Problem parsing tetrahedral stereochemistry with ring closure as last element

johnmay / beam

SMILES Toolkit

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Problem parsing tetrahedral stereochemistry with ring closure as last element #6

Closed baoilleach closed 6 years ago

baoilleach commented 6 years ago

(With CDK2.1) The following SMILES strings represent the same molecule:

[C@]1(Cl)(F)I.Br1
[C@@](Cl)1(F)I.Br1
[C@](Cl)(F)1I.Br1
[C@@](Cl)(F)(I)1.Br1

The last SMILES string triggers an exception:

org.openscience.cdk.exception.InvalidSmilesException: org.openscience.cdk.exception.InvalidSmilesException: could not parse '[C@@](Cl)(F)(I)1.Br1', Invaid number of verticies for TH1/TH2 stereo chemistry

johnmay commented 6 years ago

https://github.com/johnmay/beam/commit/335ee67bfe886613cd0ed27ae89a98150c46af13