Merge pull request #398 from BradyAJohnston/dev-new-attributes

Adds attributes `atom_id` and `occupancy`
BradyAJohnston · Jan 4, 2024 · 65229a9 · 65229a9
2 parents 2245402 + 4881ca2
commit 65229a9
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Showing 80 changed files with 255 additions and 3 deletions.
diff --git a/molecularnodes/io/load.py b/molecularnodes/io/load.py
@@ -222,6 +222,9 @@ def att_atomic_number():
             np.char.title(array.element))))
         return atomic_number
 
+    def att_atom_id():
+        return array.atom_id
+
     def att_res_id():
         return array.res_id
 
@@ -263,6 +266,9 @@ def att_entity_id():
     def att_b_factor():
         return array.b_factor
 
+    def att_occupancy():
+        return array.occupancy
+
     def att_vdw_radii():
         vdw_radii =  np.array(list(map(
             # divide by 100 to convert from picometres to angstroms which is what all of coordinates are in
@@ -357,9 +363,11 @@ def att_sec_struct():
         {'name': 'res_name',        'value': att_res_name,            'type': 'INT',     'domain': 'POINT'},
         {'name': 'atomic_number',   'value': att_atomic_number,       'type': 'INT',     'domain': 'POINT'},
         {'name': 'b_factor',        'value': att_b_factor,            'type': 'FLOAT',   'domain': 'POINT'},
+        {'name': 'occupancy',       'value': att_occupancy,           'type': 'FLOAT',   'domain': 'POINT'},
         {'name': 'vdw_radii',       'value': att_vdw_radii,           'type': 'FLOAT',   'domain': 'POINT'},
         {'name': 'chain_id',        'value': att_chain_id,            'type': 'INT',     'domain': 'POINT'},
         {'name': 'entity_id',       'value': att_entity_id,           'type': 'INT',     'domain': 'POINT'},
+        {'name': 'atom_id',         'value': att_atom_id,             'type': 'INT',     'domain': 'POINT'},
         {'name': 'atom_name',       'value': att_atom_name,           'type': 'INT',     'domain': 'POINT'},
         {'name': 'lipophobicity',   'value': att_lipophobicity,       'type': 'FLOAT',   'domain': 'POINT'},
         {'name': 'charge',          'value': att_charge,              'type': 'FLOAT',   'domain': 'POINT'},

diff --git a/molecularnodes/io/local.py b/molecularnodes/io/local.py
@@ -98,7 +98,7 @@ def open_structure_local_pdb(file_path):
 
     # returns a numpy array stack, where each array in the stack is a model in the 
     # the file. The stack will be of length = 1 if there is only one model in the file
-    mol = pdb.get_structure(file, extra_fields = ['b_factor', 'charge'], include_bonds = True)
+    mol = pdb.get_structure(file, extra_fields = ['b_factor', 'charge', 'occupancy', 'atom_id'], include_bonds = True)
     return mol, file
 
 def open_structure_local_pdbx(file_path):

diff --git a/molecularnodes/io/pdb.py b/molecularnodes/io/pdb.py
@@ -105,7 +105,7 @@ def open_structure_rcsb(pdb_code, cache_dir = None):
 
     # returns a numpy array stack, where each array in the stack is a model in the 
     # the file. The stack will be of length = 1 if there is only one model in the file
-    mol = mmtf.get_structure(file, extra_fields = ["b_factor", "charge"], include_bonds = True) 
+    mol = mmtf.get_structure(file, extra_fields = ["b_factor", "charge", 'occupancy', 'atom_id'], include_bonds = True) 
     set_atom_entity_id(mol, file)
     return mol, file
 

diff --git a/tests/constants.py b/tests/constants.py
@@ -2,5 +2,5 @@
 import os
 
 codes = ['4ozs', '8H1B', '1BNA', '8U8W']
-attributes = ['b_factor', 'vdw_radii', 'lipophobicity', 'charge', 'res_id', 'res_name', 'atomic_number', 'chain_id', 'entity_id', 'atom_name', 'sec_struct', 'Color', 'position', 'is_backbone', 'is_alpha_carbon', 'is_solvent', 'is_nucleic', 'is_peptide', 'is_hetero', 'is_carb', 'bond_type']
+attributes = ['b_factor', 'occupancy', 'vdw_radii', 'lipophobicity', 'charge', 'res_id', 'res_name', 'atomic_number', 'chain_id', 'entity_id', 'atom_id', 'atom_name', 'sec_struct', 'Color', 'position', 'is_backbone', 'is_alpha_carbon', 'is_solvent', 'is_nucleic', 'is_peptide', 'is_hetero', 'is_carb', 'bond_type']
 test_data_directory = Path(os.path.abspath(Path(__file__).parent / 'data'))
diff --git a/tests/snapshots/test_attributes/test_attribute/1BNA/att_atom_id_values.txt b/tests/snapshots/test_attributes/test_attribute/1BNA/att_atom_id_values.txt
@@ -0,0 +1,6 @@
+[407 294 421  42 249 391 134  19   1  75 340 301 241 389 377 192 164 395
+  12 140 251 411 102 374 447 212 276 277 350  49  99 289 284 359 413 463
+ 136 476 412 313 352  46 433 218 172  48 186 410 210 452 129 228 453 457
+ 387 101 434 326 408 150  50  24 302 103 336 185 250 100 264 295 331 358
+ 437 258  15 325 440 126 309 221 156 183 424  62 445 257 348 269 464  60
+ 312 449 138 160 369 431 195 248 115  71]
diff --git a/tests/snapshots/test_attributes/test_attribute/1BNA/att_occupancy_values.txt b/tests/snapshots/test_attributes/test_attribute/1BNA/att_occupancy_values.txt
@@ -0,0 +1,5 @@
+[1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1.]
diff --git a/tests/snapshots/test_attributes/test_attribute/4ozs/att_atom_id_values.txt b/tests/snapshots/test_attributes/test_attribute/4ozs/att_atom_id_values.txt
@@ -0,0 +1,8 @@
+[1182  172 1000  542   76    1  305 1364 1208  970  771  661   45  565
+ 1008  412  854 1109 1111  199  402 1160 1140  550 1256  187  876  694
+  197  748  846  519  918  410 1307  603  206   94 1212  418 1349  745
+ 1003  403 1061 1186 1327 1038   59 1304  747  508 1239  887  630  738
+ 1213  251  190 1031 1082  414  246 1252  555  646  408  784  997  463
+  289 1230  436 1076   26  393  353   35 1334  688 1149 1277 1273  633
+  774  779 1087  804  599  266 1007  111  386  873 1223  821  203  910
+  509  189]
diff --git a/tests/snapshots/test_attributes/test_attribute/4ozs/att_occupancy_values.txt b/tests/snapshots/test_attributes/test_attribute/4ozs/att_occupancy_values.txt
@@ -0,0 +1,5 @@
+[1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1.]
diff --git a/tests/snapshots/test_attributes/test_attribute/8H1B/att_atom_id_values.txt b/tests/snapshots/test_attributes/test_attribute/8H1B/att_atom_id_values.txt
@@ -0,0 +1,8 @@
+[3403 2473 3520  337 2109 3276 1123  151    2  603 2859 2525 2049 3265
+ 3163 1617 1372 3308   90 1174 2125 3438  818 3143 3727 1812 3883 2327
+ 2331 2938  392  797 2430 2390 3019 3451 3139 1139 2860 3444 2635 2953
+  367 3612 1862 1455  388 1572 3431 1796 3450 1072 1946  391 3248  814
+ 3024 2737 3416 1250  406  188 2533 3851  829 3545 2829 3892 1565 2116
+ 3564 3879  800 2231 2481 2777 3012 3809 3453 2186 3907  117 2731 1569
+ 1047 2587 1883 1310 1544 2536  496  374 2171 3758 2924 2274  822  485
+ 2624 1149]
diff --git a/tests/snapshots/test_attributes/test_attribute/8H1B/att_occupancy_values.txt b/tests/snapshots/test_attributes/test_attribute/8H1B/att_occupancy_values.txt
@@ -0,0 +1,8 @@
+[1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   0.41 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   0.5  1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 0.59 1.  ]
diff --git a/tests/snapshots/test_attributes/test_attribute/8U8W/att_atom_id_values.txt b/tests/snapshots/test_attributes/test_attribute/8U8W/att_atom_id_values.txt
@@ -0,0 +1,8 @@
+[ 342 2060 1117  152    2  610 2000 1593 1373   90 1172 2076  825 1760
+ 2278 2282  399  804 2381 2341 1143  374 1804 1439  395 1548 1744 1039
+ 1897  398  821 1248  413  194  836 1541 2067  807 2182 2137  117 1545
+ 1017 1825 1302 1528  503  381 2122 2225  829  492 1153 1344  817 1620
+ 2055  926  579  873 2212   52  787  706   70 1428 2358 1311 1599 1610
+ 2234 1659 1240  533 2075  227  773 1797 1694  407 1881 1018  378 1901
+ 1905 1621  320 2190 1811 2002 1298 1740  365  801 1144 1922 2071  719
+   76 2277]
diff --git a/tests/snapshots/test_attributes/test_attribute/8U8W/att_occupancy_values.txt b/tests/snapshots/test_attributes/test_attribute/8U8W/att_occupancy_values.txt
@@ -0,0 +1,8 @@
+[0.55 1.   0.68 0.54 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   0.8  1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.  ]
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-ball_and_stick/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-ball_and_stick/atom_id.txt
@@ -0,0 +1,6 @@
+[386 215 409 137 146 362 438  63   2 248 284 225 134 360 341  58  17 368
+  38 461 149 393 337 337 448  90 478 187 188 299 157 328 207 199 313 396
+ 336 452 285 394 243 302 150 426  99  29 158  50 392  87 395 426 115 313
+ 160 357 335 314 263 389 170 167  72 227 472 342 413 279 479  49 147 417
+ 477 329 169 217 270 312 464 396 160 482  49 262  49 416 237 103   5  46
+ 227 204 152 158 454 297 177 339 200 242]
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-ball_and_stick/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-ball_and_stick/occupancy.txt
@@ -0,0 +1,5 @@
+[1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1.]
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-preset_1/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-preset_1/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-preset_1/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-preset_1/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-ribbon/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-ribbon/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-ribbon/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-ribbon/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-spheres/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-spheres/atom_id.txt
@@ -0,0 +1,6 @@
+[448  63 379 205  29   1 114 458 367 292 250  18 213 382 155 324 420 421
+  74 151 440 432 208 476  69 332 262  73 283 320 196 348  74 154 228  77
+  36 460 157 282 380 152 402 450 393  23 282 192 470 336 238 279 460  94
+  70 391 410 156  92 475 210 244 154 297 378 174 108 467 164 408  10 148
+ 132  14 260 436 484 483 239 293 295 412 304 226  99 382  42 145 330 464
+ 311  75 345 192  70 471 349 349 297  60]
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-spheres/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-spheres/occupancy.txt
@@ -0,0 +1,5 @@
+[1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1.]
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-surface/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-surface/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-1BNA-surface/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-1BNA-surface/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-ball_and_stick/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-ball_and_stick/atom_id.txt
@@ -0,0 +1,8 @@
+[1206  673  929  232  311    2 1206 1246  883  580  412  190  267  941
+   28  708 1095 1098  782   12 1174 1143  244 1319  736  741  463  773
+  546  695  197  805  780   25  324  813  384 1252   36  540  934   14
+ 1022 1213  987  241  543  180 1293  756  365  531 1254  995  747  976
+ 1055   31  972 1314  252  390   22  601  925  105 1145 1280   65 1045
+  104 1333  215  141  454 1156 1351 1346  371  585  593 1061  630  318
+ 1053  941  452 1140  735 1269  657  798  793  181  742 1298  808  811
+  601  638]
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-ball_and_stick/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-ball_and_stick/occupancy.txt
@@ -0,0 +1,5 @@
+[1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
+ 1. 1. 1. 1.]
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-cartoon/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-cartoon/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-cartoon/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-cartoon/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-preset_1/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-preset_1/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-preset_1/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-preset_1/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-ribbon/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-ribbon/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-ribbon/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-ribbon/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-spheres/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-spheres/atom_id.txt
@@ -0,0 +1,8 @@
+[1244  902 1289  126  763 1196  415   58    1  234 1041  922  740 1192
+ 1153  589  505 1208   35  432  769 1258  316 1145 1368  653  846  848
+ 1071  149  308  886  870 1098 1263 1144  421 1041 1260  958 1076  138
+ 1324  669  530  147  572 1255  646 1262  397  701 1098  148 1185  314
+ 1100  997 1249  461  159   72  925  320 1298 1029  569  766 1306  309
+  810  905 1012 1096 1263  792   45  995  570  389  945  677  481  564
+  926  193  140  787 1065  826  317  189  956 1041  425  494 1128  313
+  599  761]
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-spheres/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-spheres/occupancy.txt
@@ -0,0 +1,6 @@
+[1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
+ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  0.5 1.  1.  1.  1.  1.  1.
+ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
+ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
+ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
+ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1. ]
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-surface/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-surface/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-4ozs-surface/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-4ozs-surface/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-ball_and_stick/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-ball_and_stick/atom_id.txt
@@ -0,0 +1,8 @@
+[3416 2015 3594 1379 1410 3221 2352  608    8 2492 2570 2094 1309 3206
+ 3051  646  311 3271  365   13 1442 3469 3341 3019 3910  913 1787 1793
+ 2704 1627 3272 1950 1888 2821 3489 3013 2799 2571 3478 2241 2727 1511
+ 3734  985  412 1605  577 3459  876 3487  954 1141 2822 1615 3180 3328
+ 2829 2396 3435  129 1686  749 2107 3379 3631 2524  566 1425 3662 3281
+ 1611 2027 2456 2803 3492 1535  471 2387  573  291 2189 1027  211  548
+ 2110 2071 1540 1513 2683 1689 3356 2025 2229 2570 3102  266 2943 3316
+  688 1398]
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-ball_and_stick/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-ball_and_stick/occupancy.txt
@@ -0,0 +1,8 @@
+[1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   0.59 1.   1.
+ 1.   0.41 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   0.44 1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   0.6  1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   0.5 ]
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-cartoon/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-cartoon/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-cartoon/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-cartoon/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-preset_1/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-preset_1/atom_id.txt
@@ -0,0 +1,8 @@
+[3919    0 3930    0    0 3907    0    0    0    0 3918    0    0 3906
+ 3896    0    0 3910    0    0    0 3923    0 3894    0    0    0 3932
+    0    0    0    0 3943 3924 3894    0 3918 3923    0 3930    0 3939
+    0    0    0    0 3922    0 3924    0    0 3943    0 3904    0 3944
+ 3902 3920    0    0    0    0    0 3933 3914    0    0 3935    0    0
+    0 3906 3941 3924    0    0 3900    0    0    0    0    0    0    0
+    0    0    0 3930    0    0    0    0 3918    0    0    0    0    0
+    0    0]
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-preset_1/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-preset_1/occupancy.txt
@@ -0,0 +1,5 @@
+[1. 0. 1. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 1. 1. 0. 0. 1. 0. 0. 0. 1. 0. 1.
+ 0. 0. 0. 1. 0. 0. 0. 0. 1. 1. 1. 0. 1. 1. 0. 1. 0. 1. 0. 0. 0. 0. 1. 0.
+ 1. 0. 0. 1. 0. 1. 0. 1. 1. 1. 0. 0. 0. 0. 0. 1. 1. 0. 0. 1. 0. 0. 0. 1.
+ 1. 1. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0.
+ 0. 0. 0. 0.]
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-ribbon/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-ribbon/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-ribbon/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-ribbon/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-spheres/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-spheres/atom_id.txt
@@ -0,0 +1,8 @@
+[3735  509 3181 1740  235    3  932 3814 3089 2452 2116  137 1819 3205
+ 1300 2721 3513 3519  595 1262 3670 3609 1765  556 2787 2217  588 2383
+ 2695 1663 2923  592 1294 1940  615  292 3827 1317 2372 3191 1267 3366
+ 3748 3297  178 2378 1617 3909 2826 2022 2353 3831  753  566 3275 3432
+ 1306  736 1789 2072 1288 2493 3173 1471  868 3882 1374 3412   79 1236
+ 1107  107 2200 3635 2033 2461 2478 3445 2551 1927  798 3204  342 1214
+ 2776 3861 2606  606 2899 1623  562 3918 2929 2936 2494  484 3378 2798
+ 3093 2017]
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-spheres/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-spheres/occupancy.txt
@@ -0,0 +1,8 @@
+[1.   1.   1.   1.   0.39 1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   0.41 1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   0.59 1.   1.   0.41 1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.  ]
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-surface/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-surface/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8H1B-surface/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8H1B-surface/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-ball_and_stick/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-ball_and_stick/atom_id.txt
@@ -0,0 +1,8 @@
+[1386 2094  639  621    9  530 2001 1386 1000  374  708 2117  236 1641
+ 1608  204  664 1507 1708 1143 1590 1311 1616  570 1836 1600  230  824
+ 1666  769  253 1298 2104  208 2279 2210  482 1304  535 1739  906 1279
+ 2035 1532 2188 2345  242 1992  678  955  224 1428 2086  397 2336  309
+ 2325  213  177   49  286 1115  917 1396 1413 2358 1486  811 2151 2117
+  897  151 1697 1540 1640 1811  537 1524 1842 1850 1429 1315 2291 1719
+ 2006  900 1611 1473  199  665 1884 2110   68  310  374 2098  574 1302
+  170  606]
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-ball_and_stick/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-ball_and_stick/occupancy.txt
@@ -0,0 +1,8 @@
+[1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   0.8  1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   0.68 1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   0.42 1.   0.8  1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.  ]
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-cartoon/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-cartoon/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-cartoon/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-cartoon/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-preset_1/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-preset_1/atom_id.txt
@@ -0,0 +1,8 @@
+[   0 2369    0    0    0    0 2363    0    0    0    0 2370    0    0
+ 2390 2390    0    0    0    0    0    0    0    0    0    0 2380    0
+    0    0    0    0    0    0 2370    0 2381 2376    0    0    0    0
+    0    0    0    0 2375 2385    0    0    0    0    0    0 2368    0
+    0    0 2383    0    0    0    0    0    0    0    0 2386    0    0
+    0 2370    0    0    0    0    0 2376    0    0 2379 2381    0    0
+ 2381    0 2363    0    0    0    0    0 2385 2370    0    0 2390    0
+    0    0]
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-preset_1/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-preset_1/occupancy.txt
@@ -0,0 +1,6 @@
+[0.  0.8 0.  0.  0.  0.  0.5 0.  0.  0.  0.  0.8 0.  0.  1.  1.  0.  0.
+ 0.  0.  0.  0.  0.  0.  0.  0.  1.  0.  0.  0.  0.  0.  0.  0.  0.8 0.
+ 1.  1.  0.  0.  0.  0.  0.  0.  0.  0.  1.  1.  0.  0.  0.  0.  0.  0.
+ 0.8 0.  0.  0.  1.  0.  0.  0.  0.  0.  0.  0.  0.  1.  0.  0.  0.  0.8
+ 0.  0.  0.  0.  0.  1.  0.  0.  1.  1.  0.  0.  1.  0.  0.5 0.  0.  0.
+ 0.  0.  1.  0.8 0.  0.  1.  0.  0.  0. ]
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-ribbon/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-ribbon/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-ribbon/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-ribbon/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-spheres/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-spheres/atom_id.txt
@@ -0,0 +1,8 @@
+[1862  258 1578  830  115    2  468 2142 1904 1532 2367 1220 1010   69
+  865 1590  632 2351 1357 1744 1747 2202  301  616 1823 1792 2257 2348
+  842 2142 1977 2213  281 1390 1069  297 1186 1344  795 1454 2257  299
+  629 2260 2055  922  311  143 1910  640 2119 1180 1583  618 1671 1871
+ 2085 2252 1636   89 2050 1183  778 1951 1405  963 1171 1912  387  286
+ 1625 2191 1704  635  378 1972 2142  850  988 2317  626 1241 1574  709
+  444 1938  669 2252 1694   40  603  541   54 2096 1052 1805 2169 2009
+ 2004  969]
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-spheres/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-spheres/occupancy.txt
@@ -0,0 +1,8 @@
+[0.42 1.   1.   1.   1.   1.   1.   1.   1.   1.   0.8  1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   0.68 1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.   1.
+ 1.   1.  ]
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-surface/atom_id.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-surface/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_1/False-8U8W-surface/occupancy.txt b/tests/snapshots/test_load/test_style_1/False-8U8W-surface/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_2/True-1BNA-ribbon/atom_id.txt b/tests/snapshots/test_load/test_style_2/True-1BNA-ribbon/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_2/True-1BNA-ribbon/occupancy.txt b/tests/snapshots/test_load/test_style_2/True-1BNA-ribbon/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
diff --git a/tests/snapshots/test_load/test_style_2/True-1BNA-surface/atom_id.txt b/tests/snapshots/test_load/test_style_2/True-1BNA-surface/atom_id.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "atom_id" not found'
diff --git a/tests/snapshots/test_load/test_style_2/True-1BNA-surface/occupancy.txt b/tests/snapshots/test_load/test_style_2/True-1BNA-surface/occupancy.txt
@@ -0,0 +1 @@
+'bpy_prop_collection[key]: key "occupancy" not found'
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		'bpy_prop_collection[key]: key "atom_id" not found'
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		'bpy_prop_collection[key]: key "occupancy" not found'