if __name__=='pymol.setting':
import traceback
import string
import types
import selector
from shortcut import Shortcut
import cmd
from cmd import _cmd,lock,lock_attempt,unlock,QuietException, \
_feedback,fb_module,fb_mask, \
DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
from cmd import is_string
import re
boolean_type = 1
int_type = 2
float_type = 3
float3_type = 4
self = cmd
class SettingIndex:
bonding_vdw_cutoff = 0
min_mesh_spacing = 1
dot_density = 2
dot_mode = 3
solvent_radius = 4
sel_counter = 5
bg_rgb = 6
ambient = 7
direct = 8
reflect = 9
light = 10
power = 11
antialias = 12
cavity_cull = 13
gl_ambient = 14
single_image = 15
movie_delay = 16
ribbon_power = 17
ribbon_power_b = 18
ribbon_sampling = 19
ribbon_radius = 20
stick_radius = 21
hash_max = 22
orthoscopic = 23
spec_reflect = 24
spec_power = 25
sweep_angle = 26
sweep_speed = 27
dot_hydrogens = 28
dot_radius = 29
ray_trace_frames = 30
cache_frames = 31
trim_dots = 32
cull_spheres = 33
test1 = 34
test2 = 35
surface_best = 36
surface_normal = 37
surface_quality = 38
surface_proximity = 39
normal_workaround = 40
stereo_angle = 41
stereo_shift = 42
line_smooth = 43
line_width = 44
half_bonds = 45
stick_quality = 46
stick_overlap = 47
stick_nub = 48
all_states = 49
pickable = 50
auto_show_lines = 51
idle_delay = 52
no_idle = 53
fast_idle = 54
slow_idle = 55
rock_delay = 56
dist_counter = 57
dash_length = 58
dash_gap = 59
auto_zoom = 60
overlay = 61
text = 62
button_mode = 63
valence = 64
nonbonded_size = 65
label_color = 66
ray_trace_fog = 67
spheroid_scale = 68
ray_trace_fog_start = 69
spheroid_smooth = 70
spheroid_fill = 71
auto_show_nonbonded = 72
cache_display = 73
mesh_radius = 74
backface_cull = 75
gamma = 76
dot_width = 77
auto_show_selections = 78
auto_hide_selections = 79
selection_width = 80
selection_overlay = 81
static_singletons = 82
max_triangles = 83
depth_cue = 84
specular = 85
shininess = 86
sphere_quality = 87
fog = 88
isomesh_auto_state = 89
mesh_width = 90
cartoon_sampling = 91
cartoon_loop_radius = 92
cartoon_loop_quality = 93
cartoon_power = 94
cartoon_power_b = 95
cartoon_rect_length = 96
cartoon_rect_width = 97
internal_gui_width = 98
internal_gui = 99
cartoon_oval_length = 100
cartoon_oval_width = 101
cartoon_oval_quality = 102
cartoon_tube_radius = 103
cartoon_tube_quality = 104
cartoon_debug = 105
ribbon_width = 106
dash_width = 107
dash_radius = 108
cgo_ray_width_scale = 109
line_radius = 110
cartoon_round_helices = 111
cartoon_refine_normals = 112
cartoon_flat_sheets = 113
cartoon_smooth_loops = 114
cartoon_dumbbell_length = 115
cartoon_dumbbell_width = 116
cartoon_dumbbell_radius = 117
cartoon_fancy_helices = 118
cartoon_fancy_sheets = 119
ignore_pdb_segi = 120
ribbon_throw = 121
cartoon_throw = 122
cartoon_refine = 123
cartoon_refine_tips = 124
cartoon_discrete_colors = 125
normalize_ccp4_maps = 126
surface_poor = 127
internal_feedback = 128
cgo_line_width = 129
cgo_line_radius = 130
logging = 131
robust_logs = 132
log_box_selections = 133
log_conformations = 134
valence_size = 135
valence_default = 135
surface_miserable = 136
ray_opaque_background = 137
transparency = 138
ray_texture = 139
ray_texture_settings = 140
suspend_updates = 141
full_screen = 142
surface_mode = 143
surface_color = 144
mesh_mode = 145
mesh_color = 146
auto_indicate_flags = 147
surface_debug = 148
ray_improve_shadows = 149
smooth_color_triangle = 150
ray_default_renderer = 151
field_of_view = 152
reflect_power = 153
preserve_chempy_ids = 154
sphere_scale = 155
two_sided_lighting = 156
secondary_structure = 157
auto_remove_hydrogens = 158
raise_exceptions = 159
stop_on_exceptions = 160
sculpting = 161
auto_sculpt = 162
sculpt_vdw_scale = 163
sculpt_vdw_scale14 = 164
sculpt_vdw_weight = 165
sculpt_vdw_weight14 = 166
sculpt_bond_weight = 167
sculpt_angl_weight = 168
sculpt_pyra_weight = 169
sculpt_plan_weight = 170
sculpting_cycles = 171
sphere_transparency = 172
sphere_color = 173
sculpt_field_mask = 174
sculpt_hb_overlap = 175
sculpt_hb_overlap_base = 176
legacy_vdw_radii = 177
sculpt_memory = 178
connect_mode = 179
cartoon_cylindrical_helices = 180
cartoon_helix_radius = 181
connect_cutoff = 182
sculpt_line_weight = 184
fit_iterations = 185
fit_tolerance = 186
batch_prefix = 187
stereo_mode = 188
cgo_sphere_quality = 189
pdb_literal_names = 190
wrap_output = 191
fog_start = 192
state = 193
frame = 194
ray_shadows = 195
ray_shadow = 195
ribbon_trace_atoms = 196
security = 197
stick_transparency = 198
ray_transparency_shadows = 199
session_version_check = 200
ray_transparency_specular = 201
stereo_double_pump_mono = 202
sphere_solvent = 203
mesh_quality = 204
mesh_solvent = 205
dot_solvent = 206
ray_shadow_fudge = 207
ray_triangle_fudge = 208
debug_pick = 209
dot_color = 210
mouse_limit = 211
mouse_scale = 212
transparency_mode = 213
clamp_colors = 214
pymol_space_max_red = 215
pymol_space_max_green = 216
pymol_space_max_blue = 217
pymol_space_min_factor = 218
roving_origin = 219
roving_lines = 220
roving_sticks = 221
roving_spheres = 222
roving_labels = 223
roving_delay = 224
roving_selection = 225
roving_byres = 226
roving_ribbon = 227
roving_cartoon = 228
roving_polar_contacts = 229
roving_polar_cutoff = 230
roving_nonbonded = 231
float_labels = 232
roving_detail = 233
roving_nb_spheres = 234
ribbon_color = 235
cartoon_color = 236
ribbon_smooth = 237
auto_color = 238
ray_interior_color = 240
cartoon_highlight_color = 241
coulomb_units_factor = 242
coulomb_dielectric = 243
ray_interior_shadows = 244
ray_interior_texture = 245
roving_map1_name = 246
roving_map2_name = 247
roving_map3_name = 248
roving_map1_level = 249
roving_map2_level = 250
roving_map3_level = 251
roving_isomesh = 252
roving_isosurface = 253
scenes_changed = 254
gaussian_b_adjust = 255
pdb_standard_order = 256
cartoon_smooth_first = 257
cartoon_smooth_last = 258
cartoon_smooth_cycles = 259
cartoon_flat_cycles = 260
max_threads = 261
show_progress = 262
use_display_lists = 263
cache_memory = 264
simplify_display_lists = 265
retain_order = 266
pdb_hetatm_sort = 267
pdb_use_ter_records = 268
cartoon_trace_atoms = 269
ray_oversample_cutoff = 270
gaussian_resolution = 271
gaussian_b_floor = 272
sculpt_nb_interval = 273
sculpt_tors_weight = 274
sculpt_tors_tolerance = 275
stick_ball = 276
stick_ball_ratio = 277
stick_fixed_radius = 278
cartoon_transparency = 279
dash_round_ends = 280
h_bond_max_angle = 281
h_bond_cutoff_center = 282
h_bond_cutoff_edge = 283
h_bond_power_a = 284
h_bond_power_b = 285
h_bond_cone = 286
ss_helix_psi_target = 287
ss_helix_psi_include = 288
ss_helix_psi_exclude = 289
ss_helix_phi_target = 290
ss_helix_phi_include = 291
ss_helix_phi_exclude = 292
ss_strand_psi_target = 293
ss_strand_psi_include = 294
ss_strand_psi_exclude = 295
ss_strand_phi_target = 296
ss_strand_phi_include = 297
ss_strand_phi_exclude = 298
movie_loop = 299
pdb_retain_ids = 300
pdb_no_end_record = 301
cgo_dot_width = 302
cgo_dot_radius = 303
defer_updates = 304
normalize_o_maps = 305
swap_dsn6_bytes = 306
pdb_insertions_go_first = 307
roving_origin_z = 308
roving_origin_z_cushion = 309
specular_intensity = 310
overlay_lines = 311
ray_transparency_spec_cut = 312
internal_prompt = 313
normalize_grd_maps = 314
ray_blend_colors = 315
ray_blend_red = 316
ray_blend_green = 317
ray_blend_blue = 318
png_screen_gamma = 319
png_file_gamma = 320
editor_label_fragments = 321
internal_gui_control_size = 322
auto_dss = 323
transparency_picking_mode = 324
virtual_trackball = 325
pdb_reformat_names_mode = 326
ray_pixel_scale = 327
label_font_id = 328
pdb_conect_all = 329
button_mode_name = 330
surface_type = 331
dot_normals = 332
session_migration = 333
mesh_normals = 334
mesh_type = 335
dot_lighting = 336
mesh_lighting = 337
surface_solvent = 338
triangle_max_passes = 339
ray_interior_reflect = 340
internal_gui_mode = 341
surface_carve_selection = 342
surface_carve_state = 343
surface_carve_cutoff = 344
surface_clear_selection = 345
surface_clear_state = 346
surface_clear_cutoff = 347
surface_trim_cutoff = 348
surface_trim_factor = 349
ray_max_passes = 350
active_selections = 351
ray_transparency_contrast = 352
seq_view = 353
mouse_selection_mode = 354
seq_view_label_spacing = 355
seq_view_label_start = 356
seq_view_format = 357
seq_view_location = 358
seq_view_overlay = 359
auto_classify_atoms = 360
cartoon_nucleic_acid_mode = 361
seq_view_color = 362
seq_view_label_mode = 363
surface_ramp_above_mode = 364
stereo = 365
wizard_prompt_mode = 366
coulomb_cutoff = 367
slice_track_camera = 368
slice_height_scale = 369
slice_height_map = 370
slice_grid = 371
slice_dynamic_grid = 372
slice_dynamic_grid_resolution = 373
pdb_insure_orthogonal = 374
ray_direct_shade = 375
stick_color = 376
cartoon_putty_radius = 377
cartoon_putty_quality = 378
cartoon_putty_scale_min = 379
cartoon_putty_scale_max = 380
cartoon_putty_scale_power = 381
cartoon_putty_range = 382
cartoon_side_chain_helper = 383
surface_optimize_subsets = 384
multiplex = 385
texture_fonts = 386
pqr_no_chain_id = 387
animation = 388
animation_duration = 389
scene_animation = 390
line_stick_helper = 391
ray_orthoscopic = 392
ribbon_side_chain_helper = 393
selection_width_max = 394
selection_width_scale = 395
scene_current_name = 396
presentation = 397
presentation_mode = 398
pdb_truncate_residue_name = 399
scene_loop = 400
sweep_mode = 401
sweep_phase = 402
scene_restart_movie_delay = 403
mouse_restart_movie_delay = 404
angle_size = 405
angle_label_position = 406
dihedral_size = 407
dihedral_label_position = 408
defer_builds_mode = 409
seq_view_discrete_by_state = 410
scene_animation_duration = 411
wildcard = 412
atom_name_wildcard = 413
ignore_case = 414
presentation_auto_quit = 415
editor_auto_dihedral = 416
presentation_auto_start = 417
validate_object_names = 418
auto_show_spheres = 420
sphere_mode = 421
sphere_point_max_size = 422
sphere_point_size = 423
pdb_honor_model_number = 424
rank_assisted_sorts = 425
ribbon_nucleic_acid_mode = 426
cartoon_ring_mode = 427
cartoon_ring_width = 428
cartoon_ring_color = 429
cartoon_ring_finder = 430
cartoon_tube_cap = 431
cartoon_loop_cap = 432
nvidia_bugs = 433
image_dots_per_inch = 434
opaque_background = 435
draw_frames = 436
show_alpha_checker = 437
matrix_mode = 438
editor_auto_origin = 439
session_file = 440
cgo_transparency = 441
legacy_mouse_zoom = 442
auto_number_selections = 443
sculpt_vdw_vis_mode = 444
sculpt_vdw_vis_min = 445
sculpt_vdw_vis_mid = 446
sculpt_vdw_vis_max = 447
cartoon_ladder_mode = 448
cartoon_ladder_radius = 449
cartoon_ladder_color = 450
cartoon_nucleic_acid_color = 451
cartoon_ring_transparency = 452
label_size = 453
spec_direct = 454
light_count = 455
light2 = 456
light3 = 457
hide_underscore_names = 458
selection_round_points = 459
distance_exclusion = 460
h_bond_exclusion = 461
label_shadow_mode = 462
light4 = 463
light5 = 464
light6 = 465
light7 = 466
label_outline_color = 467
ray_trace_mode = 468
ray_trace_gain = 469
selection_visible_only = 470
label_position = 471
ray_trace_depth_factor = 472
ray_trace_slope_factor = 473
ray_trace_disco_factor = 474
ray_shadow_decay_factor = 475
ray_interior_mode = 476
ray_legacy_lighting = 477
sculpt_auto_center = 478
pdb_discrete_chains = 479
pdb_unbond_cations = 480
sculpt_tri_scale = 481
sculpt_tri_weight = 482
sculpt_tri_min = 483
sculpt_tri_max = 484
sculpt_tri_mode = 485
pdb_echo_tags = 486
connect_bonded = 487
spec_direct_power = 488
light8 = 489
light9 = 490
ray_shadow_decay_range = 491
spec_count = 492
sculpt_min_scale = 493
sculpt_min_weight = 494
sculpt_min_min = 495
sculpt_min_max = 496
sculpt_max_scale = 497
sculpt_max_weight = 498
sculpt_max_min = 499
sculpt_max_max = 500
surface_circumscribe = 501
sculpt_avd_weight = 502
sculpt_avd_gap = 503
sculpt_avd_range = 504
sculpt_avd_excl = 505
async_builds = 506
fetch_path = 507
cartoon_ring_radius = 508
ray_color_ramps = 509
ray_hint_camera = 510
ray_hint_shadow = 511
stick_valence_scale = 512
seq_view_alignment = 513
seq_view_unaligned_mode = 514
seq_view_unaligned_color = 515
seq_view_fill_char = 516
seq_view_fill_color = 517
seq_view_label_color = 518
surface_carve_normal_cutoff = 519
trace_atoms_mode = 520
session_changed = 521
ray_clip_shadows = 522
mouse_wheel_scale = 523
nonbonded_transparency = 524
ray_spec_local = 525
line_color = 526
ray_label_specular = 527
mesh_skip = 528
label_digits = 529
label_distance_digits = 530
label_angle_digits = 531
label_dihedral_digits = 532
surface_negative_visible = 533
surface_negative_color = 534
mesh_negative_visible = 535
mesh_negative_color = 536
group_auto_mode = 537
group_full_member_names = 538
gradient_max_length = 539
gradient_min_length = 540
gradient_min_slope = 541
gradient_normal_min_dot = 542
gradient_step_size = 543
gradient_spacing = 544
gradient_symmetry = 545
ray_trace_color = 546
group_arrow_prefix = 547
suppress_hidden = 548
session_compression = 549
movie_fps = 550
ray_transparency_oblique = 551
ray_trace_trans_cutoff = 552
ray_trace_persist_cutoff = 553
ray_transparency_oblique_power = 554
ray_scatter = 555
h_bond_from_proton = 556
auto_copy_images = 557
moe_separate_chains = 558
transparency_global_sort = 559
hide_long_bonds = 560
auto_rename_duplicate_objects = 561
pdb_hetatm_guess_valences = 562
ellipsoid_quality = 563
cgo_ellipsoid_quality = 564
movie_animate_by_frame = 565
ramp_blend_nearby_colors = 566
auto_defer_builds = 567
ellipsoid_probability = 568
ellipsoid_scale = 569
ellipsoid_color = 570
ellipsoid_transparency = 571
movie_rock = 572
cache_mode = 573
dash_color = 574
angle_color = 575
dihedral_color = 576
grid_mode = 577
cache_max = 578
grid_slot = 579
grid_max = 580
cartoon_putty_transform = 581
rock = 582
cone_quality = 583
pdb_formal_charges = 584
ati_bugs = 585
geometry_export_mode = 586
mouse_grid = 587
mesh_cutoff = 588
mesh_carve_selection = 589
mesh_carve_state = 590
mesh_carve_cutoff = 591
mesh_clear_selection = 592
mesh_clear_state = 593
mesh_clear_cutoff = 594
mesh_grid_max = 595
session_cache_optimize = 596
setting_sc = Shortcut(SettingIndex.__dict__.keys())
index_list = []
name_dict = {}
name_list = SettingIndex.__dict__.keys()
name_list = filter(lambda x:x[0]!='_',name_list)
name_list.sort()
tmp_list = map(lambda x:(getattr(SettingIndex,x),x),name_list)
for a in tmp_list:
name_dict[a[0]]=a[1]
index_list.append(a[0])
boolean_dict = {
"true" : 1,
"false": 0,
"on" : 1,
"off" : 0,
"1" : 1,
"0" : 0,
"1.0" : 1,
"0.0" : 0,
}
boolean_sc = Shortcut(boolean_dict.keys())
quote_strip_re = re.compile("^\'.*\'$|^\".*\"$")
def _get_index(name):
result = setting_sc.interpret(name)
if is_string(result):
if hasattr(SettingIndex,result):
return getattr(SettingIndex,result)
else:
return -1
else:
return -1
def _get_name(index):
return name_dict.get(index,"")
def get_index_list():
return index_list
def get_name_list():
return name_list
def dump_tuples():
for idx in range(581):
print _get_name(idx), cmd.get_setting_tuple(idx)
def set_bond(name, value, selection1, selection2=None,
state=0, updates=1, log=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"set_bond" changes per-bond settings for all bonds which exist
between two selections of atoms.
USAGE
set_bond name, value, selection1 [, selection2 ]
ARGUMENTS
name = string: name of the setting
value = string: new value to use
selection1 = string: first set of atoms
selection2 = string: seconds set of atoms {default: (selection1)}
EXAMPLE
set_bond stick_transparency, 0.7, */n+c+ca+o
NOTES
The following per-bond settings are currently implemented. Others
may seem to be recognized but will currently have no effect when
set at the per-bond level.
* valence
* line_width
* line_color
* stick_radius
* stick_color
* stick_transparency
Note that if you attempt to use the "set" command with a per-bond
setting over a selection of atoms, the setting change will appear
to take, but no change will be observed.
PYMOL API
cmd.set_bond ( string name, string value,
string selection1,
string selection2,
int state, int updates, log=0, quiet=1)
'''
r = DEFAULT_ERROR
selection1 = str(selection1)
if selection2 == None:
selection2 = selection1
if log:
if ',' in str(value):
value = str(cmd.safe_list_eval(str(value)))
if len(selection2):
cmd.log("set_bond %s,%s,%s\n"%(str(name),str(value),str(selection1),str(selection2)))
else:
cmd.log("set_bond %s,%s\n"%(str(name),str(value),str(selection1)))
index = _get_index(str(name))
if(index<0):
print "Error: unknown setting '%s'."%name
raise QuietException
else:
try:
_self.lock(_self)
type = _cmd.get_setting_tuple(_self._COb,int(index),str(""),int(-1))[0]
if type==None:
print "Error: unable to get setting type."
raise QuietException
try:
if type==1:
handled = 0
if boolean_sc.interpret(str(value))==None:
try:
if not (float(value)==0.0):
handled = 1
v = (1,)
else:
handled = 1
v = (0,)
except:
pass
if not handled:
v = (boolean_dict[
boolean_sc.auto_err(
str(value),"boolean")],)
elif type==2:
if boolean_sc.has_key(str(value)):
v = (boolean_dict[
boolean_sc.auto_err(
str(value),"boolean")],)
else:
v = (int(value),)
elif type==3:
if boolean_sc.has_key(str(value)):
v = (float(boolean_dict[
boolean_sc.auto_err(
str(value),"boolean")]),)
else:
v = (float(value),)
elif type==4:
if is_string(value):
if not ',' in value:
v = string.split(value)
else:
v = eval(value)
else:
v = value
v = (float(v[0]),float(v[1]),float(v[2]))
elif type==5:
v = (str(value),)
elif type==6:
vl = str(value)
if quote_strip_re.search(vl)!=None:
vl=vl[1:-1]
v = (vl,)
v = (type,v)
if len(selection1):
selection1=selector.process(selection1)
if len(selection2):
selection2=selector.process(selection2)
r = _cmd.set_bond(_self._COb,int(index),v,
"("+selection1+")","("+selection2+")",
int(state)-1,int(quiet),
int(updates))
except:
traceback.print_exc()
if(_feedback(fb_module.cmd,fb_mask.debugging,_self)):
traceback.print_exc()
print "Error: unable to read setting value."
raise QuietException
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def set(name, value=1, selection='', state=0, updates=1, log=0,
quiet=1,_self=cmd):
'''
DESCRIPTION
"set" changes global, object, object-state, or per-atom settings.
USAGE
set name [,value [,selection [,state ]]]
ARGUMENTS
name = string: setting name
value = string: a setting value {default: 1}
selection = string: name-pattern or selection-expression
{default:'' (global)}
state = a state number {default: 0 (per-object setting)}
EXAMPLES
set orthoscopic
set line_width, 3
set surface_color, white, 1hpv
set sphere_scale, 0.5, elem C
NOTES
The default behavior (with a blank selection) is global. If the
selection is "all", then the setting entry in each individual
object will be changed. Likewise, for a given object, if state is
zero, then the object setting will be modified. Otherwise, the
setting for the indicated state within the object will be
modified.
If a selection is provided as opposed to an object name, then the
atomic setting entries are modified.
The following per-atom settings are currently implemented. Others
may seem to be recognized but will have no effect when set on a
per-atom basis.
* sphere_color
* surface_color
* mesh_color
* label_color
* dot_color
* cartoon_color
* ribbon_color
* transparency (for surfaces)
* sphere_transparency
Note that if you attempt to use the "set" command with a per-bond
setting over a selection of atoms, the setting change will appear
to take, but no change will be observed. Please use the
"set_bond" command for per-bond settings.
PYMOL API
cmd.set(string name, string value, string selection, int state,
int updates, int quiet)
SEE ALSO
get, set_bond
'''
r = DEFAULT_ERROR
selection = str(selection)
if log:
if ',' in str(value):
value = str(cmd.safe_list_eval(str(value)))
if len(selection):
cmd.log("set %s,%s,%s\n"%(str(name),str(value),str(selection)))
else:
cmd.log("set %s,%s\n"%(str(name),str(value)))
index = _get_index(str(name))
if(index<0):
print "Error: unknown setting '%s'."%name
raise QuietException
else:
try:
_self.lock(_self)
type = _cmd.get_setting_tuple(_self._COb,int(index),str(""),int(-1))[0]
if type==None:
print "Error: unable to get setting type."
raise QuietException
try:
if type==1:
handled = 0
if boolean_sc.interpret(str(value))==None:
try:
if not (float(value)==0.0):
handled = 1
v = (1,)
else:
handled = 1
v = (0,)
except:
pass
if not handled:
v = (boolean_dict[
boolean_sc.auto_err(
str(value),"boolean")],)
elif type==2:
if boolean_sc.has_key(str(value)):
v = (boolean_dict[
boolean_sc.auto_err(
str(value),"boolean")],)
else:
v = (int(value),)
elif type==3:
if boolean_sc.has_key(str(value)):
v = (float(boolean_dict[
boolean_sc.auto_err(
str(value),"boolean")]),)
else:
v = (float(value),)
elif type==4:
if is_string(value):
if not ',' in value:
v = string.split(value)
else:
v = eval(value)
else:
v = value
v = (float(v[0]),float(v[1]),float(v[2]))
elif type==5:
v = (str(value),)
elif type==6:
vl = str(value)
if quote_strip_re.search(vl)!=None:
vl=vl[1:-1]
v = (vl,)
v = (type,v)
if len(selection):
selection=selector.process(selection)
r = _cmd.set(_self._COb,int(index),v,
selection,
int(state)-1,int(quiet),
int(updates))
except:
traceback.print_exc()
if(_feedback(fb_module.cmd,fb_mask.debugging,_self)):
traceback.print_exc()
print "Error: unable to read setting value."
raise QuietException
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def unset(name, selection='', state=0, updates=1, log=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"unset" clear non-global settings and zeros out global settings.
USAGE
unset name [,selection [,state ]]
EXAMPLE
unset orthoscopic
unset surface_color, 1hpv
unset sphere_scale, elem C
NOTES
If selection is not provided, unset changes the named global
setting to a zero or off value.
If a selection is provided, then "unset" undefines per-object,
per-state, or per-atom settings.
PYMOL API
cmd.unset(string name, string selection, int state, int updates,
int log)
SEE ALSO
set, set_bond
'''
r = DEFAULT_ERROR
selection = str(selection)
if log:
if(len(selection)):
cmd.log("unset %s,%s\n"%(str(name),str(selection)))
else:
cmd.log("set %s,0\n"%(str(name)))
index = _get_index(str(name))
if(index<0):
print "Error: unknown setting '%s'."%name
raise QuietException
else:
if not len(selection):
r = set(name,0,'',state,updates,log=0,quiet=quiet,_self=_self)
else:
try:
_self.lock(_self)
try:
selection = selector.process(selection)
r = _cmd.unset(_self._COb,int(index),selection,
int(state)-1,int(quiet),
int(updates))
except:
if(_feedback(fb_module.cmd,fb_mask.debugging,_self)):
traceback.print_exc()
raise QuietException
print "Error: unable to unset setting value."
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def unset_bond(name,selection1,selection2=None,state=0,updates=1,log=0,quiet=1,_self=cmd):
'''
DESCRIPTION
"unset_bond" removes a per-bond setting for a given set of bonds.
USAGE
unset name [,selection [, selection [,state ]]]
'''
r = DEFAULT_ERROR
selection1 = str(selection1)
if selection2 == None:
selection2 = selection1
selection2 = str(selection2)
if log:
if(len(selection2)):
cmd.log("unset %s,%s\n"%(str(name),str(selection1),str(selection2)))
else:
cmd.log("set %s,%s\n"%(str(name),str(selection1)))
index = _get_index(str(name))
if(index<0):
print "Error: unknown setting '%s'."%name
raise QuietException
else:
try:
_self.lock(_self)
try:
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
r = _cmd.unset_bond(_self._COb,int(index),selection1,selection2,
int(state)-1,int(quiet),
int(updates))
except:
if(_feedback(fb_module.cmd,fb_mask.debugging,_self)):
traceback.print_exc()
raise QuietException
print "Error: unable to unset setting value."
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def get_setting(name,object='',state=0,_self=cmd):
r = DEFAULT_ERROR
if is_string(name):
i = _get_index(name)
else:
i = int(name)
if i<0:
print "Error: unknown setting"
raise QuietException
try:
_self.lock(_self)
r = _cmd.get_setting_tuple(_self._COb,i,str(object),int(state)-1)
typ = r[0]
if typ<3:
value = int(r[1][0])
elif typ<4:
value = r[1][0]
elif typ<5:
value = r[1]
else:
value = r[1]
finally:
_self.unlock(r,_self)
if is_ok(r):
return value
elif _self._raising(r,_self):
raise QuietException
return r
def get(name, selection='', state=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"get" prints out the current value of a setting.
USAGE
get name [, selection [, state ]]
EXAMPLE
get line_width
ARGUMENTS
name = string: setting name
selection = string: object name (selections not yet supported)
state = integer: state number
NOTES
"get" currently only works with global, per-object, and per-state
settings. There is currently no way to retrieve per-atom settings.
PYMOL API
cmd.get(string name, string object, int state, int quiet)
SEE ALSO
set, set_bond, get_bond
'''
r = DEFAULT_ERROR
state = int(state)
if is_string(name):
i = _get_index(name)
else:
i = int(name)
if i<0:
print "Error: unknown setting"
raise QuietException
try:
_self.lock(_self)
r = _cmd.get_setting_text(_self._COb,i,str(selection),state-1)
finally:
_self.unlock(r,_self)
if is_ok(r) and (r!=None):
r_str = str(r)
if len(string.strip(r_str))==0:
r_str = "\'"+r_str+"\'"
if not quiet:
if(selection==''):
print " get: %s = %s"%(name,r_str)
elif state<=0:
print " get: %s = %s in object %s"%(name,r_str,selection)
else:
print " get: %s = %s in object %s state %d"%(name,r_str,selection,state)
if _self._raising(r,_self): raise QuietException
return r
def get_setting_tuple(name,object='',state=0,_self=cmd):
r = DEFAULT_ERROR
if is_string(name):
i = _get_index(name)
else:
i = int(name)
if i<0:
print "Error: unknown setting"
raise QuietException
try:
_self.lock(_self)
r = _cmd.get_setting_tuple(_self._COb,i,str(object),int(state)-1)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def get_setting_boolean(name,object='',state=0,_self=cmd):
r = DEFAULT_ERROR
if is_string(name):
i = _get_index(name)
else:
i = int(name)
if i<0:
print "Error: unknown setting"
raise QuietException
try:
_self.lock(_self)
r = _cmd.get_setting_of_type(_self._COb,i,str(object),int(state)-1,1)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def get_setting_int(name,object='',state=0,_self=cmd):
r = DEFAULT_ERROR
if is_string(name):
i = _get_index(name)
else:
i = int(name)
if i<0:
print "Error: unknown setting"
raise QuietException
try:
_self.lock(_self)
r = _cmd.get_setting_of_type(_self._COb,i,str(object),int(state)-1,2)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def get_setting_float(name,object='',state=0,_self=cmd):
r = DEFAULT_ERROR
if is_string(name):
i = _get_index(name)
else:
i = int(name)
if i<0:
print "Error: unknown setting"
raise QuietException
try:
_self.lock(_self)
r = _cmd.get_setting_of_type(_self._COb,i,str(object),int(state)-1,3)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def get_setting_text(name,object='',state=0,_self=cmd):
r = DEFAULT_ERROR
if is_string(name):
i = _get_index(name)
else:
i = int(name)
if i<0:
print "Error: unknown setting"
raise QuietException
try:
_self.lock(_self)
r = _cmd.get_setting_text(_self._COb,i,str(object),int(state)-1)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def get_setting_updates(_self=cmd):
r = []
if lock_attempt(_self):
try:
r = _cmd.get_setting_updates(_self._COb)
finally:
_self.unlock(r,_self)
return r
def get_setting_legacy(name,_self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_setting(_self._COb,name)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r