Multiple molecule in some SMILES

Learning to Smell
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#1

‘.’ in SMILES should mean two seperate molecule, here in the training set, some of the rows contains ‘.’ . Some of them should be salt, but some are just two molecules, for example 498 COCC1CC=C2C(C1)C(C)CC2(C)C.COCC1CC=C2C(C)CC(C)(C)C2C1.

Here is the full list:

70 CC(C(=O)[O-])O.[Na+]
90 CCCCc1nc(C)cnc1C.CCCCc1ncc(nc1C)C
142 CC1CCc2c(C1)occ2C.CC1CCC(C(C1)OC(=O)C)C(C)C.CC1CCC(=C(C)C)C(=O)C1.CC1CCC(C(=O)C1)C(C)C.CC1CCC(C(C1)O)C(C)C.CC1CCC2(CC1)OCC2C
248 OC1C[C@H]2C([C@]1(C)CC2)(C)C.C=CC(CCC=C(C)C)C.C=CCc1ccc(c(c1)OC)OC.OC/C=C(\CCC=C(C)C)/C.O=C/C=C(\CCC=C(C)C)/C
265 [NH4+].[NH4+].[S-2]
305 OCCOc1ccc(cc1N)N.Cl.Cl
454 C(C[C@@H](C(=O)O)N)CN.Cl
462 CC(CCCC(C)(C)O)CC=O.Cc1c[nH]c2ccccc12
498 COCC1CC=C2C(C1)C(C)CC2(C)C.COCC1CC=C2C(C)CC(C)(C)C2C1
507 CC(=O)O.OCCC=C(CCC=C(C)C)C
584 CCCCCCC(CCOC(=O)C)OC(=O)C.CCCCCCC(CCO)O
648 C=C1CC[C@H]2C[C@H]1C2(C)C.Cc1ccc(cc1)C(C)C.O=CC1=CCC(=CC1)C(C)C.O=Cc1ccc(cc1)C(C)C
994 CC(=O)OC/C(=C\CC[C@]1(C)C2C[C@@H]3C1(C)C3C2)/C.CC(=O)OC/C(=C\CC[C@]1(C)[C@H]2CC[C@@H](C1=C)C2)/C
1031 CC1=C(CCO1)[S-].CC(=O)O
1066 CCO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O.COc1cc(ccc1O)C=O
1288 C=C1[C@H]2CC[C@H]3[C@]1(C)CCCC([C@H]23)(C)C.FB(F)F.OC=O
1293 OCC(O)C.CCCCCCCCCCCCCCCCCC(=O)O
1542 CCCCCCCOP(=S)(OCCCCCCC)[S-].CCCCCCCOP(=S)(OCCCCCCC)[S-].[Zn+2]
1574 CCC(C)C(=O)C(=O)[O-].[Na+]
1611 CCC(=O)CCC1C(=CCCC1(C)C)C.C#CCO
1646 CCCCCCCCCCC=O.CCCCCCCCC(C)C=O
1681 O=C1C2(C)CCC(C1(C)C)C2.COc1ccc(cc1)CC=C.C/C=C/c1ccc(cc1)OC
1801 C/C(=C/CC[C@]1(C)C2C[C@H]3C(C2)C13C)/COC(=O)C.C/C(=C/CC[C@@]1(C)C(=C)[C@@H]2CC[C@H]1C2)/COC(=O)C
1915 N.O
1995 C[C@]1(O)CC[C@@H](CC1)C(O)(C)C.O
2087 COC(=O)[C@@H](Cc1cnc[nH]1)N.Cl
2149 CCCCCCCCCCCCC(S(=O)(=O)[O-])C(=O)OCC(CCCC)CC.[Na+]
2318 Cn1cnc2c1c(=O)n(C)c(=O)n2C.Cn1cnc2c1c(=O)[nH]c(=O)n2C.Oc1cc2OC(c3ccc(c(c3)O)O)C(Cc2c(c1)O)O
2389 CCCCCCCCCCCCOS(=O)(=O)[O-].[Na+]
2493 CCCCCCC(OC(=O)C)CCOC(=O)C.CCCCCCC(CCO)O
2540 C[S+](C)CC[C@@H](C(=O)[O-])N.Cl
2587 CC(C)CC(=O)C(=O)[O-].[Na+]
2820 CC1CCC2C(C)(C)C3CC12CC(=O)C3C.CC1C2CC23C(CCCC3(CC1=O)C)(C)C
2880 CC(=O)CCC/C=C/C=C/C=C.CC(=O)CCC/C=C\C=C\C=C.CCC(=O)CC/C=C/C=C/C=C.CCC(=O)CC/C=C\C=C\C=C.CCCC(=O)C/C=C/C=C/C=C.CCCC(=O)C/C=C\C=C\C=C
2888 C=C1CC[C@H]2C[C@@H]1C2(C)C.Cc1ccc(cc1)C(C)C.O=CC1=CCC(=CC1)C(C)C.O=Cc1ccc(cc1)C(C)C
2892 C/C/1=C\CCC(=C2/C(=C\C1)/CC2)C.CC(=CCC1=C(O)C(C(=O)C(=C1O)C(=O)CC(C)C)(CC=C(C)C)CC=C(C)C)C.CC(=CCC1=C(O)C(C(=O)C(=C1O)C(=C)CC(C)C)(O)CC=C(C)C)C
2899 COc1ccc(cc1)C(=O)OCC(=O)[O-].[Na+]
3005 C/C=C/c1ccccc1.C=CCc1ccc(c(c1)OC)O
3109 CCCCCCCCCCCCCCCCCC(=O)O.CC(CO)O
3144 Cc1ccccc1C(O)O.C(C(CO)O)O
3190 CCc1cnc(C)cn1.CCc1cncc(C)n1
3216 CCC(=O)CCC1C(=CCCC1(C)C)C.OCC#C
3254 O=CC1C(C)CC(=CC1C)C.O=CC1CC(=CC(C1C)C)C
3263 OC(c1ccccc1C)O.OCC(CO)O
3347 COc1cc(ccc1[O-])/C=C/C(=O)O.[Na+]
3602 CCc1c(C)nc(C)cn1.CCc1c(C)ncc(C)n1
3671 NCCSS(=O)(=O)[O-].[Na+]
4008 CC[C@@]1(O)C(=O)OCc2c1cc1c3nc4ccc(c(c4cc3Cn1c2=O)CN(C)C)O.Cl
4014 CC(C)CC(=O)O.N
4119 CC(C(=O)O)C.CCOc1cc(C=O)ccc1[O-]
4210 CC(C)c1cnc(cn1)OC.CC(C)c1cncc(n1)OC.CC(C)c1c(nccn1)OC
4250 OC1CC(OC1COP(=O)(OP(=O)(OP(=O)(O)[O-])[O-])O)n1cnc2c1ncnc2N.[Na+].[Na+]
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#2

Another issue in the training data was the stereo bond. For example, #1015 OC1CCCC(C1)C1C[C@H]2C[C@H]1C(C2(C)C)C , the molecule looks like 企业微信截图_16010355264716 .
I don’t think these two stereo bond in the ring can be connected to one atom.

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#3

cc @guillaumegodin in case this is relevant (as it seems it is unanswered yet)

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#4

this is correct molecule it’s a real complex ring that exist in natural molecules

#5

for the molecules with . : when it salt you can remove them. you are right those mixture exist in the dataset cause the mixture was smell and describe.