Hi,
While implementing a test described by Craig for multi-fragment SMILES
canonicalization, I found this strange bug:
$ echo "[C-4]" | babel -ismi -ocan
[C-4]
1 molecule converted
16 audit log messages
$ echo "[C-4].C" | babel -ismi -ocan
C.[CH4-4]
1 molecule converted
14 audit log messages
There shouldn't be hydrogens added for the [C-4] molecule. The same bug
manifests itself when writing regular SMILES so this is not related to
canonicalization.
The test described by Craig: Take a multi-fragment SMILES string, split
this string using "." as delimiter and canonicalize the resulting
substrings. These substrings should be found in the canonical SMILES
generated from all the fragments. This test passes for all multi-fragment
SMILES from the 6.6M compounds in the eMolecules database except for a few
cases similar to the behavior illustrated above.
Any thoughts?
Tim
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