mzcore 0.1.0

Core logic for handling massspectrometry in Rust.
Documentation
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
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
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
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
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
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
215
216
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
255
256
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
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
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
389
390
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
445
446
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
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
[
    [
        1,
        "uranium linker",
        {
            "Linker": {
                "specificities": [
                    {
                        "Asymmetric": [
                            [
                                [
                                    {
                                        "AminoAcid": [
                                            [
                                                "Selenocysteine"
                                            ],
                                            "AnyCTerm"
                                        ]
                                    },
                                    {
                                        "AminoAcid": [
                                            [
                                                "GlutamicAcid"
                                            ],
                                            "Anywhere"
                                        ]
                                    }
                                ],
                                [
                                    {
                                        "AminoAcid": [
                                            [
                                                "Selenocysteine"
                                            ],
                                            "AnyNTerm"
                                        ]
                                    }
                                ]
                            ],
                            [
                                [
                                    {
                                        "elements": [
                                            [
                                                "U",
                                                null,
                                                1
                                            ]
                                        ],
                                        "additional_mass": 0.0
                                    },
                                    {
                                        "elements": [
                                            [
                                                "U",
                                                null,
                                                1
                                            ]
                                        ],
                                        "additional_mass": 0.0
                                    }
                                ]
                            ],
                            [
                                {
                                    "elements": [
                                        [
                                            "Te",
                                            null,
                                            1
                                        ]
                                    ],
                                    "additional_mass": 0.0
                                },
                                {
                                    "elements": [
                                        [
                                            "Ne",
                                            null,
                                            1
                                        ]
                                    ],
                                    "additional_mass": 0.0
                                },
                                {
                                    "elements": [
                                        [
                                            "H",
                                            null,
                                            2
                                        ],
                                        [
                                            "He",
                                            null,
                                            3
                                        ]
                                    ],
                                    "additional_mass": 0.0
                                },
                                {
                                    "elements": [
                                        [
                                            "H",
                                            null,
                                            1
                                        ],
                                        [
                                            "He",
                                            null,
                                            2
                                        ]
                                    ],
                                    "additional_mass": 0.0
                                },
                                {
                                    "elements": [
                                        [
                                            "I",
                                            null,
                                            1
                                        ],
                                        [
                                            "Er",
                                            null,
                                            1
                                        ]
                                    ],
                                    "additional_mass": 0.0
                                },
                                {
                                    "elements": [
                                        [
                                            "H",
                                            null,
                                            12
                                        ],
                                        [
                                            "C",
                                            null,
                                            12
                                        ],
                                        [
                                            "O",
                                            null,
                                            1
                                        ]
                                    ],
                                    "additional_mass": 0.0
                                }
                            ]
                        ]
                    }
                ],
                "formula": {
                    "elements": [
                        [
                            "U",
                            null,
                            2
                        ]
                    ],
                    "additional_mass": 0.0
                },
                "id": {
                    "ontology": "Custom",
                    "name": "Uranium linker",
                    "id": 1,
                    "description": "Have some uranium, its delicious!",
                    "synonyms": [],
                    "cross_ids": [
                        [
                            "Pubmed",
                            "21714143"
                        ]
                    ]
                },
                "length": 23.9
            }
        }
    ],
    [
        2,
        "helium",
        {
            "Database": {
                "specificities": [
                    [
                        [
                            {
                                "AminoAcid": [
                                    [
                                        "Alanine"
                                    ],
                                    "Anywhere"
                                ]
                            }
                        ],
                        [],
                        []
                    ],
                    [
                        [
                            {
                                "AminoAcid": [
                                    [
                                        "Methionine"
                                    ],
                                    "Anywhere"
                                ]
                            }
                        ],
                        [
                            {
                                "Loss": {
                                    "elements": [],
                                    "additional_mass": 12.0
                                }
                            }
                        ],
                        []
                    ]
                ],
                "formula": {
                    "elements": [
                        [
                            "He",
                            null,
                            2
                        ]
                    ],
                    "additional_mass": 0.0
                },
                "id": {
                    "ontology": "Custom",
                    "name": "Helium",
                    "id": 2,
                    "description": "heeeelium",
                    "synonyms": [
                        "heeeelium",
                        "funny gas"
                    ],
                    "cross_ids": [
                        [
                            "Pubmed",
                            "42"
                        ],
                        [
                            "Unimod",
                            "12"
                        ],
                        [
                            "Resid",
                            "A12"
                        ]
                    ]
                }
            }
        }
    ],
    [
        3,
        "db18",
        {
            "Database": {
                "specificities": [
                    [
                        [
                            {
                                "AminoAcid": [
                                    [
                                        "Cysteine"
                                    ],
                                    "Anywhere"
                                ]
                            }
                        ],
                        [
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 372.25
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 373.258
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 371.242
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 240.171
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 239.163
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 241.179
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 197.129
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 198.137
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 196.121
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 619.418
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 621.4343
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 649.465
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 677.497
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 618.41
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 620.426
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 648.457
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 676.489
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 620.426
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 622.442
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 650.473
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 678.504
                                }
                            },
                            {
                                "Gain": {
                                    "elements": [],
                                    "additional_mass": 28.006
                                }
                            }
                        ],
                        [
                            {
                                "elements": [],
                                "additional_mass": 372.25
                            },
                            {
                                "elements": [],
                                "additional_mass": 240.171
                            },
                            {
                                "elements": [],
                                "additional_mass": 197.129
                            },
                            {
                                "elements": [],
                                "additional_mass": 619.418
                            },
                            {
                                "elements": [],
                                "additional_mass": 621.434
                            },
                            {
                                "elements": [],
                                "additional_mass": 649.465
                            },
                            {
                                "elements": [],
                                "additional_mass": 677.497
                            }
                        ]
                    ]
                ],
                "formula": {
                    "elements": [],
                    "additional_mass": 676.489
                },
                "id": {
                    "ontology": "Custom",
                    "name": "DB18",
                    "id": 3,
                    "description": "",
                    "synonyms": [],
                    "cross_ids": []
                }
            }
        }
    ],
    [
        4,
        "disulfide",
        {
            "Linker": {
                "specificities": [
                    {
                        "Symmetric": [
                            [
                                {
                                    "AminoAcid": [
                                        [
                                            "Cysteine"
                                        ],
                                        "Anywhere"
                                    ]
                                }
                            ],
                            [
                                [
                                    {
                                        "elements": [],
                                        "additional_mass": 0.0
                                    },
                                    {
                                        "elements": [],
                                        "additional_mass": 0.0
                                    }
                                ],
                                [
                                    {
                                        "elements": [
                                            [
                                                "H",
                                                null,
                                                -1
                                            ]
                                        ],
                                        "additional_mass": 0.0
                                    },
                                    {
                                        "elements": [],
                                        "additional_mass": 0.0
                                    }
                                ],
                                [
                                    {
                                        "elements": [
                                            [
                                                "H",
                                                null,
                                                -1
                                            ]
                                        ],
                                        "additional_mass": 0.0
                                    },
                                    {
                                        "elements": [
                                            [
                                                "H",
                                                null,
                                                -1
                                            ]
                                        ],
                                        "additional_mass": 0.0
                                    }
                                ]
                            ],
                            []
                        ]
                    }
                ],
                "formula": {
                    "elements": [
                        [
                            "H",
                            null,
                            -2
                        ]
                    ],
                    "additional_mass": 0.0
                },
                "id": {
                    "ontology": "Custom",
                    "name": "Disulfide",
                    "id": 4,
                    "description": "A disulfide with all potential neutral losses",
                    "synonyms": [],
                    "cross_ids": []
                },
                "length": 0.0
            }
        }
    ],
    [
        5,
        "dsso",
        {
            "Linker": {
                "specificities": [
                    {
                        "Symmetric": [
                            [
                                {
                                    "AminoAcid": [
                                        [
                                            "Lysine"
                                        ],
                                        "Anywhere"
                                    ]
                                }
                            ],
                            [
                                [
                                    {
                                        "elements": [
                                            [
                                                "H",
                                                null,
                                                1
                                            ],
                                            [
                                                "C",
                                                null,
                                                3
                                            ],
                                            [
                                                "N",
                                                null,
                                                -1
                                            ],
                                            [
                                                "O",
                                                null,
                                                3
                                            ],
                                            [
                                                "S",
                                                null,
                                                1
                                            ]
                                        ],
                                        "additional_mass": 0.0
                                    },
                                    {
                                        "elements": [
                                            [
                                                "H",
                                                null,
                                                1
                                            ],
                                            [
                                                "C",
                                                null,
                                                3
                                            ],
                                            [
                                                "N",
                                                null,
                                                -1
                                            ],
                                            [
                                                "O",
                                                null,
                                                2
                                            ]
                                        ],
                                        "additional_mass": 0.0
                                    }
                                ]
                            ],
                            []
                        ]
                    }
                ],
                "formula": {
                    "elements": [
                        [
                            "H",
                            null,
                            2
                        ],
                        [
                            "C",
                            null,
                            6
                        ],
                        [
                            "N",
                            null,
                            -2
                        ],
                        [
                            "O",
                            null,
                            5
                        ],
                        [
                            "S",
                            null,
                            1
                        ]
                    ],
                    "additional_mass": 0.0
                },
                "id": {
                    "ontology": "Custom",
                    "name": "DSSO",
                    "id": 5,
                    "description": "",
                    "synonyms": [],
                    "cross_ids": []
                },
                "length": 0.0
            }
        }
    ]
]