1 2 3#-------------------------------------------------------------------- 4from .importing import \ 5 finish_object, \ 6 load, \ 7 loadall, \ 8 load_brick, \ 9 load_callback, \ 10 load_cgo, \ 11 load_coords, \ 12 load_coordset, \ 13 load_embedded, \ 14 load_map, \ 15 load_model, \ 16 load_mtz, \ 17 load_object, \ 18 load_traj, \ 19 load_raw, \ 20 loadable, \ 21 read_mmodstr, \ 22 read_molstr, \ 23 read_sdfstr, \ 24 read_pdbstr, \ 25 read_xplorstr, \ 26 fetch, \ 27 set_session, \ 28 space 29 30#-------------------------------------------------------------------- 31from . import creating 32from .creating import \ 33 copy, \ 34 create, \ 35 extract, \ 36 fragment, \ 37 group, \ 38 gradient, \ 39 isodot, \ 40 isolevel, \ 41 isomesh, \ 42 isosurface, \ 43 join_states, \ 44 map_generate, \ 45 map_new, \ 46 pseudoatom, \ 47 set_raw_alignment, \ 48 slice_new, \ 49 symexp, \ 50 ramp_new, \ 51 ramp_update, \ 52 ungroup, \ 53 volume 54 55#-------------------------------------------------------------------- 56from .colorramping import \ 57 volume_ramp_new, \ 58 volume_panel, \ 59 volume_color 60 61#-------------------------------------------------------------------- 62from . import commanding 63from .commanding import \ 64 async_, \ 65 cls, \ 66 delete, \ 67 do, \ 68 log, \ 69 log_close, \ 70 log_open, \ 71 quit, \ 72 resume, \ 73 splash, \ 74 reinitialize, \ 75 sync 76 77#-------------------------------------------------------------------- 78from . import controlling 79from .controlling import \ 80 button, \ 81 config_mouse, \ 82 mouse, \ 83 mask, \ 84 order, \ 85 set_key, \ 86 unmask, \ 87 edit_mode 88 89#-------------------------------------------------------------------- 90from .querying import \ 91 angle, \ 92 auto_measure, \ 93 centerofmass, \ 94 count_atoms, \ 95 count_frames, \ 96 count_states, \ 97 count_discrete, \ 98 dist, \ 99 dihedral, \ 100 distance, \ 101 find_pairs, \ 102 get_angle, \ 103 get_area, \ 104 get_assembly_ids, \ 105 get_bonds, \ 106 get_chains, \ 107 get_collada, \ 108 get_color_index, \ 109 get_color_indices, \ 110 get_object_color_index, \ 111 get_object_list, \ 112 get_object_settings,\ 113 get_object_state, \ 114 get_color_tuple, \ 115 get_atom_coords, \ 116 get_coords, \ 117 get_coordset, \ 118 get_dihedral, \ 119 get_distance, \ 120 get_drag_object_name, \ 121 get_extent, \ 122 get_gltf, \ 123 get_idtf, \ 124 get_modal_draw, \ 125 get_model, \ 126 get_movie_locked, \ 127 get_movie_length, \ 128 get_names, \ 129 get_names_of_type, \ 130 get_legal_name, \ 131 get_unused_name, \ 132 get_object_matrix, \ 133 get_object_ttt, \ 134 get_mtl_obj, \ 135 get_phipsi, \ 136 get_position, \ 137 get_povray, \ 138 get_raw_alignment, \ 139 get_renderer, \ 140 get_selection_state,\ 141 get_symmetry, \ 142 get_title, \ 143 get_type, \ 144 get_version, \ 145 get_volume_field, \ 146 get_volume_histogram, \ 147 get_vrml, \ 148 id_atom, \ 149 identify, \ 150 index, \ 151 overlap, \ 152 pi_interactions, \ 153 phi_psi 154 155#-------------------------------------------------------------------- 156from .selecting import \ 157 deselect, \ 158 indicate, \ 159 select, \ 160 select_list, \ 161 pop 162 163#-------------------------------------------------------------------- 164from . import exporting 165from .exporting import \ 166 copy_image, \ 167 cache, \ 168 get_str, \ 169 get_bytes, \ 170 get_pdbstr, \ 171 get_cifstr, \ 172 get_session, \ 173 get_fastastr, \ 174 multifilesave, \ 175 multifilenamegen, \ 176 multisave, \ 177 png, \ 178 save 179 180#-------------------------------------------------------------------- 181from . import editing 182from .editing import \ 183 add_bond, \ 184 alter, \ 185 alter_list, \ 186 alter_state, \ 187 alphatoall, \ 188 attach, \ 189 bond, \ 190 copy_to, \ 191 cycle_valence, \ 192 deprotect, \ 193 drag, \ 194 dss, \ 195 edit, \ 196 fix_chemistry, \ 197 flag, \ 198 fuse, \ 199 get_editor_scheme, \ 200 h_add, \ 201 h_fill, \ 202 h_fix, \ 203 invert, \ 204 iterate, \ 205 iterate_state, \ 206 map_set, \ 207 map_set_border, \ 208 map_double, \ 209 map_halve, \ 210 map_trim, \ 211 matrix_copy, \ 212 matrix_reset, \ 213 mse2met, \ 214 protect, \ 215 push_undo, \ 216 rebond, \ 217 reference, \ 218 redo, \ 219 remove, \ 220 remove_picked, \ 221 rename, \ 222 replace, \ 223 rotate, \ 224 sculpt_purge, \ 225 sculpt_deactivate, \ 226 sculpt_activate, \ 227 sculpt_iterate, \ 228 set_dihedral, \ 229 set_name, \ 230 set_geometry, \ 231 set_object_color, \ 232 set_object_ttt, \ 233 set_state_order, \ 234 set_symmetry, \ 235 set_title, \ 236 smooth, \ 237 sort, \ 238 split_chains, \ 239 split_states, \ 240 symmetry_copy, \ 241 torsion, \ 242 transform_object, \ 243 transform_selection,\ 244 translate, \ 245 translate_atom, \ 246 unbond, \ 247 undo, \ 248 uniquify, \ 249 unpick, \ 250 update, \ 251 valence, \ 252 vdw_fit 253 254from .editor import \ 255 fab 256 257from .computing import \ 258 clean 259 260matrix_transfer = matrix_copy # legacy 261 262#-------------------------------------------------------------------- 263 264from .externing import \ 265 cd, \ 266 ls, \ 267 paste, \ 268 pwd, \ 269 system 270 271#-------------------------------------------------------------------- 272from . import wizarding 273from .wizarding import \ 274 get_wizard, \ 275 get_wizard_stack, \ 276 refresh_wizard, \ 277 replace_wizard, \ 278 set_wizard, \ 279 set_wizard_stack, \ 280 dirty_wizard, \ 281 wizard 282 283#-------------------------------------------------------------------- 284from .fitting import \ 285 align, \ 286 alignto, \ 287 extra_fit, \ 288 fit, \ 289 super, \ 290 rms, \ 291 rms_cur, \ 292 intra_fit, \ 293 intra_rms, \ 294 intra_rms_cur, \ 295 cealign, \ 296 pair_fit 297 298#-------------------------------------------------------------------- 299# ARE ALL OF THESE UNUSED AND/OR DEPRECATED (?) 300from .preset import \ 301 simple, \ 302 technical, \ 303 pretty, \ 304 publication 305 306#-------------------------------------------------------------------- 307from .morphing import \ 308 morph 309 310#-------------------------------------------------------------------- 311from . import moving 312from .moving import \ 313 madd, \ 314 mcopy, \ 315 mdelete, \ 316 mmove, \ 317 minsert, \ 318 mset, \ 319 mclear, \ 320 mdo, \ 321 mappend, \ 322 mmatrix, \ 323 mdump, \ 324 accept, \ 325 decline, \ 326 mpng, \ 327 mview, \ 328 forward, \ 329 backward, \ 330 rewind, \ 331 middle, \ 332 ending, \ 333 mplay, \ 334 mtoggle, \ 335 mstop, \ 336 mpng, \ 337 frame, \ 338 get_movie_playing, \ 339 set_frame, \ 340 get_state, \ 341 get_frame 342 343#-------------------------------------------------------------------- 344from . import viewing 345from .viewing import \ 346 show_as, \ 347 bg_color, \ 348 bg_colour, \ 349 cartoon, \ 350 capture, \ 351 clip, \ 352 color, \ 353 color_deep, \ 354 colour, \ 355 del_colorection, \ 356 dirty, \ 357 disable, \ 358 draw, \ 359 enable, \ 360 full_screen, \ 361 get_colorection, \ 362 get_view, \ 363 get_viewport, \ 364 get_vis, \ 365 get_scene_list, \ 366 hide, \ 367 label, \ 368 label2, \ 369 load_png, \ 370 meter_reset, \ 371 move, \ 372 orient, \ 373 origin, \ 374 center, \ 375 ray, \ 376 rebuild, \ 377 recolor, \ 378 recolour, \ 379 refresh, \ 380 reset, \ 381 rock, \ 382 scene, \ 383 scene_order, \ 384 scene_recall_message, \ 385 set_color, \ 386 set_colour, \ 387 set_colorection, \ 388 set_vis, \ 389 set_view, \ 390 show, \ 391 spectrum, \ 392 stereo, \ 393 toggle, \ 394 turn, \ 395 view, \ 396 viewport, \ 397 window, \ 398 zoom 399 400#-------------------------------------------------------------------- 401from . import setting 402from .setting import \ 403 set, \ 404 set_bond, \ 405 get_bond, \ 406 get, \ 407 unset, \ 408 unset_bond, \ 409 unset_deep, \ 410 get_setting_boolean, \ 411 get_setting_int, \ 412 get_setting_float, \ 413 get_setting_float as get_setting_legacy, \ 414 get_setting_tuple, \ 415 get_setting_updates, \ 416 get_setting_text 417 418#-------------------------------------------------------------------- 419from .parsing import \ 420 run, \ 421 spawn 422 423#-------------------------------------------------------------------- 424from . import helping 425from .helping import \ 426 abort, \ 427 api, \ 428 show_help, \ 429 help, \ 430 help_setting, \ 431 commands 432 433#-------------------------------------------------------------------- 434from .experimenting import \ 435 check, \ 436 dump, \ 437 get_bond_print, \ 438 fast_minimize, \ 439 mem, \ 440 minimize, \ 441 spheroid, \ 442 focal_blur, \ 443 callout, \ 444 desaturate, \ 445 test 446 447from .internal import \ 448 download_chem_comp, \ 449 file_read 450 451from .util import \ 452 get_sasa_relative 453 454from .stereochemistry import \ 455 assign_stereo 456 457#-------------------------------------------------------------------- 458# Modules which contain programs used explicity as "module.xxx" 459 460from . import util 461from . import movie 462from . import gui 463