datasets
DataSet
dataclass
Source code in hdxms_datasets/datasets.py
447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 |
|
data_files: dict[str, DataFile]
instance-attribute
Dictionary of data files
data_id: str
instance-attribute
Unique identifier for the dataset
hdx_specification: dict
instance-attribute
Dictionary with HDX-MS state specification
peptides_per_state: dict[str, list[str]]
property
Dictionary of state names and list of peptide sets for each state
protein_spec: dict[str, ProteinInfo]
property
Access the protein section of the specification
cite()
Returns citation information
Source code in hdxms_datasets/datasets.py
611 612 613 614 615 616 617 618 619 620 |
|
get_state(state)
Get a specific state by name or index
Source code in hdxms_datasets/datasets.py
532 533 534 535 536 537 538 539 540 541 |
|
DataState
dataclass
Encapsulates all data for a specific protein state
Source code in hdxms_datasets/datasets.py
391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 |
|
name: str
instance-attribute
Name of the state
peptides: dict[str, Peptides]
instance-attribute
Dictionary of peptide sets for this state
protein: ProteinInfo
instance-attribute
Protein information for this state
structure: Structure
instance-attribute
Optional structure file information for this state
compute_uptake_metrics()
Compute uptake metrics for this state
Source code in hdxms_datasets/datasets.py
425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 |
|
get_peptides(peptide_set)
Get a specific peptide set
Source code in hdxms_datasets/datasets.py
407 408 409 410 411 412 |
|
get_protein_property(property_name)
Get a specific protein property
Source code in hdxms_datasets/datasets.py
418 419 420 421 422 423 |
|
get_sequence()
Get the protein sequence for this state
Source code in hdxms_datasets/datasets.py
414 415 416 |
|
PeptideMetadata
Bases: TypedDict
TypedDict for peptide metadata
Source code in hdxms_datasets/datasets.py
157 158 159 160 161 162 |
|
PeptideTableFile
dataclass
Bases: DataFile
Source code in hdxms_datasets/datasets.py
83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 |
|
extension: Optional[str] = None
class-attribute
instance-attribute
File extension, e.g. .csv, in case of a file-like object
Peptides
dataclass
Source code in hdxms_datasets/datasets.py
316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 |
|
get_pH()
Get the pH of the experiment
Source code in hdxms_datasets/datasets.py
382 383 384 385 386 387 388 |
|
get_temperature()
Get the temperature of the experiment
Source code in hdxms_datasets/datasets.py
371 372 373 374 375 376 377 378 379 380 |
|
ProteinInfo
Bases: TypedDict
TypedDict for protein information in a state
Source code in hdxms_datasets/datasets.py
143 144 145 146 147 148 149 150 151 152 153 154 |
|
Structure
dataclass
Source code in hdxms_datasets/datasets.py
165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 |
|
null_structure()
classmethod
Returns a null structure with no data. This is useful for cases where no structure is available.
Source code in hdxms_datasets/datasets.py
199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 |
|
pdbemolstar_custom_data()
Returns a dictionary with custom data for PDBeMolstar visualization.
Source code in hdxms_datasets/datasets.py
171 172 173 174 175 176 |
|
StructureFile
dataclass
Bases: DataFile
Source code in hdxms_datasets/datasets.py
107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 |
|
extension: Optional[str] = None
class-attribute
instance-attribute
File extension, e.g. .pdf, in case of a file-like object
pdbemolstar_custom_data()
Returns a dictionary with custom data for PDBeMolstar visualization.
Source code in hdxms_datasets/datasets.py
118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 |
|
allow_missing_fields(allow=True)
Context manager to temporarily allow missing protein information
Source code in hdxms_datasets/datasets.py
30 31 32 33 34 35 36 37 38 39 |
|
create_dataset(target_dir, author_name, tag=None, template_dir=TEMPLATE_DIR)
Create a dataset in the specified target directory.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
target_dir
|
Path
|
The directory where the dataset will be created. |
required |
author_name
|
str
|
The name of the author of the dataset. |
required |
tag
|
Optional[str]
|
An optional tag to append to the directory name. Defaults to None. |
None
|
template_dir
|
Path
|
The directory containing the template files for the dataset. Defaults to TEMPLATE_DIR. |
TEMPLATE_DIR
|
Returns:
Type | Description |
---|---|
str
|
The id of the created dataset. |
Source code in hdxms_datasets/datasets.py
42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 |
|
parse_data_files(data_file_spec, data_dir)
Parse data file specifications from a YAML file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data_file_spec
|
dict
|
Dictionary with data file specifications. |
required |
data_dir
|
Path
|
Path to data directory. |
required |
Returns:
Type | Description |
---|---|
dict[str, DataFile]
|
Dictionary with parsed data file specifications. |
Source code in hdxms_datasets/datasets.py
217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 |
|
parse_peptides(peptides_spec, data_files)
Parse the peptides specification and return a dictionary of PeptideTableFile objects.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
peptides_spec
|
dict[str, Any]
|
Dictionary containing peptide specifications. |
required |
data_files
|
dict[str, PeptideTableFile]
|
Dictionary of available data files. |
required |
Returns:
Type | Description |
---|---|
dict[str, dict[str, Peptides]]
|
Dictionary of Peptides dictionaries. |
Source code in hdxms_datasets/datasets.py
257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 |
|
parse_structures(structures_spec, data_files)
Parse the structures specification and return a dictionary of Structure objects.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
structures_spec
|
dict[str, Any]
|
Dictionary containing structure specifications. |
required |
data_files
|
dict[str, StructureFile]
|
Dictionary of available data files. |
required |
Returns:
Type | Description |
---|---|
dict[str, Structure]
|
Dictionary of Structure objects keyed by structure name. |
Source code in hdxms_datasets/datasets.py
291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 |
|