@datagrok/sequence-translator 0.0.4 → 0.0.8

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Files changed (16) hide show
  1. package/.eslintrc.json +39 -0
  2. package/detectors.js +2 -12
  3. package/package.json +7 -3
  4. package/src/axolabsMap.ts +101 -99
  5. package/src/defineAxolabsPattern.ts +240 -211
  6. package/src/drawAxolabsPattern.ts +127 -92
  7. package/src/package-test.ts +6 -7
  8. package/src/package.ts +301 -604
  9. package/src/salts.ts +2 -0
  10. package/src/structures-works/converters.ts +288 -0
  11. package/src/structures-works/from-monomers.ts +73 -0
  12. package/src/structures-works/map.ts +540 -0
  13. package/src/structures-works/save-sense-antisense.ts +44 -0
  14. package/src/structures-works/sequence-codes-tools.ts +236 -0
  15. package/src/tests/smiles-tests.ts +448 -7
  16. package/src/map.ts +0 -534
package/src/map.ts DELETED
@@ -1,534 +0,0 @@
1
- export const SYNTHESIZERS = {
2
- RAW_NUCLEOTIDES: "Raw Nucleotides",
3
- BIOSPRING: "BioSpring Codes",
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- GCRS: "Janssen GCRS Codes",
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- AXOLABS: "Axolabs Codes",
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- MERMADE_12: "Mermade 12"
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- };
8
- export const TECHNOLOGIES = {
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- DNA: "DNA",
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- RNA: "RNA",
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- ASO_GAPMERS: "For ASO Gapmers",
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- SI_RNA: "For 2'-OMe and 2'-F modified siRNA"
13
- };
14
- // interface CODES {
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- // }
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- export const MODIFICATIONS: {[index: string]: {left: string, right: string}} = {
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- "(invabasic)": {
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- left: "OC1CCOC1COP(=O)(S[H])O",
19
- right: "OP(=O)(S[H])OCC1OCCC1O"
20
- },
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- "(GalNAc-2-JNJ)": {
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- left: "C(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)NC(=O)CCCC(=O)NCC(O)CO",
23
- right: "OCC(O)CNC(=O)CCCC(=O)NC(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)"
24
- }
25
- };
26
- export const stadardPhosphateLinkSmiles = 'OP(=O)(O)O';
27
- export const map: {[synthesizer: string]: {[technology: string]: {[code: string]: {"name": string, "weight": number, "normalized": string, "SMILES": string}}}} = {
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- "Raw Nucleotides": {
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- "DNA": {
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- "A": {
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- "name": "Adenine",
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- "weight": 313.21,
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- "normalized": "dA",
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- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[C@@H]1O"
35
- },
36
- "T": {
37
- "name": "Tyrosine",
38
- "weight": 304.2,
39
- "normalized": "dT",
40
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O"
41
- },
42
- "G": {
43
- "name": "Guanine",
44
- "weight": 329.21,
45
- "normalized": "dG",
46
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O"
47
- },
48
- "C": {
49
- "name": "Cytosine",
50
- "weight": 289.18,
51
- "normalized": "dC",
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- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))C[C@@H]1O"
53
- }
54
- },
55
- "RNA": {
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- "A": {
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- "name": "Adenine",
58
- "weight": 313.21,
59
- "normalized": "dA",
60
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[C@@H]1O"
61
- },
62
- "U": {
63
- "name": "Uracil",
64
- "weight": 306.17,
65
- "normalized": "rU",
66
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](O)[C@@H]1O"
67
- },
68
- "G": {
69
- "name": "Guanine",
70
- "weight": 329.21,
71
- "normalized": "dG",
72
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O"
73
- },
74
- "C": {
75
- "name": "Cytosine",
76
- "weight": 289.18,
77
- "normalized": "dC",
78
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))C[C@@H]1O"
79
- }
80
- }
81
- },
82
- "BioSpring Codes": {
83
- 'For ASO Gapmers': {
84
- "5": {
85
- "name": "2'MOE-5Me-rU",
86
- "weight": 378.27,
87
- "normalized": "rU",
88
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))[C@H](OCCOC)[C@@H]1O"
89
- },
90
- "6": {
91
- "name": "2'MOE-rA",
92
- "weight": 387.29,
93
- "normalized": "rA",
94
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OCCOC)[C@@H]1O"
95
- },
96
- "7": {
97
- "name": "2'MOE-5Me-rC",
98
- "weight": 377.29,
99
- "normalized": "rC",
100
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(N)=NC2(=O))[C@H](OCCOC)[C@@H]1O"
101
- },
102
- "8": {
103
- "name": "2'MOE-rG",
104
- "weight": 403.28,
105
- "normalized": "rG",
106
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OCCOC)[C@@H]1O"
107
- },
108
- "9": {
109
- "name": "5-Methyl-dC",
110
- "weight": 303.21,
111
- "normalized": "dC",
112
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(N)=NC2(=O))C[C@@H]1O"
113
- },
114
- "*": {
115
- "name": "ps linkage",
116
- "weight": 16.07,
117
- "normalized": "",
118
- "SMILES": "OP(=O)(S)O"
119
- },
120
- "A": {
121
- "name": "Adenine",
122
- "weight": 313.21,
123
- "normalized": "dA",
124
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[C@@H]1O"
125
- },
126
- "C": {
127
- "name": "Cytosine",
128
- "weight": 289.18,
129
- "normalized": "dC",
130
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))C[C@@H]1O"
131
- },
132
- "G": {
133
- "name": "Guanine",
134
- "weight": 329.21,
135
- "normalized": "dG",
136
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O"
137
- },
138
- "T": {
139
- "name": "Tyrosine",
140
- "weight": 304.2,
141
- "normalized": "dT",
142
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O"
143
- }
144
- },
145
- "For 2'-OMe and 2'-F modified siRNA": {
146
- "1": {
147
- "name": "2'-fluoro-U",
148
- "weight": 308.16,
149
- "normalized": "rU",
150
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1O"
151
- },
152
- "2": {
153
- "name": "2'-fluoro-A",
154
- "weight": 331.2,
155
- "normalized": "rA",
156
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1O"
157
- },
158
- "3": {
159
- "name": "2'-fluoro-C",
160
- "weight": 307.18,
161
- "normalized": "rC",
162
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](F)[C@@H]1O"
163
- },
164
- "4": {
165
- "name": "2'-fluoro-G",
166
- "weight": 347.19,
167
- "normalized": "rG",
168
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](F)[C@@H]1O"
169
- },
170
- "5": {
171
- "name": "2'OMe-rU",
172
- "weight": 320.2,
173
- "normalized": "rU",
174
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1O"
175
- },
176
- "6": {
177
- "name": "2'OMe-rA",
178
- "weight": 343.24,
179
- "normalized": "rA",
180
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1O"
181
- },
182
- "7": {
183
- "name": "2'OMe-rC",
184
- "weight": 319.21,
185
- "normalized": "rC",
186
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1O"
187
- },
188
- "8": {
189
- "name": "2'OMe-rG",
190
- "weight": 359.24,
191
- "normalized": "rG",
192
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1O"
193
- },
194
- "*": {
195
- "name": "ps linkage",
196
- "weight": 16.07,
197
- "normalized": "",
198
- "SMILES": "OP(=O)(S)O"
199
- }
200
- }
201
- },
202
- "Axolabs Codes": {
203
- "For 2'-OMe and 2'-F modified siRNA": {
204
- "Uf": {
205
- "name": "2'-fluoro-U",
206
- "weight": 308.16,
207
- "normalized": "rU",
208
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1O"
209
- },
210
- "Af": {
211
- "name": "2'-fluoro-A",
212
- "weight": 331.2,
213
- "normalized": "rA",
214
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1O"
215
- },
216
- "Cf": {
217
- "name": "2'-fluoro-C",
218
- "weight": 307.18,
219
- "normalized": "rC",
220
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](F)[C@@H]1O"
221
- },
222
- "Gf": {
223
- "name": "2'-fluoro-G",
224
- "weight": 347.19,
225
- "normalized": "rG",
226
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](F)[C@@H]1O"
227
- },
228
- "u": {
229
- "name": "2'OMe-rU",
230
- "weight": 320.2,
231
- "normalized": "rU",
232
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1O"
233
- },
234
- "a": {
235
- "name": "2'OMe-rA",
236
- "weight": 343.24,
237
- "normalized": "rA",
238
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1O"
239
- },
240
- "c": {
241
- "name": "2'OMe-rC",
242
- "weight": 319.21,
243
- "normalized": "rC",
244
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1O"
245
- },
246
- "g": {
247
- "name": "2'OMe-rG",
248
- "weight": 359.,
249
- "normalized": "rG",
250
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1O"
251
- },
252
- "s": {
253
- "name": "ps linkage",
254
- "weight": 16.07,
255
- "normalized": "",
256
- "SMILES": "OP(=O)(S)O"
257
- }
258
- }
259
- },
260
- "Janssen GCRS Codes": {
261
- "For ASO Gapmers": {
262
- "moeT": {
263
- "name": "2'MOE-5Me-rU",
264
- "weight": 378.27,
265
- "normalized": "rU",
266
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))[C@H](OCCOC)[C@@H]1O"
267
- },
268
- "moeA": {
269
- "name": "2'MOE-rA",
270
- "weight": 387.29,
271
- "normalized": "rA",
272
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OCCOC)[C@@H]1O"
273
- },
274
- "moe5mC": {
275
- "name": "2'MOE-5Me-rC",
276
- "weight": 377.29,
277
- "normalized": "rC",
278
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(N)=NC2(=O))[C@H](OCCOC)[C@@H]1O"
279
- },
280
- "(5m)moeC": {
281
- "name": "2'MOE-5Me-rC",
282
- "weight": 377.29,
283
- "normalized": "rC",
284
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(N)=NC2(=O))[C@H](OCCOC)[C@@H]1O"
285
- },
286
- "moeG": {
287
- "name": "2'MOE-rG",
288
- "weight": 403.28,
289
- "normalized": "rG",
290
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OCCOC)[C@@H]1O"
291
- },
292
- "5mC": {
293
- "name": "5-Methyl-dC",
294
- "weight": 303.28,
295
- "normalized": "dC",
296
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(N)=NC2(=O))C[C@@H]1O"
297
- },
298
- "(5m)C": {
299
- "name": "5-Methyl-dC",
300
- "weight": 303.28,
301
- "normalized": "dC",
302
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(N)=NC2(=O))C[C@@H]1O"
303
- },
304
- "ps": {
305
- "name": "ps linkage",
306
- "weight": 16.07,
307
- "normalized": "",
308
- "SMILES": "OP(=O)(S)O"
309
- },
310
- "A": {
311
- "name": "Adenine",
312
- "weight": 313.21,
313
- "normalized": "dA",
314
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[C@@H]1O"
315
- },
316
- "dA": {
317
- "name": "Adenine",
318
- "weight": 313.21,
319
- "normalized": "dA",
320
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[C@@H]1O"
321
- },
322
- "C": {
323
- "name": "Cytosine",
324
- "weight": 289.18,
325
- "normalized": "dC",
326
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))C[C@@H]1O"
327
- },
328
- "dC": {
329
- "name": "Cytosine",
330
- "weight": 289.18,
331
- "normalized": "dC",
332
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))C[C@@H]1O"
333
- },
334
- "G": {
335
- "name": "Guanine",
336
- "weight": 329.21,
337
- "normalized": "dG",
338
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O"
339
- },
340
- "dG": {
341
- "name": "Guanine",
342
- "weight": 329.21,
343
- "normalized": "dG",
344
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O"
345
- },
346
- "T": {
347
- "name": "Tyrosine",
348
- "weight": 304.2,
349
- "normalized": "dT",
350
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O"
351
- },
352
- "dT": {
353
- "name": "Tyrosine",
354
- "weight": 304.2,
355
- "normalized": "dT",
356
- "SMILES": "OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O"
357
- },
358
- "rA": {
359
- "name": "Adenine",
360
- "weight": 329.21,
361
- "normalized": "rA",
362
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](O)[C@@H]1O"
363
- },
364
- "rC": {
365
- "name": "Cytosine",
366
- "weight": 305.18,
367
- "normalized": "rC",
368
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](O)[C@@H]1O"
369
- },
370
- "rG": {
371
- "name": "Guanine",
372
- "weight": 345.21,
373
- "normalized": "rG",
374
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](O)[C@@H]1O"
375
- },
376
- "rU": {
377
- "name": "Uracil",
378
- "weight": 306.17,
379
- "normalized": "rU",
380
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](O)[C@@H]1O"
381
- }
382
- },
383
- "For 2'-OMe and 2'-F modified siRNA": {
384
- "fU": {
385
- "name": "2'-fluoro-U",
386
- "weight": 308.16,
387
- "normalized": "rU",
388
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1O"
389
- },
390
- "fA": {
391
- "name": "2'-fluoro-A",
392
- "weight": 331.2,
393
- "normalized": "rA",
394
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1O"
395
- },
396
- "fC": {
397
- "name": "2'-fluoro-C",
398
- "weight": 307.18,
399
- "normalized": "rC",
400
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](F)[C@@H]1O"
401
- },
402
- "fG": {
403
- "name": "2'-fluoro-G",
404
- "weight": 347.19,
405
- "normalized": "rG",
406
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](F)[C@@H]1O"
407
- },
408
- "mU": {
409
- "name": "2'OMe-rU",
410
- "weight": 320.2,
411
- "normalized": "rU",
412
- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1O"
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- },
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415
- "name": "2'OMe-rA",
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- "weight": 343.24,
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- "normalized": "rA",
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- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1O"
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- },
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- "weight": 319.21,
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- "normalized": "rC",
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- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1O"
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- },
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- "weight": 359.24,
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- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1O"
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- }
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- }
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- },
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- "Mermade 12": {
435
- "For 2'-OMe and 2'-F modified siRNA": {
436
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437
- "name": "2'OMe-rA-ps",
438
- "weight": 359.31,
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- "weight": 335.28,
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- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1OP(=O)(S)O"
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- },
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- "name": "2'-fluoro-A-ps",
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- "weight": 347.27,
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- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1OP(=O)(S)O"
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- },
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- "l": {
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- },
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- "weight": 363.26,
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- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](F)[C@@H]1OP(=O)(S)O"
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- },
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- "weight": 323.25,
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483
- },
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486
- "weight": 308.16,
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- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1O"
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- },
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491
- "name": "2'-fluoro-A",
492
- "weight": 331.2,
493
- "normalized": "rA",
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- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1O"
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- },
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- "weight": 307.18,
499
- "normalized": "rC",
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- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](F)[C@@H]1O"
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- },
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503
- "name": "2'-fluoro-G",
504
- "weight": 347.19,
505
- "normalized": "rG",
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- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](F)[C@@H]1O"
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- "weight": 320.2,
511
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- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1O"
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- },
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- "E": {
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- "weight": 343.24,
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- "SMILES": "OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1O"
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- },
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- "weight": 319.21,
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- "normalized": "rC",
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- "SMILES": "OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1O"
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- },
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- "G": {
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- "weight": 359.24,
529
- "normalized": "rG",
530
- "SMILES": "OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1O"
531
- }
532
- }
533
- }
534
- };