_axis(), apps::pilot::AlignChunkMover.get_superposition_transformation(), get_superposition_transformation(), identity_matrix(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his_clamp(), binder.is_callback_structure_constructible(), binder.is_callback_structure_needed(), main(), map_morph(), matrix3f_to_xyzMatrix(), binder::ClassBinder.maybe_base_classes(), numeric::NearestSelector< R, T, bool >.nearest(), numeric::NearestSelector< R, T, true >.nearest(), numeric.nearest(), ObjexxFCL::NearestSelector< R, T, bool >.nearest(), ObjexxFCL::NearestSelector< R, T, true >.nearest(), ObjexxFCL.nearest(), numeric.operator<<(), numeric.operator>>(), pdb_to_silent_file_simple(), numeric.quat2R(), numeric.R2quat(), randomly_shift_and_tilt_pose(), randomly_shift_and_tilt_poses(), refold_second(), CrystFFTDock.resample_maps_and_get_self(), numeric::geometry.residual_squared_of_points_to_plane(), numeric::model_quality.rms_fit(), numeric::model_quality.rmsfitca2(), numeric::kinematic_closure.rotateX(), numeric::kinematic_closure::radians.rotateX(), numeric::kinematic_closure.rotateY(), numeric::kinematic_closure::radians.rotateY(), numeric::kinematic_closure.rotateZ(), numeric::kinematic_closure::radians.rotateZ(), numeric.rotation_angle(), numeric.rotation_axis_angle(), run_diiron_glu(), numeric::fourier::SHT.sharm_invTransform(), numeric::fourier::SHT.sharm_transform(), numeric::fourier::SHT.so3_correlate(), SpacegroupHit.SpacegroupHit(), numeric::fourier::SHT.sph_standardize(), superimpose_pose_transform(), test_chi_xform(), numeric::kinematic_closure.test_frame(), testone(), SpacegroupHit.to_string(), InterfaceHit.to_string(), CrystFFTDock.transform_pdb(), unsatisfied_buried_polars(), numeric::urs_Quat.urs_Quat(), numeric.urs_R2ang(), visualize(), and wrap_CXXRecordDecl().
Referenced by main(), and randomize1().
Referenced by main(), and randomize2().
| docking.recover_sidechains = protocols.simple_moves.ReturnSidechainMover(starting_p) |
Referenced by recover_sidechains().
Referenced by ObjexxFCL::format.A(), ObjexxFCL::internal::ObserverMediator.accumulate(), ObjexxFCL::internal::ObserverMediator.acyclic(), utility::json_spirit.add_esc_char(), utility::json_spirit.add_esc_chars(), PoseWrap.add_floating_sc_csts(), binder.add_relevant_includes(), align_pdbs(), analyze_base_pair_test(), anglestats_local(), utility::json_spirit.append_esc_char_and_incr_iter(), PhProtocol.apply(), HolesTrainingDataMover.apply(), CrystFFTDock.apply(), ui::network.as_hexadecimal(), ui::widgets.as_number(), ObjexxFCL::format::Bite< T >.assign(), assign_stack_faces(), ObjexxFCL::FArray1A< T >.attach(), ObjexxFCL::FArray1P< T >.attach(), ObjexxFCL::FArray2A< T >.attach(), ObjexxFCL::FArray2P< T >.attach(), ObjexxFCL::FArray3A< T >.attach(), ObjexxFCL::FArray3P< T >.attach(), ObjexxFCL::FArray4A< T >.attach(), ObjexxFCL::FArray4P< T >.attach(), ObjexxFCL::FArray5A< T >.attach(), ObjexxFCL::FArray5P< T >.attach(), ObjexxFCL::FArray6A< T >.attach(), ObjexxFCL::FArray6P< T >.attach(), ObjexxFCL::FArray< T >.attach(), base_pair_to_base_pair_test(), benzene_pair_score_test(), bin2string(), binder::ClassBinder.bind(), bind_T12_insertion_operator(), bind_T12_insertion_operator_1(), bind_T12_insertion_operator_2(), bind_T12_insertion_operator_3(), bind_T12_insertion_operator_4(), bind_T31_include_for_class_incl_a_include(), binder.binding_public_data_members(), binder.binding_public_member_functions(), utility::graph.breadth_first_search_prune(), utility::graph.breadth_first_visit_prune(), build_next_nucleotide_test(), MatchSet.c2_linker_check_dist(), calc_ddg(), calculate_distances(), basic::TracerImpl.calculate_tracer_level(), utility::options::VectorOption_T_< K, T >.can_hold_another(), ObjexxFCL.center(), ObjexxFCL.centered(), numeric::kinematic_closure.chainXYZ(), numeric::kinematic_closure::radians.chainXYZ(), ObjexxFCL.char_of(), detail.check_format_string(), check_structures(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >.chrono_formatter(), utility::options::OptionCollection.cleaned(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), cluster_rotamers(), coarse_frag_test(), detail.code_point_index(), detail.compile_string_to_view(), ObjexxFCL.compress(), pointGroupHit.contains_symmop(), SomeThingGetter.convert(), convert_to_coarse_test(), detail.count_code_points(), binder::Context.create_all_nested_namespaces(), create_ensemble(), MatchSet.cross(), cst_relax_test(), ObjexxFCL::Cstring.Cstring(), dab_sasa(), ObjexxFCL.date(), dinucleotide_test(), ObjexxFCL.dncase(), do_the_match(), dock(), doit(), dot_sasa(), ObjexxFCL.double_of(), utility.down_cast(), dump_energy_kinemage(), PoseWrap.dump_pdb(), dump_sequences(), dump_unique_atoms(), ObjexxFCL::Fstring.equal(), ObjexxFCL.equal(), ObjexxFCL.equali(), utility::file.equali(), basic::Emitter.escape_string(), basic.execute(), expand_chi_for_silent_structs(), binder.expresion_to_string(), figure_out_icoord_test(), fill_input_poses(), ObjexxFCL::Fstring.find(), ObjexxFCL::Fstring.find_first_not_of(), ObjexxFCL::Fstring.find_first_of(), ObjexxFCL::Fstring.find_last(), ObjexxFCL::Fstring.find_last_not_of(), ObjexxFCL::Fstring.find_last_of(), first_preminimized_namer(), ObjexxFCL.float_of(), ObjexxFCL.floops(), utility.fmt_real(), utility::py.foo_all(), utility::py.foo_all_sp(), utility::py::Base.foo_string(), binder::ClassBinder.for_public_nested_classes(), numeric::xyzTransform< T >.from_quaternion(), ui::task::Task.from_string(), utility.from_string(), ObjexxFCL::Fstring.Fstring(), ga_main(), binder::Context.generate(), generate_from_fiber(), rosetta_binders.generic_add_on_binder_maybe_has_insertion_operator(), get_axis_angle(), MatchSet.get_contacting_stub(), TCDock.get_contacts_by_component(), detail.get_data(), get_dots_area(), CrystFFTDock.get_interfaces_allatom(), detail.get_milliseconds(), utility.get_resnum_and_chain(), utility.get_resnum_and_chain_and_segid(), utility.get_resnum_and_segid(), get_rmsd(), SomeThing.get_score(), utility::sql_database::DatabaseSessionManager.get_session_mysql(), utility::sql_database::DatabaseSessionManager.get_session_postgres(), utility::sql_database::DatabaseSessionManager.get_session_sqlite3(), get_vallfrags(), getline(), getxform(), ObjexxFCL::Fstring.has(), ObjexxFCL.has(), ObjexxFCL::Cstring.has_any_of(), ObjexxFCL::Fstring.has_any_of(), ObjexxFCL.has_any_of(), utility::options::ScalarOption_T_< K, T >.has_any_of_characters(), utility::options::VectorOption_T_< K, T >.has_any_of_characters(), ObjexxFCL::Fstring.has_prefix(), ObjexxFCL.has_prefix(), ObjexxFCL.has_suffix(), ObjexxFCL.head(), hermann_phase_two_minimize(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >.hour(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >.hour12(), numeric.hsv_to_rgb(), ObjexxFCL.IACHAR(), ObjexxFCL.ICHAR(), basic::TracerImpl.in(), binder::Config.includes_code(), ObjexxFCL.index(), MatchSet.init(), abbinding.init_options(), PhDocking.init_options(), PhProtocol.init_options(), insert_stage_tag(), ObjexxFCL.int_of(), ObjexxFCL.ints_of(), ObjexxFCL.is_any_of(), ObjexxFCL.is_blank(), ObjexxFCL::format.is_blank_string(), ObjexxFCL.is_bool(), ObjexxFCL.is_char(), ObjexxFCL.is_double(), ObjexxFCL.is_float(), ObjexxFCL.is_int(), ObjexxFCL.is_ints(), ObjexxFCL.is_long(), ObjexxFCL.is_longdouble(), binder::Config.is_namespace_binding_requested(), binder::Config.is_namespace_skipping_requested(), ObjexxFCL.is_short(), ObjexxFCL.is_type(), ObjexxFCL.is_type< char >(), ObjexxFCL.is_uint(), ObjexxFCL.is_ulong(), ObjexxFCL.is_ushort(), ObjexxFCL.is_whitespace(), jacobi(), numeric.jacobi_rotation(), utility.join(), lariat_modeling(), ObjexxFCL.last_index(), ObjexxFCL.left_justified(), ObjexxFCL.left_justify(), utility::options::ScalarOption_T_< K, T >.legal_string(), utility::options::VectorOption_T_< K, T >.legal_string(), ObjexxFCL.len(), ObjexxFCL.len_trim(), ObjexxFCL.len_trim_whitespace(), ObjexxFCL.lge(), ObjexxFCL.lgt(), rosetta_binders.list_add_on_binder_maybe_has_insertion_operator(), ObjexxFCL.ljust(), ObjexxFCL.lle(), ObjexxFCL.llt(), load_models(), ObjexxFCL.long_of(), ObjexxFCL.longdouble_of(), utility.lower(), ObjexxFCL.lowercase(), ObjexxFCL.lowercased(), ObjexxFCL.lpad(), ObjexxFCL.lpadded(), ObjexxFCL.lstrip(), ObjexxFCL.lstrip_whitespace(), ObjexxFCL.lstripped(), ObjexxFCL.lstripped_whitespace(), utility.ltrim(), m_inv_gen(), main(), make_frag_set(), make_pose(), make_symm_data(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_default_constructible(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_has_insertion_operator(), measure_sequence_recovery(), utility::options::OptionCollection.merged(), methane_pair_score_test(), minimize_poses(), minimize_with_constraints(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >.minute(), modeler_map_test(), molten_get_vallfrags(), myasserteq(), utility::options::OptionCollection.n_part(), utility::options::OptionCollection.n_part_prefix_match(), ObjexxFCL.not_blank(), utility::keys::KeyLookup< K >.not_blank(), ObjexxFCL.not_whitespace(), ObjexxFCL::internal::ObserverMediator.notify(), nucleobase_probe_score_test(), numeric::kinematic_closure.numchanges(), numeric::kinematic_closure.numroots(), ObjexxFCL::internal::ObserverGraph.ObserverGraph(), detail::int_writer< OutputIt, Char, UInt >.on_num(), detail::get_cstring< Char >.operator()(), utility::signals::SignalHub< ReturnType, Signal >.operator()(), utility::BitSet< B >.operator+=(), utility::BitVector< B >.operator+=(), ObjexxFCL::Cstring.operator+=(), utility::BitSet< B >.operator-=(), utility::BitVector< B >.operator-=(), operator<<(), bbbb.operator<<(), basic::Report.operator<<(), detail::fill_t< Char >.operator=(), ObjexxFCL::Cstring.operator=(), ObjexxFCL::FArraySection< T >.operator=(), ObjexxFCL::Fstring.operator=(), ObjexxFCL::Fsubstring.operator=(), operator>>(), utility::BitSet< B >.operator|=(), utility::BitVector< B >.operator|=(), utility::json_spirit::Generator< Value_type, Ostream_type >.output(), output_centroid_silent_struct(), output_minipose_coords_test(), output_to_silent(), ObjexxFCL::Fstring.overlay(), ObjexxFCL.overlay(), ObjexxFCL.pad(), utility.pad_atom_name(), utility.pad_left(), utility.pad_right(), ObjexxFCL.padded(), ConstraintConfig.parse_config_file(), parse_pathway_test(), ConstraintConfig.parse_residues(), ConstraintConfig.parse_sequence(), pdb_to_silent_file(), pdb_to_silent_file_simple(), pdbstats_test(), ConstraintConfig.pick_sequence(), pose2frags(), pose_from_scratch(), utility::options::OptionCollection.prefix(), basic::sampling::orientations::Quaternion.Print(), basic::sampling::orientations::QuatSet.Print(), basic::database::schema_generator::Index.print(), print_all_torsions_test(), print_secstruct_test(), print_string_stdout(), print_verbose_ddgs(), printbits(), basic::sampling::orientations::Quaternion.PrintEuler(), ObjexxFCL::internal::ObserverGraph.push(), numeric::BodyPosition< T >.q_refresh(), quick_score_test(), basic::YamlEmitter.quote_string(), basic::JsonEmitter.quote_string(), utility.quoted_split(), numeric::linear_algebra.qzhes(), numeric::linear_algebra.qzit(), numeric::linear_algebra.qzval(), numeric::linear_algebra.qzvec(), read_ignore_comments(), read_pose(), utility::json_spirit.read_string(), utility::json_spirit.read_string_or_throw(), reduce_fa_rep(), numeric.remainder_conversion(), ObjexxFCL.remainder_conversion(), remove_dashes(), detail::dragonbox.remove_trailing_zeros(), repack_minimize_test(), repackmin(), binder.replace_(), utility.replace_in(), replace_string(), ConstraintConfig.residue_names_from_sequence(), reverse_doublet_test(), ObjexxFCL.right_justified(), ObjexxFCL.right_justify(), ObjexxFCL.rjust(), rna_assemble_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_denovo(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_fullatom_score_test(), rna_lores_score_silent_test(), rna_o2prime_test(), nacl_rosetta::RosettaInstance.RosettaThread(), rotamerize_rna_test(), numeric::kinematic_closure.rotateX(), numeric::kinematic_closure::radians.rotateX(), numeric::kinematic_closure.rotateY(), numeric::kinematic_closure::radians.rotateY(), numeric::kinematic_closure.rotateZ(), numeric::kinematic_closure::radians.rotateZ(), round_minimized_namer(), round_resampled_namer(), ObjexxFCL.rpad(), ObjexxFCL.rpadded(), ObjexxFCL.rstrip(), ObjexxFCL.rstrip_whitespace(), ObjexxFCL.rstripped(), ObjexxFCL.rstripped_whitespace(), utility.rtrim(), run_mc(), score12_plot_test(), score_and_minimize(), search_translations(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >.second(), second_preminimized_namer(), utility::signals::LinkUnit.send(), utility::signals::SignalHub< ReturnType, Signal >.send(), utility::signals::SignalHub< ReturnType, Signal >.send_signal(), sequence_tolerance_main(), sequence_tolerance_mf_main(), rosetta_binders.set_add_on_binder(), rosetta_binders.set_add_on_binder_maybe_has_insertion_operator(), basic::Emitter.set_indent(), set_temp_based_on_ens_diversity(), setargs(), CL.setargs(), ui::task::FileTableModel.setData(), setup_ca_constraints(), ObjexxFCL.short_of(), utility::options::ScalarOption_T_< K, T >.shortd(), utility::options::VectorOption_T_< K, T >.shortd(), sicdock_thread_num(), utility::signals::BufferedSignalHub< ReturnType, Signal >.signal_allowed(), simple_rotamer_recovery(), ObjexxFCL.size(), ObjexxFCL.sized(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), utility::keys::ClassKeyVector< K, T, C >.sort(), utility::options::OptionCollection.space_prefixed(), spanfile_from_pdb(), numeric::fourier::SHT.sph_standardize(), sphere_coverage(), utility.split(), utility.split_by_newlines(), binder.split_in_two(), utility.split_to_list(), utility.split_to_set(), utility.split_whitespace(), ConstraintConfig.ssstr(), store_energies(), str(), ObjexxFCL.str_dn(), ObjexxFCL.str_up(), ObjexxFCL.string_of(), rosetta_binders.stringstream_add_on_binder(), ObjexxFCL.strip(), utility.strip(), ObjexxFCL.strip_whitespace(), ObjexxFCL.stripped(), ObjexxFCL.stripped_whitespace(), utility::keys::KeyLookup< K >.stripped_whitespace(), utility::options::OptionCollection.suffix(), basic::svd::SVD_Solver.svbksb(), basic::svd::SVD_Solver.svdcmp(), numeric::linear_algebra.svdcmp(), ObjexxFCL::format.SW(), utility::BitSet< B >.swap(), utility::BitVector< B >.swap(), ObjexxFCL::Cstring.swap(), basic::TracerImpl::TracerProxyImpl.t_flush(), basic::ComparingTracer.t_flush(), basic::TracerToFile.t_flush(), utility::options::OptionCollection.tab_prefixed(), binder.template_argument_to_string(), IsctFast.test(), TEST(), test_actcoord(), test_chi_xform(), test_function(), FunctorTest.test_functor_async_sequence(), FunctorTest.test_functor_sequence(), third_preminimized_namer(), utility.timestamp_millis(), utility.timestamp_millis_short(), to_integer(), to_string_view(), numeric::expression_parser.to_uppercase(), numeric::kinematic_closure.torsion(), numeric::kinematic_closure::radians.torsion(), ObjexxFCL.trim(), utility.trim(), utility::options::OptionCollection.trim(), binder.trim(), ObjexxFCL.trim_whitespace(), ObjexxFCL.trimmed(), utility::options::OptionCollection.trimmed(), ObjexxFCL.trimmed_whitespace(), ObjexxFCL.type_of(), ObjexxFCL.type_of< char >(), ObjexxFCL.type_of< std::string >(), ObjexxFCL.uint_of(), ObjexxFCL.ulong_of(), ObjexxFCL.unique(), ObjexxFCL.uniqued(), ObjexxFCL.upcase(), utility.upper(), ObjexxFCL.uppercase(), ObjexxFCL.uppercased(), ObjexxFCL.ushort_of(), detail.utf8_decode(), detail::utf8_to_utf16.utf8_to_utf16(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.utility_vector_binder(), utility::options::OptionCollection.wrapped(), detail::arg_formatter_base< OutputIt, Char, ErrorHandler >.write(), detail.write(), write_base_pair_step_to_silent_struct(), basic::Emitter.write_raw(), xform_pose(), xform_pose_rev(), xform_rsd_gl2(), and detail::formatbuf< Char >.xsputn().
| docking.scorefxn = rosetta.get_fa_scorefxn() |
| docking.scorefxn_high = create_score_function('docking') |
| docking.scorefxn_high_min = create_score_function('docking','docking_min') |
| docking.scorefxn_low = create_score_function('interchain_cen') |
| docking.slide_into_contact = protocols.docking.DockingSlideIntoContact( dock_jump ) |
Referenced by CenRotDockingMover.init().
| docking.starting_p = Pose() |
| docking.starting_p_centroid = Pose() |
| docking.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover('centroid') |
| docking.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover('fa_standard') |
| docking.U = rosetta.numeric.xyzMatrix_double() |
Referenced by numeric.angle_of(), numeric::kinematic_closure.chainXYZ(), numeric::kinematic_closure::radians.chainXYZ(), numeric.cos_of(), numeric::kinematic_closure.dixon_eig(), numeric::kinematic_closure.frame(), numeric::kinematic_closure::radians.frame(), numeric::linear_algebra.minimum_bounding_ellipse(), detail::arg_converter< T, Context >.operator()(), numeric.sin_of(), numeric::kinematic_closure.test_frame(), test_MAT_VEC(), and numeric::random.uniform_vector_sphere().
1.9.1