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Describe the bug Certain isomeric SMILES strings exhibit cyclical canonicalization.
This is related to this and this issue, but I did not see this specific problem mentioned.
To Reproduce The code snippet below checks if canonicalization 1+3 and 2+4 times gives the same SMILES representation.
from rdkit import Chem def check_canon(smi): can1 = Chem.CanonSmiles(smi) can2 = Chem.CanonSmiles(can1) can3 = Chem.CanonSmiles(can2) can4 = Chem.CanonSmiles(can3) cyc1 = can1 == can3 cyc2 = can2 == can4 if cyc1 and cyc2: return True smi = r"CC1=C\C/C=C(\C)CC[C@H]2C(C)(C)[C@@H](\\C=C/1)CC[C@]2(C)O" print(check_canon(smi))
These SMILES also exhibit this behaviour:
COC1=N\C2=CC(=O)c3c(c(O)c(C)c4c3C(=O)C(C)(O/C=C/C(OC)C(C)C(OC(C)=O)C(C)C(O)C(C)C(O)C(C)/C=C\C=C/1C)O4)C2=O CC1C2c3cc4/c5c6c7c8c9c%10c6c4c4c3C3=C6c%11c%12c%13c%14c%15c(c9c9c%16c8c(c8/c(c%17c%18c%19c(c(c%11c%11c%19c%19c%17c8c%16c(c%149)c%19c%13%11)C62)C1C%181C[N+](C)(C)C1)=C\C\C=5)C7)C%10C4C31C[N+](C)(C)CC%12%151 CC1=C\[C@H](C)C[C@@]2(C)CC[C@@H](O2)[C@@]23CC[C@@](C)(C[C@@H](O2)[C@H]2O[C@](C)(CC2=O)[C@@H](O)[C@@H]2CC[C@@]4(CCC[C@H](O4)[C@@H](C)C(=O)O[C@@H]4C[C@@H]([C@@]5(O)OCC[C@@H](C)[C@H]5O)O[C@@H]4/C=C/1)O2)O3 CC1=C/[C@H]2O[C@@H](C/C=C/C=C/C(=O)O[C@@H]3C[C@@H](/C=C/C/C=C/1)O[C@@H](C/C=C\CCO)[C@]3(C)CO)C[C@H](O)[C@H]2C CC(=O)OCC1=C\CC/C(C)=C/CC[C@@]2(C)CC[C@@](C(C)C)(/C=C/1)O2 CC1=C\C/C=C(\C)CC[C@H]2C(C)(C)[C@@H](\C=C/1)CC[C@]2(C)O CC(=O)OCC1=C/[C@@H]2OC(=O)[C@H](C)[C@@]2(O)[C@@H](OC(C)=O)[C@H]2[C@]3(CC[C@H](OC(C)=O)[C@]2(C)[C@@H](OC(=O)COC(=O)CC(C)C)\C=C/1)CO3 CC(=O)OCC1=C/[C@@H]2OC(=O)[C@H](C)[C@@]2(O)[C@@H](OC(C)=O)[C@H]2[C@]3(CC[C@H](OC(C)=O)[C@]2(C)[C@@H](OC(C)=O)\C=C/1)CO3 C=Cc1c(C)/c2[nH]/c1=C\C1=N/C(=C\C3=C(C)C4C(=O)N(Cc5cccc(C#Cc6cccc(Nc7ncnc8cc(OCCOC)c(OCCOC)cc78)c6)c5)C(=O)/C(=C5/N=C(/C=2)[C@@H](C)[C@@H]5CCC(=O)OC)C4N3)C(CC)=C1C CC1=C\C[C@H](O)/C=C/C(C)=C/[C@@H](NC(=O)[C@H](C)O)[C@]2(C)C(=O)O[C@H](C[C@H](O)/C=C/1)[C@@H](C)C2=O CC1=C/[C@H]2O[C@@H](C/C=C/C=C/C(=O)O[C@@H]3C[C@@H](/C=C/C/C=C/1)O[C@@H](C/C=C\C[C@@H](O)C(=O)O)[C@]3(C)CO)C[C@H](O)[C@H]2C c1ccc2/c3[nH]/c(c2c1)=N\c1ccc(cc1)-c1nc2cc(ccc2o1)/N=c1/[nH]/c(c2ccccc12)=N/c1ccc2nc(oc2c1)-c1ccc(cc1)/N=3 c1ccc2/c3[nH]/c(c2c1)=N\c1ccc(cc1)-c1nc2ccc(cc2o1)/N=c1/[nH]/c(c2ccccc12)=N/c1ccc2nc(oc2c1)-c1ccc(cc1)/N=3 CC1=C/[C@@H](C)C[C@]2(C)CC[C@H](O2)[C@]23CC[C@](C)(C[C@H](O2)[C@@H]2O[C@@](C)(CC2=O)[C@@H](O)[C@H]2CC[C@@]4(CCC[C@@H](O4)[C@H](C)C(=O)O[C@H]4C[C@H]([C@]5(O)OCC[C@H](C)[C@@H]5O)O[C@H]4\C=C/1)O2)O3 CC1=C/[C@@H](C)C[C@]2(C)CC[C@H](O2)[C@]23CC[C@](C(=O)O)(C[C@H](O2)[C@@H]2O[C@@](C)(CC2=O)[C@@H](O)[C@H]2CC[C@@]4(CCC[C@@H](O4)[C@H](C)C(=O)O[C@H]4C[C@H]([C@]5(O)OCC[C@H](C)[C@@H]5O)O[C@H]4\C=C/1)O2)O3 CC1=C/[C@@H](C)C[C@]2(C)CC[C@H](O2)[C@]23CC[C@](CO)(C[C@H](O2)[C@@H]2O[C@@](C)(CC2=O)[C@@H](O)[C@H]2CC[C@@]4(CCC[C@@H](O4)[C@H](C)C(=O)O[C@H]4C[C@H]([C@]5(O)OCC[C@H](C)[C@@H]5O)O[C@H]4\C=C/1)O2)O3 COC(=O)C1=C/c2cc3c(cc2-c2c(cc(OC)c(OC)c2OC)\C=C/1C(=O)OC)OCO3
Expected behavior Stacking Chem.CanonSmiles calls should provide the same SMILES representation rather than exhibiting cyclical behaviour.
Chem.CanonSmiles
Configuration (please complete the following information):
The text was updated successfully, but these errors were encountered:
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Describe the bug
Certain isomeric SMILES strings exhibit cyclical canonicalization.
This is related to this and this issue, but I did not see this specific problem mentioned.
To Reproduce
The code snippet below checks if canonicalization 1+3 and 2+4 times gives the same SMILES representation.
These SMILES also exhibit this behaviour:
Expected behavior
Stacking
Chem.CanonSmilescalls should provide the same SMILES representation rather than exhibiting cyclical behaviour.Configuration (please complete the following information):
The text was updated successfully, but these errors were encountered: