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WIP: adding display SMILES for polyketide motifs
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‎src/retromol/data/mxn.yml‎

Lines changed: 66 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,260 +1,326 @@
11
- name: A1
22
smiles: "O=C(O)CC(=O)SO"
3+
display_smiles: "O=C(CC([1*])=O)S[2*]"
34
pseudonyms: ["PK_A", "PK"]
45
- name: A1
56
smiles: "O=C(O)C=C(O)SO"
7+
display_smiles: "O=C(CC([1*])=O)S[2*]"
68
pseudonyms: ["PK_A", "PK"]
79

810
- name: A2^R
911
smiles: "C[C@@H](C(SO)=O)C(O)=O"
12+
display_smiles: "C[C@@H](C(S[2*])=O)C([1*])=O"
1013
stereochemistry: true
1114
pseudonyms: ["A2", "PK_A", "PK"]
1215
- name: A2^S
1316
smiles: "C[C@H](C(SO)=O)C(O)=O"
17+
display_smiles: "C[C@H](C(S[2*])=O)C([1*])=O"
1418
stereochemistry: true
1519
pseudonyms: ["A2", "PK_A", "PK"]
1620
- name: A2
1721
smiles: "CC(C(=O)O)C(=O)SO"
22+
display_smiles: "O=C(C(C)C([1*])=O)S[2*]"
1823
pseudonyms: ["PK_A", "PK"]
1924
- name: A2
2025
smiles: "CC(C(=O)O)=C(O)SO"
26+
display_smiles: "O=C(C(C)C([1*])=O)S[2*]"
2127
pseudonyms: ["PK_A", "PK"]
2228

2329
- name: A3
2430
smiles: "CC(C)(C(=O)O)C(=O)SO"
31+
display_smiles: "CC(C)(C(=O)[1*])C(=O)S[2*]"
2532
pseudonyms: ["PK_A", "PK"]
2633

2734
- name: A4^R
2835
smiles: "CC[C@@H](C(SO)=O)C(O)=O"
36+
display_smiles: "CC[C@@H](C(S[2*])=O)C([1*])=O"
2937
stereochemistry: true
3038
pseudonyms: ["A4", "PK_A", "PK"]
3139
- name: A4^S
3240
smiles: "CC[C@H](C(SO)=O)C(O)=O"
41+
display_smiles: "CC[C@H](C(S[2*])=O)C([1*])=O"
3342
stereochemistry: true
3443
pseudonyms: ["A4", "PK_A", "PK"]
3544
- name: A4
3645
smiles: "CCC(C(=O)O)C(=O)SO"
46+
display_smiles: "CCC(C(=O)[1*])C(=O)S[2*]"
3747
pseudonyms: ["PK_A", "PK"]
3848

3949
- name: A5^R
4050
smiles: "O=C([C@H](C(SO)=O)O)O"
51+
display_smiles: "O=C([C@H](C(S[2*])=O)O)[1*]"
4152
stereochemistry: true
4253
pseudonyms: ["A5", "PK_A", "PK"]
4354
- name: A5^S
4455
smiles: "O=C([C@@H](C(SO)=O)O)O"
56+
display_smiles: "O=C([C@@H](C(S[2*])=O)O)[1*]"
4557
stereochemistry: true
4658
pseudonyms: ["A5", "PK_A", "PK"]
4759
- name: A5
4860
smiles: "O=C(O)C(O)C(=O)SO"
61+
display_smiles: "O=C(C(C(S[2*])=O)O)[1*]"
4962
pseudonyms: ["PK_A", "PK"]
5063
- name: A5
5164
smiles: "O=C(C(O)=C(SO)O)O"
65+
display_smiles: "O=C(C(C(S[2*])=O)O)[1*]"
5266
pseudonyms: ["PK_A", "PK"]
5367

5468
- name: A6^R
5569
smiles: "C[C@@](C(O)=O)(C(SO)=O)O"
70+
display_smiles: "C[C@@](C([1*])=O)(C(S[2*])=O)O"
5671
stereochemistry: true
5772
pseudonyms: ["A6", "PK_A", "PK"]
5873
- name: A6^S
5974
smiles: "C[C@](C(O)=O)(C(SO)=O)O"
75+
display_smiles: "C[C@](C([1*])=O)(C(S[2*])=O)O"
6076
stereochemistry: true
6177
pseudonyms: ["A6", "PK_A", "PK"]
6278
- name: A6
6379
smiles: "CC(O)(C(=O)O)C(=O)SO"
80+
display_smiles: "CC(C([1*])=O)(C(S[2*])=O)O"
6481
pseudonyms: ["PK_A", "PK"]
6582

6683
- name: A7^R
6784
smiles: "O=C([C@H](C(SO)=O)CO)O"
85+
display_smiles: "O=C([C@H](C(S[2*])=O)CO)[1*]"
6886
stereochemistry: true
6987
pseudonyms: ["A7", "PK_A", "PK"]
7088
- name: A7^S
7189
smiles: "O=C([C@@H](C(SO)=O)CO)O"
90+
display_smiles: "O=C([C@@H](C(S[2*])=O)CO)[1*]"
7291
stereochemistry: true
7392
pseudonyms: ["A7", "PK_A", "PK"]
7493
- name: A7
7594
smiles: "O=C(O)C(CO)C(=O)SO"
95+
display_smiles: "O=C(C(C(S[2*])=O)CO)[1*]"
7696
pseudonyms: ["PK_A", "PK"]
7797
- name: A7
7898
smiles: "O=C(O)C(CO)=C(O)SO"
99+
display_smiles: "O=C(C(C(S[2*])=O)CO)[1*]"
79100
pseudonyms: ["PK_A", "PK"]
80101

81102
- name: A8
82103
smiles: "C=C(CC(=O)O)SO"
104+
display_smiles: "C=C(CC(=O)[1*])S[2*]"
83105
pseudonyms: ["PK_A", "PK"]
84106
- name: A8
85107
smiles: "CC(=CC(=O)O)SO"
108+
display_smiles: "C=C(CC(=O)[1*])S[2*]"
86109
pseudonyms: ["PK_A", "PK"]
87110

88111
- name: A9^R
89112
smiles: "C=C([C@@H](C(O)=O)C)SO"
113+
display_smiles: "C=C([C@@H](C([1*])=O)C)S[2*]"
90114
stereochemistry: true
91115
pseudonyms: ["A9", "PK_A", "PK"]
92116
- name: A9^S
93117
smiles: "C=C([C@H](C(O)=O)C)SO"
118+
display_smiles: "C=C([C@H](C([1*])=O)C)S[2*]"
94119
stereochemistry: true
95120
pseudonyms: ["A9", "PK_A", "PK"]
96121
- name: A9
97122
smiles: "C=C(SO)C(C)C(=O)O"
123+
display_smiles: "C=C(C(C([1*])=O)C)S[2*]"
98124
pseudonyms: ["PK_A", "PK"]
99125

100126
- name: A10^R
101127
smiles: "C=C([C@@H](C(O)=O)O)SO"
128+
display_smiles: "C=C([C@@H](C([1*])=O)O)S[2*]"
102129
stereochemistry: true
103130
pseudonyms: ["A10", "PK_A", "PK"]
104131
- name: A10^S
105132
smiles: "C=C([C@H](C(O)=O)O)SO"
133+
display_smiles: "C=C([C@H](C([1*])=O)O)S[2*]"
106134
stereochemistry: true
107135
pseudonyms: ["A10", "PK_A", "PK"]
108136
- name: A10
109137
smiles: "C=C(SO)C(O)C(=O)O"
138+
display_smiles: "C=C(C(C([1*])=O)O)S[2*]"
110139
pseudonyms: ["PK_A", "PK"]
111140

112141
- name: A11
113142
smiles: "C=C(SO)C(=O)C(=O)O"
143+
display_smiles: "C=C(S[2*])C(=O)C(=O)[1*]"
114144
pseudonyms: ["PK_A", "PK"]
115145

116146
- name: B^R1
117147
smiles: "O=C(C[C@@H](SO)O)O"
148+
display_smiles: "O=C(C[C@@H](S[2*])O)[1*]"
118149
stereochemistry: true
119150
pseudonyms: ["B1", "PK_B", "PK"]
120151
- name: B^S1
121152
smiles: "O=C(C[C@H](SO)O)O"
153+
display_smiles: "O=C(C[C@H](S[2*])O)[1*]"
122154
stereochemistry: true
123155
pseudonyms: ["B1", "PK_B", "PK"]
124156
- name: B1
125157
smiles: "O=C(O)CC(O)SO"
158+
display_smiles: "O=C(CC(S[2*])O)[1*]"
126159
pseudonyms: ["PK_B", "PK"]
127160

128161
- name: B^R2^R
129162
smiles: "C[C@@H]([C@@H](SO)O)C(O)=O"
163+
display_smiles: "C[C@@H]([C@@H](S[2*])O)C([1*])=O"
130164
stereochemistry: true
131165
pseudonyms: ["B2", "PK_B", "PK"]
132166
- name: B^R2^S
133167
smiles: "C[C@H]([C@@H](SO)O)C(O)=O"
168+
display_smiles: "C[C@H]([C@@H](S[2*])O)C([1*])=O"
134169
stereochemistry: true
135170
pseudonyms: ["B2", "PK_B", "PK"]
136171
- name: B^R2
137172
smiles: "CC([C@@H](SO)O)C(O)=O"
173+
display_smiles: "CC([C@@H](S[2*])O)C([1*])=O"
138174
stereochemistry: true
139175
pseudonyms: ["B2", "PK_B", "PK"]
140176
- name: B^S2^R
141177
smiles: "C[C@@H]([C@H](SO)O)C(O)=O"
178+
display_smiles: "C[C@@H]([C@H](S[2*])O)C([1*])=O"
142179
stereochemistry: true
143180
pseudonyms: ["B2", "PK_B", "PK"]
144181
- name: B^S2^S
145182
smiles: "C[C@H]([C@H](SO)O)C(O)=O"
183+
display_smiles: "C[C@H]([C@H](S[2*])O)C([1*])=O"
146184
stereochemistry: true
147185
pseudonyms: ["B2", "PK_B", "PK"]
148186
- name: B^S2
149187
smiles: "CC([C@H](SO)O)C(O)=O"
188+
display_smiles: "CC([C@H](S[2*])O)C([1*])=O"
150189
stereochemistry: true
151190
pseudonyms: ["B2", "PK_B", "PK"]
152191
- name: B2
153192
smiles: "CC(C(=O)O)C(O)SO"
193+
display_smiles: "CC(C(=O)[1*])C(O)S[2*]"
154194
pseudonyms: ["PK_B", "PK"]
155195

156196
- name: B^R3
157197
smiles: "CC(C(O)=O)([C@@H](SO)O)C"
198+
display_smiles: "CC(C([1*])=O)([C@@H](S[2*])O)C"
158199
stereochemistry: true
159200
pseudonyms: ["B3", "PK_B", "PK"]
160201
- name: B^S3
161202
smiles: "CC(C(O)=O)([C@H](SO)O)C"
203+
display_smiles: "CC(C([1*])=O)([C@H](S[2*])O)C"
162204
stereochemistry: true
163205
pseudonyms: ["B3", "PK_B", "PK"]
164206
- name: B3
165207
smiles: "CC(C)(C(=O)O)C(O)SO"
208+
display_smiles: "CC(C)(C(=O)[1*])C(O)S[2*]"
166209
pseudonyms: ["PK_B", "PK"]
167210

168211
- name: B^R4^R
169212
smiles: "CC[C@@H]([C@@H](SO)O)C(O)=O"
213+
display_smiles: "CC[C@@H]([C@@H](S[2*])O)C([1*])=O"
170214
stereochemistry: true
171215
pseudonyms: ["B4", "PK_B", "PK"]
172216
- name: B^R4^S
173217
smiles: "CC[C@H]([C@@H](SO)O)C(O)=O"
218+
display_smiles: "CC[C@H]([C@@H](S[2*])O)C([1*])=O"
174219
stereochemistry: true
175220
pseudonyms: ["B4", "PK_B", "PK"]
176221
- name: B^S4^R
177222
smiles: "CC[C@@H]([C@H](SO)O)C(O)=O"
223+
display_smiles: "CC[C@@H]([C@H](S[2*])O)C([1*])=O"
178224
stereochemistry: true
179225
pseudonyms: ["B4", "PK_B", "PK"]
180226
- name: B^S4^S
181227
smiles: "CC[C@H]([C@H](SO)O)C(O)=O"
228+
display_smiles: "CC[C@H]([C@H](S[2*])O)C([1*])=O"
182229
stereochemistry: true
183230
pseudonyms: ["B4", "PK_B", "PK"]
184231
- name: B4
185232
smiles: "CCC(C(=O)O)C(O)SO"
233+
display_smiles: "CCC(C(=O)[1*])C(O)S[2*]"
186234
pseudonyms: ["PK_B", "PK"]
187235

188236
- name: B^R5^R
189237
smiles: "O=C([C@H]([C@@H](SO)O)O)O"
238+
display_smiles: "O=C([C@H]([C@@H](S[2*])O)O)[1*]"
190239
stereochemistry: true
191240
pseudonyms: ["B5", "PK_B", "PK"]
192241
- name: B^R5^S
193242
smiles: "O=C([C@@H]([C@@H](SO)O)O)O"
243+
display_smiles: "O=C([C@@H]([C@@H](S[2*])O)O)[1*]"
194244
stereochemistry: true
195245
pseudonyms: ["B5", "PK_B", "PK"]
196246
- name: B^S5^R
197247
smiles: "O=C([C@H]([C@H](SO)O)O)O"
248+
display_smiles: "O=C([C@H]([C@H](S[2*])O)O)[1*]"
198249
stereochemistry: true
199250
pseudonyms: ["B5", "PK_B", "PK"]
200251
- name: B^S5^S
201252
smiles: "O=C([C@@H]([C@H](SO)O)O)O"
253+
display_smiles: "O=C([C@@H]([C@H](S[2*])O)O)[1*]"
202254
stereochemistry: true
203255
pseudonyms: ["B5", "PK_B", "PK"]
204256
- name: B5
205257
smiles: "O=C(O)C(O)C(O)SO"
258+
display_smiles: "O=C([1*])C(O)C(O)S[2*]"
206259
pseudonyms: ["PK_B", "PK"]
207260

208261
- name: B^R6^R
209262
smiles: "C[C@@](C(O)=O)([C@@H](SO)O)O"
263+
display_smiles: "C[C@@](C([1*])=O)([C@@H](S[2*])O)O"
210264
stereochemistry: true
211265
pseudonyms: ["B6", "PK_B", "PK"]
212266
- name: B^R6^S
213267
smiles: "C[C@](C(O)=O)([C@@H](SO)O)O"
268+
display_smiles: "C[C@](C([1*])=O)([C@@H](S[2*])O)O"
214269
stereochemistry: true
215270
pseudonyms: ["B6", "PK_B", "PK"]
216271
- name: B^S6^R
217272
smiles: "C[C@@](C(O)=O)([C@H](SO)O)O"
273+
display_smiles: "C[C@@](C([1*])=O)([C@H](S[2*])O)O"
218274
stereochemistry: true
219275
pseudonyms: ["B6", "PK_B", "PK"]
220276
- name: B^S6^S
221277
smiles: "C[C@](C(O)=O)([C@H](SO)O)O"
278+
display_smiles: "C[C@](C([1*])=O)([C@H](S[2*])O)O"
222279
stereochemistry: true
223280
pseudonyms: ["B6", "PK_B", "PK"]
224281
- name: B6
225282
smiles: "CC(O)(C(=O)O)C(O)SO"
283+
display_smiles: "CC(O)(C(=O)[1*])C(O)S[2*]"
226284
pseudonyms: ["PK_B", "PK"]
227285

228286
- name: B^R7^R
229287
smiles: "O=C([C@H]([C@@H](SO)O)CO)O"
288+
display_smiles: "O=C([C@H]([C@@H](S[2*])O)CO)[1*]"
230289
stereochemistry: true
231290
pseudonyms: ["B7", "PK_B", "PK"]
232291
- name: B^R7^S
233292
smiles: "O=C([C@@H]([C@@H](SO)O)CO)O"
293+
display_smiles: "O=C([C@@H]([C@@H](S[2*])O)CO)[1*]"
234294
stereochemistry: true
235295
pseudonyms: ["B7", "PK_B", "PK"]
236296
- name: B^S7^R
237297
smiles: "O=C([C@H]([C@H](SO)O)CO)O"
298+
display_smiles: "O=C([C@H]([C@H](S[2*])O)CO)[1*]"
238299
stereochemistry: true
239300
pseudonyms: ["B7", "PK_B", "PK"]
240301
- name: B^S7^S
241302
smiles: "O=C([C@@H]([C@H](SO)O)CO)O"
303+
display_smiles: "O=C([C@@H]([C@H](S[2*])O)CO)[1*]"
242304
stereochemistry: true
243305
pseudonyms: ["B7", "PK_B", "PK"]
244306
- name: B7
245307
smiles: "O=C(O)C(CO)C(O)SO"
308+
display_smiles: "O=C([1*])C(CO)C(O)S[2*]"
246309
pseudonyms: ["PK_B", "PK"]
247310

248311
- name: B^R8
249312
smiles: "C[C@](CC(O)=O)(SO)O"
313+
display_smiles: "C[C@](CC([1*])=O)(S[2*])O"
250314
stereochemistry: true
251315
pseudonyms: ["B8", "PK_B", "PK"]
252316
- name: B^S8
253317
smiles: "C[C@@](CC(O)=O)(SO)O"
318+
display_smiles: "C[C@@](CC([1*])=O)(S[2*])O"
254319
stereochemistry: true
255320
pseudonyms: ["B8", "PK_B", "PK"]
256321
- name: B8
257322
smiles: "CC(O)(CC(=O)O)SO"
323+
display_smiles: "CC(O)(CC(=O)[1*])S[2*]"
258324
pseudonyms: ["PK_B", "PK"]
259325

260326
- name: B^R9^R

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