Index

A

add_argument_unless_exists() (in module rpxdock.app.options) add_hier_score() (rpxdock.motif.pairscore.ResPairScore method) add_rots_to_respairdat() (in module rpxdock.motif.frames) add_xbin_to_respairdat() (in module rpxdock.motif.frames) align_around_axis() (in module rpxdock.homog) align_lines_isect_axis2() (in module rpxdock.homog) align_vector() (in module rpxdock.homog) align_vectors() (in module rpxdock.homog) alltimes() (rpxdock.util.timer.Timer method) analyze_ori_hier() (in module rpxdock.tests.sampling.test_xform_hierarchy) aname_to_elem() (in module rpxdock.io.io) angle() (in module rpxdock.homog) angle_degrees() (in module rpxdock.homog) angle_of() (in module rpxdock.homog)

angle_of_3x3() (in module rpxdock.homog) assert_results_close() (in module rpxdock.search.result) assign_rotamers() (in module rpxdock.rotamer.rotamer) asym_get_sample_hierarchy() (in module rpxdock.search.asym) AsymEvaluator (class in rpxdock.search.asym) axis() (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) (rpxdock.sampling.xform_hierarchy.RotHier_f4 property) (rpxdock.sampling.xform_hierarchy.RotHier_f8 property) axis_ang_cen_of() (in module rpxdock.homog) axis_ang_cen_of_eig() (in module rpxdock.homog) axis_ang_cen_of_planes() (in module rpxdock.homog) axis_angle_of() (in module rpxdock.homog) axis_angle_of_3x3() (in module rpxdock.homog)

B

bb_stubs() (in module rpxdock.motif.frames) BCC3 (class in rpxdock.geom.bcc) BCC3_float (class in rpxdock.geom.bcc) BCC6 (class in rpxdock.geom.bcc) BCC6_float (class in rpxdock.geom.bcc) bin_get_all_data() (rpxdock.motif.pairscore.ResPairScore method) bin_respairs() (rpxdock.motif.pairscore.ResPairScore method) bin_score() (rpxdock.motif.pairscore.ResPairScore method) bincen_of() (rpxdock.xbin.xbin.Xbin_double method) (rpxdock.xbin.xbin.Xbin_float method) Body (class in rpxdock.body.body) BodyPairEvalComponent (class in rpxdock.score.body_pair_eval) BodyPairEvaluator (class in rpxdock.score.body_pair_eval) Bunch (class in rpxdock.util.bunch) bunchify() (in module rpxdock.util.bunch) bvh_bvh_isect7d() (in module rpxdock.bvh.bvh_nd) bvh_bvh_isect7d_naive() (in module rpxdock.bvh.bvh_nd) bvh_collect_pairs() (in module rpxdock.bvh.bvh) bvh_collect_pairs_range_vec() (in module rpxdock.bvh.bvh)

bvh_collect_pairs_vec() (in module rpxdock.bvh.bvh) bvh_count_pairs() (in module rpxdock.bvh.bvh) bvh_count_pairs_vec() (in module rpxdock.bvh.bvh) bvh_isect() (in module rpxdock.bvh.bvh) bvh_isect7d() (in module rpxdock.bvh.bvh_nd) bvh_isect7d_naive() (in module rpxdock.bvh.bvh_nd) bvh_isect_fixed() (in module rpxdock.bvh.bvh) bvh_isect_fixed_range_vec() (in module rpxdock.bvh.bvh) bvh_isect_vec() (in module rpxdock.bvh.bvh) bvh_min_dist() (in module rpxdock.bvh.bvh) bvh_min_dist_fixed() (in module rpxdock.bvh.bvh) bvh_min_dist_one() (in module rpxdock.bvh.bvh) bvh_min_dist_vec() (in module rpxdock.bvh.bvh) bvh_mindist4d() (in module rpxdock.bvh.bvh_nd) bvh_mindist4d_naive() (in module rpxdock.bvh.bvh_nd) bvh_mindist7d() (in module rpxdock.bvh.bvh_nd) bvh_mindist7d_naive() (in module rpxdock.bvh.bvh_nd) bvh_print() (in module rpxdock.bvh.bvh) bvh_slide() (in module rpxdock.bvh.bvh) bvh_slide_vec() (in module rpxdock.bvh.bvh)

C

Cache (class in rpxdock.util.cache) CachedProxy (class in rpxdock.util.cache) calc_dihedral_angle() (in module rpxdock.homog) can_pickle() (in module rpxdock.util.util) cart_bs() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) cart_bs_() (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) cart_bs_pref_prod_() (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) cart_cell_width() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) cart_cell_width_() (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) cart_lb() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) cart_ncell() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) cart_resl() (rpxdock.xbin.xbin.Xbin_double property) (rpxdock.xbin.xbin.Xbin_float property) cart_ub() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) CartHier1D_f4 (class in rpxdock.sampling.xform_hierarchy) CartHier1D_f8 (class in rpxdock.sampling.xform_hierarchy) CartHier2D_f4 (class in rpxdock.sampling.xform_hierarchy) CartHier2D_f8 (class in rpxdock.sampling.xform_hierarchy) CartHier3D_f4 (class in rpxdock.sampling.xform_hierarchy) CartHier3D_f8 (class in rpxdock.sampling.xform_hierarchy) CartHier4D_f4 (class in rpxdock.sampling.xform_hierarchy) CartHier4D_f8 (class in rpxdock.sampling.xform_hierarchy) CartHier5D_f4 (class in rpxdock.sampling.xform_hierarchy) CartHier5D_f8 (class in rpxdock.sampling.xform_hierarchy) CartHier6D_f4 (class in rpxdock.sampling.xform_hierarchy) CartHier6D_f8 (class in rpxdock.sampling.xform_hierarchy) cell_index_of() (rpxdock.sampling.compound.CompoundHier method) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method) cellsize() (rpxdock.sampling.compound.CompoundHier method) (rpxdock.sampling.compound.ZeroDHier method) center() (rpxdock.bvh.bvh.SphereBVH_double method) (rpxdock.bvh.bvh_nd.SphereBVH4D method) (rpxdock.bvh.bvh_nd.SphereBVH7D method) centers() (rpxdock.bvh.bvh.SphereBVH_double method) (rpxdock.bvh.bvh_nd.SphereBVH4D method) (rpxdock.bvh.bvh_nd.SphereBVH7D method)

check_indices() (rpxdock.sampling.compound.CompoundHier method) check_needs_update() (in module rpxdock.util.parallel_build_modules) check_rotamer_deviation() (in module rpxdock.rotamer.rotamer) check_scores() (in module rpxdock.tests.xbin.test_smear) check_validity() (rpxdock.score.body_pair_eval.BodyPairEvalComponent method) checkpoint() (rpxdock.util.cache.Cache method) (rpxdock.util.timer.Timer method) child_of_begin() (rpxdock.sampling.xform_hierarchy.DummyHier_f4 method) (rpxdock.sampling.xform_hierarchy.DummyHier_f8 method) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method) child_of_end() (rpxdock.sampling.xform_hierarchy.DummyHier_f4 method) (rpxdock.sampling.xform_hierarchy.DummyHier_f8 method) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method) clash_ok() (rpxdock.body.body.Body method) coeffs3zorder() (in module rpxdock.sampling.xform_hierarchy) coeffs6zorder() (in module rpxdock.sampling.xform_hierarchy) com() (rpxdock.body.body.Body method) (rpxdock.bvh.bvh.SphereBVH_double method) (rpxdock.bvh.bvh_nd.SphereBVH4D method) (rpxdock.bvh.bvh_nd.SphereBVH7D method) combine_xforms() (rpxdock.sampling.compound.ProductHier method) (rpxdock.sampling.lattice_hier.LatticeHier method) CompoundHier (class in rpxdock.sampling.compound) concat_results() (in module rpxdock.search.result) concat_rotamer_space() (in module rpxdock.rotamer.richardson) contact_count() (rpxdock.body.body.Body method) contact_pairs() (rpxdock.body.body.Body method) cookie_cutter() (in module rpxdock.cluster.cookie_cutter) copy() (rpxdock.body.body.Body method) (rpxdock.search.result.Result method) (rpxdock.util.bunch.Bunch method) copy_with_sym() (rpxdock.body.body.Body method) copy_xformed() (rpxdock.body.body.Body method) cpu_count() (in module rpxdock.util.util) crappy_xform_hierarchy_resl_sanity_check() (in module rpxdock.tests.sampling.test_xform_hierarchy) create_bvh4d() (in module rpxdock.bvh.bvh_nd) create_bvh7d() (in module rpxdock.bvh.bvh_nd) create_bvh_quat() (in module rpxdock.bvh.bvh_nd) create_bvh_xform() (in module rpxdock.bvh.bvh_nd) create_OriCart1Hier_4f_nside() (in module rpxdock.sampling.xform_hierarchy) create_OriHier_nside_f4() (in module rpxdock.sampling.xform_hierarchy) create_OriHier_nside_f8() (in module rpxdock.sampling.xform_hierarchy) create_res_pair_score() (in module rpxdock.motif.pairscore) create_res_pair_score_map() (in module rpxdock.motif.pairscore) create_RotHier_nside_f4() (in module rpxdock.sampling.xform_hierarchy) create_RotHier_nside_f8() (in module rpxdock.sampling.xform_hierarchy) create_xbin_even_nside() (in module rpxdock.motif.rpxgen) create_Xbin_nside_double() (in module rpxdock.xbin.xbin) create_Xbin_nside_float() (in module rpxdock.xbin.xbin) create_XformHier_nside_f4() (in module rpxdock.sampling.xform_hierarchy) create_XformHier_nside_f8() (in module rpxdock.sampling.xform_hierarchy) CyclicEvaluator (class in rpxdock.search.cyclic)

D

default() (rpxdock.phmap.phmap.PHMap_u4f4 property) (rpxdock.phmap.phmap.PHMap_u8f4 property) (rpxdock.phmap.phmap.PHMap_u8f8 property) (rpxdock.phmap.phmap.PHMap_u8u8 property) default_cli_parser() (in module rpxdock.app.options) defaults() (in module rpxdock.app.options) dict_coherent_entries() (in module rpxdock.search.result) dihedral() (in module rpxdock.homog) dim() (rpxdock.sampling.xform_hierarchy.CartHier1D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier1D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier2D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier2D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier3D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier3D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier4D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier4D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier5D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier5D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier6D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier6D_f8 property) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) (rpxdock.sampling.xform_hierarchy.RotHier_f4 property) (rpxdock.sampling.xform_hierarchy.RotHier_f8 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property)

distance_to() (rpxdock.body.body.Body method) dock_cyclic() (in module rpxdock.app.dock) dock_multicomp() (in module rpxdock.app.dock) dock_onecomp() (in module rpxdock.app.dock) DockSpec1CompCage (class in rpxdock.search.dockspec) DockSpec1CompMirrorLayer (class in rpxdock.search.dockspec) DockSpec2CompCage (class in rpxdock.search.dockspec) DockSpec3CompCage (class in rpxdock.search.dockspec) DockSpec3CompLayer (class in rpxdock.search.dockspec) DockSpecMonomerToCyclic (class in rpxdock.search.dockspec) dummy_result() (in module rpxdock.search.result) dummyclass (class in rpxdock.tests.util.test_util) dummyfunc() (in module rpxdock.tests.util.test_util) DummyHier_f4 (class in rpxdock.sampling.xform_hierarchy) DummyHier_f8 (class in rpxdock.sampling.xform_hierarchy) dump() (in module rpxdock.util.util) dump_pdb() (rpxdock.body.body.Body method) (rpxdock.search.result.Result method) dump_pdb_from_bodies() (in module rpxdock.io.io_body) dump_pdb_from_points() (in module rpxdock.io.io) dump_pdbs() (rpxdock.search.result.Result method) dump_pdbs_top_score() (rpxdock.search.result.Result method) dump_pdbs_top_score_each() (rpxdock.search.result.Result method) dump_str() (in module rpxdock.util.util)

E

eval_trim_one() (rpxdock.search.multicomp.TwoCompEvaluatorWithTrim method) evaluate_positions() (in module rpxdock.search.basic) evaluate_positions_executor() (in module rpxdock.search.basic) expand_samples() (in module rpxdock.search.hierarchical) expand_top_N() (rpxdock.sampling.compound.CompoundHier method) (rpxdock.sampling.compound.ProductHier method) (rpxdock.sampling.lattice_hier.LatticeHier method) (rpxdock.sampling.xform_hierarchy.DummyHier_f4 method) (rpxdock.sampling.xform_hierarchy.DummyHier_f8 method) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method)

expand_xforms() (in module rpxdock.homog) extra_fields (rpxdock.score.body_pair_eval.BodyPairEvalComponent attribute) extract_2comp_dofs() (in module rpxdock.cluster.prune)

F

F6_to_xform() (rpxdock.xbin.xbin.Xbin_double method) (rpxdock.xbin.xbin.Xbin_float method) fa() (in module rpxdock.tests.phmap.test_phmap) fast_axis_of() (in module rpxdock.homog) files_needing_rebuild() (in module rpxdock.util.parallel_build_modules) filter_pairs() (rpxdock.body.body.Body method)

filter_quaternion_set_axis_within() (in module rpxdock.sampling.orientations) filter_redundancy() (in module rpxdock.filter.redundancy) find_connected_1xCyclic_slide() (in module rpxdock.search.gridslide) find_connected_2xCyclic_slide() (in module rpxdock.search.gridslide) find_connected_monomer_to_cyclic_slide() (in module rpxdock.search.gridslide) from_dict() (rpxdock.util.bunch.Bunch static method) fullname_from_path() (in module rpxdock.util.parallel_build_modules)

G

get_arg() (in module rpxdock.tests.search.test_cyclic) (in module rpxdock.tests.search.test_multicomp) get_bb_coords() (in module rpxdock.rosetta.rosetta_util) get_body() (in module rpxdock.data.data) get_cached() (rpxdock.util.cache.Cache method) get_cb_coords() (in module rpxdock.rosetta.rosetta_util) get_cli_args() (in module rpxdock.app.options) get_opts() (in module rpxdock.app.genrate_motif_scores) (in module rpxdock.app.rpx_score) get_ori() (rpxdock.sampling.xform_hierarchy.OriHier_f4 method) (rpxdock.sampling.xform_hierarchy.OriHier_f8 method) (rpxdock.sampling.xform_hierarchy.RotHier_f4 method) (rpxdock.sampling.xform_hierarchy.RotHier_f8 method) get_pair_keys() (in module rpxdock.motif.frames) get_pair_keys_ss_py() (in module rpxdock.tests.motif.test_motif) get_plotter() (in module rpxdock.util.plot) get_rotamer_index() (in module rpxdock.rotamer.richardson) get_rotamer_space() (in module rpxdock.rotamer.richardson) get_rotamer_space_raw() (in module rpxdock.rotamer.richardson) get_rpxdock_args() (in module rpxdock.app.dock) get_sc_coords() (in module rpxdock.rosetta.rosetta_util) get_spec() (in module rpxdock.app.dock) get_sphere_samples() (in module rpxdock.sampling.sphere) get_test_data() (in module rpxdock.data.data) get_trans() (rpxdock.sampling.xform_hierarchy.CartHier1D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier1D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier2D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier2D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier3D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier3D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier4D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier4D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier5D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier5D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier6D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier6D_f8 method)

get_xforms() (rpxdock.sampling.compound.CompoundHier method) (rpxdock.sampling.compound.ProductHier method) (rpxdock.sampling.compound.SlideHier method) (rpxdock.sampling.compound.ZeroDHier method) (rpxdock.sampling.lattice_hier.LatticeHier method) (rpxdock.sampling.xform_hier.LineHier method) (rpxdock.sampling.xform_hierarchy.CartHier1D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier1D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier2D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier2D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier3D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier3D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier4D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier4D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier5D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier5D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier6D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier6D_f8 method) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.RotHier_f4 method) (rpxdock.sampling.xform_hierarchy.RotHier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method) getstate() (rpxdock.search.result.Result method) grid6() (rpxdock.xbin.xbin.Xbin_double property) (rpxdock.xbin.xbin.Xbin_float property) grid_search() (in module rpxdock.search.basic) grid_sym_axis() (in module rpxdock.sampling.xform_grid) guess_is_degrees() (in module rpxdock.homog)

H

h_rand_points() (in module rpxdock.homog) has() (rpxdock.motif.pairscore.Xmap method) (rpxdock.phmap.phmap.PHMap_u4f4 method) (rpxdock.phmap.phmap.PHMap_u8f4 method) (rpxdock.phmap.phmap.PHMap_u8f8 method) (rpxdock.phmap.phmap.PHMap_u8u8 method) hash_str_to_int() (in module rpxdock.util.util) hcross() (in module rpxdock.homog) hdot() (in module rpxdock.homog) helix_get_sample_hierarchy() (in module rpxdock.search.helix) HelixEvaluator (class in rpxdock.search.helix) hier_axis_sampler() (in module rpxdock.sampling.xform_hier) hier_index_of() (rpxdock.sampling.compound.CompoundHier method) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method)

hier_mindis() (rpxdock.score.rpxhier.RpxHier method) hier_mirror_lattice_sampler() (in module rpxdock.sampling.xform_hier) hier_multi_axis_sampler() (in module rpxdock.sampling.xform_hier) hier_score() (rpxdock.motif.pairscore.ResPairScore method) hier_search() (in module rpxdock.search.hierarchical) hinv() (in module rpxdock.homog) hist() (in module rpxdock.util.plot) hnorm() (in module rpxdock.homog) hnorm2() (in module rpxdock.homog) hnormalized() (in module rpxdock.homog) hpoint() (in module rpxdock.homog) hray() (in module rpxdock.homog) hrot() (in module rpxdock.homog) hstub() (in module rpxdock.homog) htrans() (in module rpxdock.homog) hvec() (in module rpxdock.homog)

I

iface_scores() (rpxdock.search.plug.PlugEvaluator method) init_coords() (rpxdock.body.body.Body method) InProcessExecutor (class in rpxdock.util.util) intersect() (rpxdock.body.body.Body method) intersect_planes() (in module rpxdock.homog) intersect_range() (rpxdock.body.body.Body method) iresls() (rpxdock.score.rpxhier.RpxHier method) is_broadcastable() (in module rpxdock.homog) is_homog_xform() (in module rpxdock.homog) is_valid_quat_rot() (in module rpxdock.homog)

is_valid_rays() (in module rpxdock.homog) isect_range() (in module rpxdock.bvh.bvh) isect_range_single() (in module rpxdock.bvh.bvh) items() (rpxdock.phmap.phmap.PHMap_u4f4 method) (rpxdock.phmap.phmap.PHMap_u8f4 method) (rpxdock.phmap.phmap.PHMap_u8f8 method) (rpxdock.phmap.phmap.PHMap_u8u8 method) items_array() (rpxdock.phmap.phmap.PHMap_u4f4 method) (rpxdock.phmap.phmap.PHMap_u8f4 method) (rpxdock.phmap.phmap.PHMap_u8f8 method) (rpxdock.phmap.phmap.PHMap_u8u8 method)

K

karney_data_path() (in module rpxdock.sampling.orientations) karney_name_by_radius() (in module rpxdock.sampling.orientations) key_of() (rpxdock.motif.pairscore.Xmap method) (rpxdock.util.cache.Cache method) (rpxdock.xbin.xbin.Xbin_double method) (rpxdock.xbin.xbin.Xbin_float method) key_of_pairs() (in module rpxdock.xbin.xbin_util) key_of_selected_pairs() (in module rpxdock.xbin.xbin_util) keys() (rpxdock.geom.bcc.BCC3 method) (rpxdock.geom.bcc.BCC3_float method) (rpxdock.geom.bcc.BCC6 method) (rpxdock.geom.bcc.BCC6_float method) (rpxdock.motif.pairscore.Xmap method) (rpxdock.phmap.phmap.PHMap_u4f4 method) (rpxdock.phmap.phmap.PHMap_u8f4 method) (rpxdock.phmap.phmap.PHMap_u8f8 method) (rpxdock.phmap.phmap.PHMap_u8u8 method)

keys_have_changed_since_checkpoint() (rpxdock.util.cache.Cache method)

L

LatticeHier (class in rpxdock.sampling.lattice_hier) lb() (rpxdock.sampling.xform_hierarchy.RotHier_f4 property) (rpxdock.sampling.xform_hierarchy.RotHier_f8 property) line_angle() (in module rpxdock.homog) line_angle_degrees() (in module rpxdock.homog) line_line_closest_points() (in module rpxdock.homog) line_line_closest_points_pa() (in module rpxdock.homog) line_line_distance() (in module rpxdock.homog) line_line_distance_pa() (in module rpxdock.homog) LineHier (class in rpxdock.sampling.xform_hier)

load() (in module rpxdock.util.util) (rpxdock.util.cache.Cache method) load_threads() (in module rpxdock.util.util) localpath() (in module rpxdock.rotamer.richardson) long_axis() (rpxdock.body.body.Body method) long_axis_z_angle() (rpxdock.body.body.Body method) lower() (rpxdock.geom.bcc.BCC3 property) (rpxdock.geom.bcc.BCC3_float property) (rpxdock.geom.bcc.BCC6 property) (rpxdock.geom.bcc.BCC6_float property)

M

main() (in module rpxdock.app.dock) (in module rpxdock.app.dump_results) (in module rpxdock.app.genrate_motif_scores) (in module rpxdock.app.rpx_score) (in module rpxdock.tests.search.test_asym) (in module rpxdock.tests.search.test_helix) (in module rpxdock.tests.search.test_onecomp) make_and_dump_hier_score_tables() (in module rpxdock.motif.rpxgen) make_argv_with_atfiles() (in module rpxdock.app.options) make_asym() (in module rpxdock.search.asym) make_cyclic() (in module rpxdock.search.cyclic) make_cyclic_hier_sampler() (in module rpxdock.search.cyclic) make_helix() (in module rpxdock.search.helix) make_hscore_single() (in module rpxdock.motif.rpxgen) make_multicomp() (in module rpxdock.search.multicomp) make_onecomp() (in module rpxdock.search.onecomp) make_pdb_from_bodies() (in module rpxdock.io.io_body) make_plugs() (in module rpxdock.search.plug) make_respairdat_subsets() (in module rpxdock.motif.frames) make_score_files_moveme() (in module rpxdock.tests.motif.test_pairscore) map_of_selected_pairs() (in module rpxdock.xbin.xbin_util) map_pairs_multipos() (in module rpxdock.xbin.xbin_util) max_cart() (rpxdock.xbin.xbin.Xbin_double property) (rpxdock.xbin.xbin.Xbin_float property) max_id() (rpxdock.bvh.bvh.SphereBVH_double method) max_ub() (rpxdock.bvh.bvh.SphereBVH_double method) maybe_build() (in module rpxdock.util.parallel_build_modules) merge() (rpxdock.util.timer.Timer method) merge_on_chi() (in module rpxdock.rotamer.richardson) min_lb() (rpxdock.bvh.bvh.SphereBVH_double method) miniball() (in module rpxdock.geom.miniball) miniball_test() (in module rpxdock.geom.miniball) module rpxdock rpxdock.app rpxdock.app.dock rpxdock.app.dump_results rpxdock.app.genrate_motif_scores rpxdock.app.options rpxdock.app.rpx_score rpxdock.body rpxdock.body.body rpxdock.bvh rpxdock.bvh.bvh rpxdock.bvh.bvh_nd rpxdock.bvh.bvh_test rpxdock.cluster rpxdock.cluster.cookie_cutter rpxdock.cluster.prune rpxdock.data rpxdock.data.data rpxdock.filter rpxdock.filter.redundancy rpxdock.geom rpxdock.geom.bcc rpxdock.geom.miniball rpxdock.geom.porosity rpxdock.geom.primitive_test rpxdock.geom.sym rpxdock.geom.xform_dist rpxdock.homog rpxdock.io rpxdock.io.io rpxdock.io.io_body rpxdock.motif rpxdock.motif.frames rpxdock.motif.pairdat rpxdock.motif.pairscore rpxdock.motif.rpxgen rpxdock.phmap rpxdock.phmap.phmap rpxdock.rosetta rpxdock.rosetta.rosetta_util rpxdock.rotamer rpxdock.rotamer.richardson rpxdock.rotamer.rotamer rpxdock.sampling rpxdock.sampling.compound rpxdock.sampling.lattice_hier rpxdock.sampling.orientations rpxdock.sampling.sphere rpxdock.sampling.xform_grid rpxdock.sampling.xform_hier rpxdock.sampling.xform_hierarchy rpxdock.sampling.xhier_util rpxdock.score rpxdock.score.body_pair_eval rpxdock.score.rpxhier rpxdock.search rpxdock.search.asym rpxdock.search.basic rpxdock.search.cyclic rpxdock.search.dockspec rpxdock.search.gridslide rpxdock.search.helix rpxdock.search.hierarchical rpxdock.search.multicomp rpxdock.search.onecomp rpxdock.search.plug rpxdock.search.result rpxdock.tests rpxdock.tests.app rpxdock.tests.app.test_options rpxdock.tests.bvh rpxdock.tests.bvh.test_bvh rpxdock.tests.bvh.test_bvh_nd rpxdock.tests.cluster rpxdock.tests.cluster.test_cluster rpxdock.tests.geom rpxdock.tests.geom.test_bcc rpxdock.tests.geom.test_geom rpxdock.tests.geom.test_quat rpxdock.tests.geom.test_sym rpxdock.tests.motif rpxdock.tests.motif.test_motif rpxdock.tests.motif.test_pairdat rpxdock.tests.motif.test_pairscore rpxdock.tests.phmap rpxdock.tests.phmap.test_phmap rpxdock.tests.rotamer rpxdock.tests.rotamer.test_richardson rpxdock.tests.sampling rpxdock.tests.sampling.test_compound rpxdock.tests.sampling.test_orientations rpxdock.tests.sampling.test_xform_grid rpxdock.tests.sampling.test_xform_hierarchy rpxdock.tests.search rpxdock.tests.search.test_asym rpxdock.tests.search.test_cyclic rpxdock.tests.search.test_dockspec rpxdock.tests.search.test_gridslide rpxdock.tests.search.test_helix rpxdock.tests.search.test_hierarchical rpxdock.tests.search.test_multicomp rpxdock.tests.search.test_onecomp rpxdock.tests.search.test_plug rpxdock.tests.search.test_result rpxdock.tests.test_homog rpxdock.tests.util rpxdock.tests.util.test_bunch rpxdock.tests.util.test_cache rpxdock.tests.util.test_numeric rpxdock.tests.util.test_pybind_types rpxdock.tests.util.test_timer rpxdock.tests.util.test_util rpxdock.tests.xbin rpxdock.tests.xbin.test_smear rpxdock.tests.xbin.test_xbin rpxdock.tests.xbin.test_xbin_util rpxdock.util rpxdock.util.bunch rpxdock.util.cache rpxdock.util.dilated_int_test rpxdock.util.numeric rpxdock.util.parallel_build_modules rpxdock.util.plot rpxdock.util.pybind_types_test rpxdock.util.timer rpxdock.util.util rpxdock.xbin rpxdock.xbin.smear rpxdock.xbin.xbin rpxdock.xbin.xbin_test rpxdock.xbin.xbin_util

move_by() (rpxdock.body.body.Body method) move_to() (rpxdock.body.body.Body method) move_to_canonical_unit() (rpxdock.search.dockspec.DockSpec2CompCage method) move_to_center() (rpxdock.body.body.Body method) MultiCompEvaluator (class in rpxdock.search.multicomp) MultiCompEvaluatorBase (class in rpxdock.search.multicomp)

N

naive_collect_pairs() (in module rpxdock.bvh.bvh) naive_isect() (in module rpxdock.bvh.bvh) naive_isect_fixed() (in module rpxdock.bvh.bvh) naive_isect_range() (in module rpxdock.bvh.bvh) naive_min_dist() (in module rpxdock.bvh.bvh) naive_min_dist_fixed() (in module rpxdock.bvh.bvh) ncell() (rpxdock.sampling.xform_hierarchy.CartHier1D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier1D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier2D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier2D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier3D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier3D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier4D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier4D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier5D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier5D_f8 property) (rpxdock.sampling.xform_hierarchy.CartHier6D_f4 property) (rpxdock.sampling.xform_hierarchy.CartHier6D_f8 property) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.OriHier_f4 property) (rpxdock.sampling.xform_hierarchy.OriHier_f8 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) (rpxdock.sampling.xform_hierarchy.RotHier_f4 property) (rpxdock.sampling.xform_hierarchy.RotHier_f8 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) ndocks() (rpxdock.search.result.Result property)

neighbor_radius_square_cut() (rpxdock.geom.bcc.BCC3 method) (rpxdock.geom.bcc.BCC3_float method) (rpxdock.geom.bcc.BCC6 method) (rpxdock.geom.bcc.BCC6_float method) neighbor_sphere_radius_square_cut() (rpxdock.geom.bcc.BCC3 method) (rpxdock.geom.bcc.BCC3_float method) (rpxdock.geom.bcc.BCC6 method) (rpxdock.geom.bcc.BCC6_float method) neighbors_3() (rpxdock.geom.bcc.BCC3 method) (rpxdock.geom.bcc.BCC3_float method) neighbors_3_dist() (rpxdock.geom.bcc.BCC3 method) (rpxdock.geom.bcc.BCC3_float method) (rpxdock.geom.bcc.BCC6 method) (rpxdock.geom.bcc.BCC6_float method) neighbors_6_3() (rpxdock.geom.bcc.BCC6 method) (rpxdock.geom.bcc.BCC6_float method) neighbors_6_3_dist() (rpxdock.geom.bcc.BCC3 method) (rpxdock.geom.bcc.BCC3_float method) (rpxdock.geom.bcc.BCC6 method) (rpxdock.geom.bcc.BCC6_float method) NOCACHE() (in module rpxdock.util.cache) NonFuture (class in rpxdock.util.util) nside() (rpxdock.geom.bcc.BCC3 property) (rpxdock.geom.bcc.BCC3_float property) (rpxdock.geom.bcc.BCC6 property) (rpxdock.geom.bcc.BCC6_float property) num_digits() (in module rpxdock.util.util) numpy_stub_from_rosetta_stub() (in module rpxdock.rosetta.rosetta_util)

O

obj_id() (rpxdock.bvh.bvh.SphereBVH_double method) OneCompEvaluator (class in rpxdock.search.onecomp) only_whats_needed() (rpxdock.motif.pairdat.ResPairData method) ori_cell_of() (rpxdock.xbin.xbin.Xbin_double method) (rpxdock.xbin.xbin.Xbin_float method) ori_ncell() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) ori_nside() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.OriHier_f4 property) (rpxdock.sampling.xform_hierarchy.OriHier_f8 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) (rpxdock.xbin.xbin.Xbin_double property) (rpxdock.xbin.xbin.Xbin_float property)

ori_resl() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f4 property) (rpxdock.sampling.xform_hierarchy.XformHier_f8 property) (rpxdock.xbin.xbin.Xbin_double property) (rpxdock.xbin.xbin.Xbin_float property) OriCart1Hier_f4 (class in rpxdock.sampling.xform_hierarchy) OriHier_f4 (class in rpxdock.sampling.xform_hierarchy) OriHier_f8 (class in rpxdock.sampling.xform_hierarchy)

P

pack_zorder() (in module rpxdock.sampling.xform_hierarchy) pair_key_ss_py() (in module rpxdock.tests.motif.test_motif) parallel_build_modules() (in module rpxdock.util.parallel_build_modules) parent_of() (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method) parse_list_of_strtuple() (in module rpxdock.app.options) pca() (in module rpxdock.util.numeric) pca_eig() (in module rpxdock.util.numeric) pdb_format_atom() (in module rpxdock.io.io) PHMap_u4f4 (class in rpxdock.phmap.phmap) PHMap_u8f4 (class in rpxdock.phmap.phmap) PHMap_u8f8 (class in rpxdock.phmap.phmap) PHMap_u8u8 (class in rpxdock.phmap.phmap) pickle_analysis() (in module rpxdock.util.util) pickle_time() (in module rpxdock.util.util) place_along_axes() (rpxdock.search.dockspec.DockSpec2CompCage method) place_along_axis() (rpxdock.search.dockspec.DockSpec1CompCage method) (rpxdock.search.dockspec.DockSpecMonomerToCyclic method)

placements() (rpxdock.search.dockspec.DockSpec1CompCage method) placements1() (rpxdock.search.dockspec.DockSpec2CompCage method) placements2() (rpxdock.search.dockspec.DockSpec2CompCage method) placements_second() (rpxdock.search.dockspec.DockSpec1CompCage method) (rpxdock.search.dockspec.DockSpecMonomerToCyclic method) plug_get_sample_hierarchy() (in module rpxdock.search.plug) plug_test_hier_sampler() (in module rpxdock.search.plug) PlugEvaluator (class in rpxdock.search.plug) point_in_plane() (in module rpxdock.homog) positioned_cen() (rpxdock.body.body.Body method) positioned_coord() (rpxdock.body.body.Body method) positioned_coord_atomno() (rpxdock.body.body.Body method) positioned_orig_coords() (rpxdock.body.body.Body method) print_full() (in module rpxdock.rotamer.richardson) process_cart_bounds() (in module rpxdock.app.options) process_cli_args() (in module rpxdock.app.options) ProductHier (class in rpxdock.sampling.compound) proj_perp() (in module rpxdock.homog) prune_results_2comp() (in module rpxdock.cluster.prune)

Q

quat_multiply() (in module rpxdock.homog) quat_to_rot() (in module rpxdock.homog) quat_to_upper_half() (in module rpxdock.homog)

quat_to_xform() (in module rpxdock.homog) quaternion_set_by_name() (in module rpxdock.sampling.orientations) quaternion_set_with_covering_radius_degrees() (in module rpxdock.sampling.orientations) quats_from_karney_file() (in module rpxdock.sampling.orientations)

R

radius() (rpxdock.bvh.bvh.SphereBVH_double method) (rpxdock.bvh.bvh_nd.SphereBVH4D method) (rpxdock.bvh.bvh_nd.SphereBVH7D method) radius_max() (rpxdock.body.body.Body method) radius_xy_max() (rpxdock.body.body.Body method) rand_point() (in module rpxdock.homog) rand_quat() (in module rpxdock.homog) rand_ray() (in module rpxdock.homog) rand_unit() (in module rpxdock.homog) rand_vec() (in module rpxdock.homog) rand_xform() (in module rpxdock.homog) rand_xform_aac() (in module rpxdock.homog) random_walk() (in module rpxdock.tests.bvh.test_bvh) ray_in_plane() (in module rpxdock.homog) remove() (rpxdock.util.cache.Cache method) remove_proxy() (in module rpxdock.util.cache) remove_redundant_pdbs() (in module rpxdock.motif.frames) report() (rpxdock.util.timer.Timer method) report_dict() (rpxdock.util.timer.Timer method) ResPairData (class in rpxdock.motif.pairdat) ResPairScore (class in rpxdock.motif.pairscore) Result (class in rpxdock.search.result) result() (rpxdock.util.util.NonFuture method) rg() (rpxdock.body.body.Body method) rg_xy() (rpxdock.body.body.Body method) rg_z() (rpxdock.body.body.Body method) rosetta_init() (in module rpxdock.rosetta.rosetta_util) rot() (in module rpxdock.homog) rot_cell_width() (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) (rpxdock.sampling.xform_hierarchy.RotHier_f4 property) (rpxdock.sampling.xform_hierarchy.RotHier_f8 property) rot_lb() (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) rot_ncell() (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) (rpxdock.sampling.xform_hierarchy.RotHier_f4 property) (rpxdock.sampling.xform_hierarchy.RotHier_f8 property) rot_to_quat() (in module rpxdock.homog) rot_ub() (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 property) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 property) rotation_around_dof_for_target_angle() (in module rpxdock.homog) RotCart1Hier_f4 (class in rpxdock.sampling.xform_hierarchy) RotCart1Hier_f8 (class in rpxdock.sampling.xform_hierarchy) RotHier_f4 (class in rpxdock.sampling.xform_hierarchy) RotHier_f8 (class in rpxdock.sampling.xform_hierarchy) rpxdock module rpxdock.app module rpxdock.app.dock module rpxdock.app.dump_results module rpxdock.app.genrate_motif_scores module rpxdock.app.options module rpxdock.app.rpx_score module rpxdock.body module rpxdock.body.body module rpxdock.bvh module rpxdock.bvh.bvh module rpxdock.bvh.bvh_nd module rpxdock.bvh.bvh_test module rpxdock.cluster module rpxdock.cluster.cookie_cutter module rpxdock.cluster.prune module rpxdock.data module rpxdock.data.data module rpxdock.filter module rpxdock.filter.redundancy module rpxdock.geom module rpxdock.geom.bcc module rpxdock.geom.miniball module rpxdock.geom.porosity module rpxdock.geom.primitive_test module rpxdock.geom.sym module rpxdock.geom.xform_dist module rpxdock.homog module rpxdock.io module rpxdock.io.io module rpxdock.io.io_body module rpxdock.motif module rpxdock.motif.frames module rpxdock.motif.pairdat module rpxdock.motif.pairscore module rpxdock.motif.rpxgen module rpxdock.phmap module rpxdock.phmap.phmap module rpxdock.rosetta module rpxdock.rosetta.rosetta_util module rpxdock.rotamer module rpxdock.rotamer.richardson module rpxdock.rotamer.rotamer module rpxdock.sampling module rpxdock.sampling.compound module rpxdock.sampling.lattice_hier module rpxdock.sampling.orientations module rpxdock.sampling.sphere module rpxdock.sampling.xform_grid module rpxdock.sampling.xform_hier module rpxdock.sampling.xform_hierarchy module rpxdock.sampling.xhier_util module rpxdock.score module rpxdock.score.body_pair_eval module

rpxdock.score.rpxhier module rpxdock.search module rpxdock.search.asym module rpxdock.search.basic module rpxdock.search.cyclic module rpxdock.search.dockspec module rpxdock.search.gridslide module rpxdock.search.helix module rpxdock.search.hierarchical module rpxdock.search.multicomp module rpxdock.search.onecomp module rpxdock.search.plug module rpxdock.search.result module rpxdock.tests module rpxdock.tests.app module rpxdock.tests.app.test_options module rpxdock.tests.bvh module rpxdock.tests.bvh.test_bvh module rpxdock.tests.bvh.test_bvh_nd module rpxdock.tests.cluster module rpxdock.tests.cluster.test_cluster module rpxdock.tests.geom module rpxdock.tests.geom.test_bcc module rpxdock.tests.geom.test_geom module rpxdock.tests.geom.test_quat module rpxdock.tests.geom.test_sym module rpxdock.tests.motif module rpxdock.tests.motif.test_motif module rpxdock.tests.motif.test_pairdat module rpxdock.tests.motif.test_pairscore module rpxdock.tests.phmap module rpxdock.tests.phmap.test_phmap module rpxdock.tests.rotamer module rpxdock.tests.rotamer.test_richardson module rpxdock.tests.sampling module rpxdock.tests.sampling.test_compound module rpxdock.tests.sampling.test_orientations module rpxdock.tests.sampling.test_xform_grid module rpxdock.tests.sampling.test_xform_hierarchy module rpxdock.tests.search module rpxdock.tests.search.test_asym module rpxdock.tests.search.test_cyclic module rpxdock.tests.search.test_dockspec module rpxdock.tests.search.test_gridslide module rpxdock.tests.search.test_helix module rpxdock.tests.search.test_hierarchical module rpxdock.tests.search.test_multicomp module rpxdock.tests.search.test_onecomp module rpxdock.tests.search.test_plug module rpxdock.tests.search.test_result module rpxdock.tests.test_homog module rpxdock.tests.util module rpxdock.tests.util.test_bunch module rpxdock.tests.util.test_cache module rpxdock.tests.util.test_numeric module rpxdock.tests.util.test_pybind_types module rpxdock.tests.util.test_timer module rpxdock.tests.util.test_util module rpxdock.tests.xbin module rpxdock.tests.xbin.test_smear module rpxdock.tests.xbin.test_xbin module rpxdock.tests.xbin.test_xbin_util module rpxdock.util module rpxdock.util.bunch module rpxdock.util.cache module rpxdock.util.dilated_int_test module rpxdock.util.numeric module rpxdock.util.parallel_build_modules module rpxdock.util.plot module rpxdock.util.pybind_types_test module rpxdock.util.timer module rpxdock.util.util module rpxdock.xbin module rpxdock.xbin.smear module rpxdock.xbin.xbin module rpxdock.xbin.xbin_test module rpxdock.xbin.xbin_util module RpxHier (class in rpxdock.score.rpxhier)

S

sample_rotamer_space() (in module rpxdock.rotamer.richardson) samples_1xCyclic() (in module rpxdock.search.gridslide) samples_1xMonomer_orientations() (in module rpxdock.search.gridslide) samples_2xCyclic_slide() (in module rpxdock.search.gridslide) sanitize_for_pickle() (in module rpxdock.util.util) sanity_check() (rpxdock.motif.pairdat.ResPairData method) (rpxdock.sampling.xform_hierarchy.CartHier1D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier1D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier2D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier2D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier3D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier3D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier4D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier4D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier5D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier5D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier6D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier6D_f8 method) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method) save() (rpxdock.util.cache.Cache method) scatter() (in module rpxdock.util.plot) score() (rpxdock.score.rpxhier.RpxHier method) score_all() (rpxdock.score.rpxhier.RpxHier method) score_base() (rpxdock.score.rpxhier.RpxHier method) score_by_resl() (rpxdock.score.rpxhier.RpxHier method) score_fields (rpxdock.score.body_pair_eval.BodyPairEvalComponent attribute) score_matrix_inter() (rpxdock.score.rpxhier.RpxHier method) score_matrix_intra() (rpxdock.score.rpxhier.RpxHier method) score_onebody() (in module rpxdock.app.rpx_score) score_twobody() (in module rpxdock.app.rpx_score) scorepos() (rpxdock.score.rpxhier.RpxHier method) sel() (rpxdock.search.result.Result method) set_asym_body() (rpxdock.body.body.Body method) set_loglevel() (in module rpxdock.app.options) setstate() (rpxdock.search.result.Result method) show() (in module rpxdock.util.plot) size() (rpxdock.sampling.compound.CompoundHier method) (rpxdock.sampling.compound.ZeroDHier method) (rpxdock.sampling.xform_hierarchy.CartHier1D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier1D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier2D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier2D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier3D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier3D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier4D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier4D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier5D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier5D_f8 method) (rpxdock.sampling.xform_hierarchy.CartHier6D_f4 method) (rpxdock.sampling.xform_hierarchy.CartHier6D_f8 method) (rpxdock.sampling.xform_hierarchy.DummyHier_f4 method) (rpxdock.sampling.xform_hierarchy.DummyHier_f8 method) (rpxdock.sampling.xform_hierarchy.OriCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.OriHier_f4 method) (rpxdock.sampling.xform_hierarchy.OriHier_f8 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f4 method) (rpxdock.sampling.xform_hierarchy.RotCart1Hier_f8 method) (rpxdock.sampling.xform_hierarchy.RotHier_f4 method) (rpxdock.sampling.xform_hierarchy.RotHier_f8 method) (rpxdock.sampling.xform_hierarchy.XformHier_f4 method) (rpxdock.sampling.xform_hierarchy.XformHier_f8 method)

slide_dir() (rpxdock.search.dockspec.DockSpec1CompCage method) (rpxdock.search.dockspec.DockSpec2CompCage method) (rpxdock.search.dockspec.DockSpecMonomerToCyclic method) slide_to() (rpxdock.body.body.Body method) SlideHier (class in rpxdock.sampling.compound) slow_test_ori_hier_rand_nside4() (in module rpxdock.tests.sampling.test_xform_hierarchy) small_hscore() (in module rpxdock.data.data) small_respairdat() (in module rpxdock.data.data) small_respairscore() (in module rpxdock.data.data) smear() (in module rpxdock.xbin.smear) smear_bench() (in module rpxdock.tests.xbin.test_smear) sortby() (rpxdock.search.result.Result method) sphere_porosity() (in module rpxdock.geom.porosity) SphereBVH4D (class in rpxdock.bvh.bvh_nd) SphereBVH7D (class in rpxdock.bvh.bvh_nd) SphereBVH_double (class in rpxdock.bvh.bvh) split_by_pdb() (rpxdock.motif.pairdat.ResPairData method) split_indices() (rpxdock.sampling.compound.CompoundHier method) split_indices_cell() (rpxdock.sampling.compound.CompoundHier method) split_indices_hier() (rpxdock.sampling.compound.CompoundHier method) ss_to_ssid() (in module rpxdock.motif.frames) sskey_of_selected_pairs() (in module rpxdock.xbin.xbin_util) ssmap_of_selected_pairs() (in module rpxdock.xbin.xbin_util) ssmap_pairs_multipos() (in module rpxdock.xbin.xbin_util) start() (rpxdock.util.timer.Timer method) stop() (rpxdock.util.timer.Timer method) str2bool() (in module rpxdock.app.options) str_pdb() (rpxdock.body.body.Body method) strip_data() (rpxdock.body.body.Body method) stub_from_points() (in module rpxdock.motif.frames) sub() (rpxdock.util.bunch.Bunch method) submit() (rpxdock.util.util.InProcessExecutor method) subplots() (in module rpxdock.util.plot) subset_by_aa() (rpxdock.motif.pairdat.ResPairData method) subset_by_pair() (rpxdock.motif.pairdat.ResPairData method) subset_by_pdb() (rpxdock.motif.pairdat.ResPairData method) subset_by_res() (rpxdock.motif.pairdat.ResPairData method) subset_by_ss() (rpxdock.motif.pairdat.ResPairData method) sum_() (in module rpxdock.tests.util.test_cache) svd() (in module rpxdock.util.numeric) symframes() (in module rpxdock.geom.sym) (rpxdock.search.dockspec.DockSpec1CompCage method) (rpxdock.search.dockspec.DockSpec2CompCage method) (rpxdock.search.dockspec.DockSpecMonomerToCyclic method)

T

terrible_sanity_check() (in module rpxdock.tests.motif.test_pairscore) test_accessors() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_align_around_axis() (in module rpxdock.tests.test_homog) test_align_lines_dof_dihedral_basic() (in module rpxdock.tests.test_homog) test_align_lines_dof_dihedral_rand() (in module rpxdock.tests.test_homog) test_align_lines_dof_dihedral_rand_3D() (in module rpxdock.tests.test_homog) test_align_lines_dof_dihedral_rand_single() (in module rpxdock.tests.test_homog) test_align_vectors_minangle() (in module rpxdock.tests.test_homog) test_align_vectors_una_case() (in module rpxdock.tests.test_homog) test_angle() (in module rpxdock.tests.test_homog) test_asym() (in module rpxdock.tests.search.test_asym) test_asym_trim() (in module rpxdock.tests.search.test_asym) test_avg_dist() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_axis_ang_cen_of_rand() (in module rpxdock.tests.test_homog) test_axis_angle_of() (in module rpxdock.tests.test_homog) test_axis_angle_of_rand() (in module rpxdock.tests.test_homog) test_bcc_neighbor_radous() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_3() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_3_exhalf() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_3_exhalf_sphere() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_3_sphere() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_6_3() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_6_3_extrahalf() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_6_3_oddlast3() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_6_3_oddlast3_extrahalf() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_6_3_oddlast3_sphere() (in module rpxdock.tests.geom.test_bcc) test_bcc_neighbors_6_3_oddlast3_sphere_extrahalf() (in module rpxdock.tests.geom.test_bcc) test_bin_get_all_data() (in module rpxdock.tests.motif.test_pairscore) test_bin_score() (in module rpxdock.tests.motif.test_pairscore) test_bunch_init() (in module rpxdock.tests.util.test_bunch) test_bunch_items() (in module rpxdock.tests.util.test_bunch) test_bunch_pickle() (in module rpxdock.tests.util.test_bunch) test_bunch_sub() (in module rpxdock.tests.util.test_bunch) test_bvh_accessors() (in module rpxdock.tests.bvh.test_bvh) test_bvh_bvh_isect7() (in module rpxdock.tests.bvh.test_bvh_nd) test_bvh_isect() (in module rpxdock.tests.bvh.test_bvh) test_bvh_isect7() (in module rpxdock.tests.bvh.test_bvh_nd) test_bvh_isect_cpp() (in module rpxdock.tests.bvh.test_bvh) test_bvh_isect_fixed() (in module rpxdock.tests.bvh.test_bvh) test_bvh_isect_fixed_range() (in module rpxdock.tests.bvh.test_bvh) test_bvh_isect_range() (in module rpxdock.tests.bvh.test_bvh) test_bvh_isect_range_ids() (in module rpxdock.tests.bvh.test_bvh) test_bvh_isect_range_lb_ub() (in module rpxdock.tests.bvh.test_bvh) test_bvh_min_cpp() (in module rpxdock.tests.bvh.test_bvh) test_bvh_min_dist() (in module rpxdock.tests.bvh.test_bvh) test_bvh_min_dist_fixed() (in module rpxdock.tests.bvh.test_bvh) test_bvh_min_dist_floormin() (in module rpxdock.tests.bvh.test_bvh) test_bvh_mindist4() (in module rpxdock.tests.bvh.test_bvh_nd) test_bvh_mindist7() (in module rpxdock.tests.bvh.test_bvh_nd) test_bvh_pickle() (in module rpxdock.tests.bvh.test_bvh) test_bvh_slide_single() (in module rpxdock.tests.bvh.test_bvh) test_bvh_slide_single_inline() (in module rpxdock.tests.bvh.test_bvh) test_bvh_slide_single_xform() (in module rpxdock.tests.bvh.test_bvh) test_bvh_slide_whole() (in module rpxdock.tests.bvh.test_bvh) TEST_bvh_test_isect() (in module rpxdock.bvh.bvh_test) TEST_bvh_test_min() (in module rpxdock.bvh.bvh_test) test_bvh_threading_isect_may_fail() (in module rpxdock.tests.bvh.test_bvh) test_bvh_threading_mindist_may_fail() (in module rpxdock.tests.bvh.test_bvh) test_cache() (in module rpxdock.tests.util.test_cache) test_cage_hier_3comp() (in module rpxdock.tests.search.test_multicomp) test_cage_hier_D3_2_onecomp_notrim() (in module rpxdock.tests.search.test_onecomp) test_cage_hier_D3_onecomp_notrim() (in module rpxdock.tests.search.test_onecomp) test_cage_hier_no_trim() (in module rpxdock.tests.search.test_multicomp) test_cage_hier_onecomp_notrim() (in module rpxdock.tests.search.test_onecomp) test_cage_hier_trim() (in module rpxdock.tests.search.test_multicomp) test_calc_dihedral_angle() (in module rpxdock.tests.test_homog) test_can_pickle() (in module rpxdock.tests.util.test_util) test_cart_hier1() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_cluster() (in module rpxdock.tests.cluster.test_cluster) test_cluster_rand() (in module rpxdock.tests.cluster.test_cluster) test_collect_pairs() (in module rpxdock.tests.bvh.test_bvh) test_collect_pairs_range() (in module rpxdock.tests.bvh.test_bvh) test_collect_pairs_range_sym() (in module rpxdock.tests.bvh.test_bvh) test_collect_pairs_simple() (in module rpxdock.tests.bvh.test_bvh) test_collect_pairs_simple_selection() (in module rpxdock.tests.bvh.test_bvh) test_compound_basic_indexing() (in module rpxdock.tests.sampling.test_compound) test_compound_get_xforms() (in module rpxdock.tests.sampling.test_compound) test_compound_ncell_dim() (in module rpxdock.tests.sampling.test_compound) test_compound_product_hier() (in module rpxdock.tests.sampling.test_compound) test_compound_single() (in module rpxdock.tests.sampling.test_compound) test_compound_split() (in module rpxdock.tests.sampling.test_compound) test_compound_split_cell() (in module rpxdock.tests.sampling.test_compound) test_compound_split_hier() (in module rpxdock.tests.sampling.test_compound) test_create_binner() (in module rpxdock.tests.xbin.test_xbin) test_create_res_pair_score() (in module rpxdock.tests.motif.test_pairscore) test_defaults() (in module rpxdock.tests.app.test_options) test_dihedral() (in module rpxdock.tests.test_homog) test_dilated_int() (in module rpxdock.tests.util.test_util) TEST_dilated_int_64bit() (in module rpxdock.util.dilated_int_test) test_dockspec() (in module rpxdock.tests.search.test_dockspec) test_eig_svd() (in module rpxdock.tests.util.test_numeric) test_expand_xforms_basic() (in module rpxdock.tests.test_homog) TEST_geom_primitive_sphere() (in module rpxdock.geom.primitive_test) TEST_geom_primitive_welzl_bounding_sphere() (in module rpxdock.geom.primitive_test) test_geom_sphere() (in module rpxdock.tests.geom.test_geom) test_geom_welzl_sphere() (in module rpxdock.tests.geom.test_geom) test_get_cli_args() (in module rpxdock.tests.app.test_options) test_grid_sym_axis() (in module rpxdock.tests.sampling.test_xform_grid) test_grid_sym_axis_flip() (in module rpxdock.tests.sampling.test_xform_grid) test_hcross() (in module rpxdock.tests.test_homog) test_helix() (in module rpxdock.tests.search.test_helix) test_hinv_rand() (in module rpxdock.tests.test_homog) test_homo_rotation_angle() (in module rpxdock.tests.test_homog) test_homo_rotation_array() (in module rpxdock.tests.test_homog) test_homo_rotation_center() (in module rpxdock.tests.test_homog) test_homo_rotation_single() (in module rpxdock.tests.test_homog) test_hstub() (in module rpxdock.tests.test_homog) test_htrans() (in module rpxdock.tests.test_homog) test_intersect_planes() (in module rpxdock.tests.test_homog) test_intersect_planes_rand() (in module rpxdock.tests.test_homog) test_is_valid_rays() (in module rpxdock.tests.test_homog) test_jagged_bin() (in module rpxdock.tests.motif.test_motif) test_jagged_bin_zero() (in module rpxdock.tests.motif.test_motif) test_karney_10() (in module rpxdock.tests.sampling.test_orientations) test_karney_by_covrad() (in module rpxdock.tests.sampling.test_orientations) test_karney_lengths_weights() (in module rpxdock.tests.sampling.test_orientations)

test_karney_oddball() (in module rpxdock.tests.sampling.test_orientations) test_key_of() (in module rpxdock.tests.xbin.test_xbin) test_key_of_pairs() (in module rpxdock.tests.xbin.test_xbin_util) test_layer_hier_3comp() (in module rpxdock.tests.search.test_multicomp) test_line_line_closest_points() (in module rpxdock.tests.test_homog) test_line_line_dist() (in module rpxdock.tests.test_homog) test_load_threads() (in module rpxdock.tests.util.test_util) test_make_cyclic_hier() (in module rpxdock.tests.search.test_cyclic) test_make_cyclic_hier_trim() (in module rpxdock.tests.search.test_cyclic) test_map_of_selected_pairs() (in module rpxdock.tests.xbin.test_xbin_util) test_miniball_cpp() (in module rpxdock.tests.geom.test_geom) test_miniball_py() (in module rpxdock.tests.geom.test_geom) test_mismatch_len() (in module rpxdock.tests.search.test_result) test_mod_phmap_inplace() (in module rpxdock.phmap.phmap) test_num_digits() (in module rpxdock.tests.util.test_util) test_ori_hier_1cell() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_ori_hier_all2() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_ori_hier_angresl() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_ori_hier_rand() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_ori_hier_rand_nside() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_OriCart1_hierarchy_product() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_orientation_cpp() (in module rpxdock.tests.sampling.test_orientations) test_pair_key() (in module rpxdock.tests.motif.test_motif) test_pair_key_ss() (in module rpxdock.tests.motif.test_motif) test_pair_score() (in module rpxdock.tests.motif.test_pairscore) test_pairdat_subset_by_aa() (in module rpxdock.tests.motif.test_pairdat) test_pairdat_subset_by_ss() (in module rpxdock.tests.motif.test_pairdat) test_pca() (in module rpxdock.tests.util.test_numeric) test_phmap() (in module rpxdock.tests.phmap.test_phmap) test_phmap_contains() (in module rpxdock.tests.phmap.test_phmap) test_phmap_cpp_roundtrip() (in module rpxdock.tests.phmap.test_phmap) test_phmap_dump_load() (in module rpxdock.tests.phmap.test_phmap) test_phmap_eq() (in module rpxdock.tests.phmap.test_phmap) test_phmap_items() (in module rpxdock.tests.phmap.test_phmap) test_phmap_items_array() (in module rpxdock.tests.phmap.test_phmap) test_pickle() (in module rpxdock.tests.xbin.test_xbin) test_place_lines_to_isect_F432() (in module rpxdock.tests.test_homog) test_place_lines_to_isect_F432_null() (in module rpxdock.tests.test_homog) test_place_lines_to_isect_onecase() (in module rpxdock.tests.test_homog) test_plug_hier() (in module rpxdock.tests.search.test_plug) test_plug_hier_trim() (in module rpxdock.tests.search.test_plug) test_plug_olig_grid() (in module rpxdock.tests.search.test_plug) test_plug_olig_hier() (in module rpxdock.tests.search.test_plug) test_point_in_plane() (in module rpxdock.tests.test_homog) test_product_hier() (in module rpxdock.tests.sampling.test_compound) test_proj_prep() (in module rpxdock.tests.test_homog) test_quat_mult() (in module rpxdock.tests.geom.test_quat) test_rand_quat() (in module rpxdock.tests.geom.test_quat) test_rand_ray() (in module rpxdock.tests.test_homog) test_ray_in_plane() (in module rpxdock.tests.test_homog) test_read_karney_orientations() (in module rpxdock.tests.sampling.test_orientations) test_remove_redundant_pdbs() (in module rpxdock.tests.motif.test_motif) test_res_pair_score_pickle() (in module rpxdock.tests.motif.test_pairscore) test_respairdat_addrots() (in module rpxdock.tests.motif.test_motif) test_result() (in module rpxdock.tests.search.test_result) test_result_attrs() (in module rpxdock.tests.search.test_result) test_result_no_body_label() (in module rpxdock.tests.search.test_result) test_result_pickle() (in module rpxdock.tests.search.test_result) test_richardson_space() (in module rpxdock.tests.rotamer.test_richardson) test_richardson_space_cache() (in module rpxdock.tests.rotamer.test_richardson) test_richardson_space_concat() (in module rpxdock.tests.rotamer.test_richardson) test_richardson_space_nchi() (in module rpxdock.tests.rotamer.test_richardson) test_rot_hier() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_rot_hier_multicell() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_rot_quat_conversion_cases() (in module rpxdock.tests.geom.test_quat) test_rot_quat_conversion_rand() (in module rpxdock.tests.geom.test_quat) test_rotcart1_hier() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_rotcart1_hier_expand_top_N() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_rotcart1_hier_multicell() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_RotCart1Hier_pickle() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_sanitize_for_pickle() (in module rpxdock.tests.util.test_util) test_selected_pairs_pos() (in module rpxdock.tests.xbin.test_xbin_util) test_slide_collect_pairs() (in module rpxdock.tests.bvh.test_bvh) test_smear_multiple() (in module rpxdock.tests.xbin.test_smear) test_smear_one() (in module rpxdock.tests.xbin.test_smear) test_smear_one_bounding() (in module rpxdock.tests.xbin.test_smear) test_smear_one_exhalf_oddori_sphere() (in module rpxdock.tests.xbin.test_smear) test_smear_one_kernel() (in module rpxdock.tests.xbin.test_smear) test_smear_one_oddori() (in module rpxdock.tests.xbin.test_smear) test_smear_one_oddori_sphere() (in module rpxdock.tests.xbin.test_smear) test_smear_two() (in module rpxdock.tests.xbin.test_smear) test_sskey_of_selected_pairs() (in module rpxdock.tests.xbin.test_xbin_util) test_ssmap_of_selected_pairs() (in module rpxdock.tests.xbin.test_xbin_util) test_summary() (in module rpxdock.tests.util.test_timer) test_sym() (in module rpxdock.tests.geom.test_sym) (in module rpxdock.tests.test_homog) test_symframes() (in module rpxdock.tests.geom.test_sym) test_timer() (in module rpxdock.tests.util.test_timer) test_tiny_subset_by_aa_pdb_removal_2pdb() (in module rpxdock.tests.motif.test_pairdat) test_tiny_subset_by_aa_pdb_removal_3pdb() (in module rpxdock.tests.motif.test_pairdat) test_top_each() (in module rpxdock.tests.search.test_result) test_xbin_covrad() (in module rpxdock.tests.xbin.test_xbin) test_xbin_covrad_ori() (in module rpxdock.tests.xbin.test_xbin) test_xbin_cpp() (in module rpxdock.tests.xbin.test_xbin) test_xform_dist() (in module rpxdock.tests.geom.test_geom) test_xform_hierarchy_ctor() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_xform_hierarchy_expand_top_N() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_xform_hierarchy_expand_top_N_nullval() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_xform_hierarchy_get_xforms() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_xform_hierarchy_get_xforms_bs() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_xform_hierarchy_plug_bug() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_xform_hierarchy_product() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_xform_hierarchy_product_zorder() (in module rpxdock.tests.sampling.test_xform_hierarchy) test_xform_round_trip() (in module rpxdock.tests.util.test_pybind_types) (in module rpxdock.util.pybind_types_test) test_xform_round_trip_2d() (in module rpxdock.tests.util.test_pybind_types) TEST_XformHash_XformHash_bt24_BCC6() (in module rpxdock.xbin.xbin_test) test_zorder() (in module rpxdock.tests.sampling.test_xform_hierarchy) testarg() (in module rpxdock.tests.search.test_asym) (in module rpxdock.tests.search.test_helix) (in module rpxdock.tests.search.test_plug) Timer (class in rpxdock.util.timer) toDict() (rpxdock.util.bunch.Bunch method) top_each() (rpxdock.search.result.Result method) total() (rpxdock.util.timer.Timer property) trim_ok() (in module rpxdock.search.basic) TwoCompEvaluatorWithTrim (class in rpxdock.search.multicomp)

U

ua() (in module rpxdock.tests.phmap.test_phmap) ub() (rpxdock.sampling.xform_hierarchy.RotHier_f4 property) (rpxdock.sampling.xform_hierarchy.RotHier_f8 property) unbunchify() (in module rpxdock.util.bunch) unpack_zorder() (in module rpxdock.sampling.xform_hierarchy)

upper() (rpxdock.geom.bcc.BCC3 property) (rpxdock.geom.bcc.BCC3_float property) (rpxdock.geom.bcc.BCC6 property) (rpxdock.geom.bcc.BCC6_float property) urandint() (in module rpxdock.tests.sampling.test_xform_hierarchy) urange() (in module rpxdock.tests.sampling.test_xform_hierarchy)

V

vals() (rpxdock.geom.bcc.BCC3 method) (rpxdock.geom.bcc.BCC3_float method) (rpxdock.geom.bcc.BCC6 method) (rpxdock.geom.bcc.BCC6_float method)

vol_lb() (rpxdock.bvh.bvh.SphereBVH_double method) vol_ub() (rpxdock.bvh.bvh.SphereBVH_double method)

W

width() (rpxdock.geom.bcc.BCC3 property) (rpxdock.geom.bcc.BCC3_float property) (rpxdock.geom.bcc.BCC6 property) (rpxdock.geom.bcc.BCC6_float property)

X

Xbin_double (class in rpxdock.xbin.xbin) Xbin_float (class in rpxdock.xbin.xbin) xform_around_dof_for_vector_target_angle() (in module rpxdock.homog) xform_dist2() (in module rpxdock.geom) xform_dist2_split() (in module rpxdock.geom.xform_dist) xform_hier_guess_sampling_covrads() (in module rpxdock.sampling.xhier_util)

xform_to_F6() (rpxdock.xbin.xbin.Xbin_double method) (rpxdock.xbin.xbin.Xbin_float method) xform_to_quat() (in module rpxdock.homog) XformHier_f4 (class in rpxdock.sampling.xform_hierarchy) XformHier_f8 (class in rpxdock.sampling.xform_hierarchy) xforms() (rpxdock.motif.pairscore.Xmap method) Xmap (class in rpxdock.motif.pairscore)

Z

ZeroDHier (class in rpxdock.sampling.compound)

zorder3coeffs() (in module rpxdock.sampling.xform_hierarchy) zorder6coeffs() (in module rpxdock.sampling.xform_hierarchy)