#875 canonicalization of disconnected SMILES

[Jeff Janes]

(Discussed on openbabel-discuss mailing list, under same subject)

I'm using Open Babel 2.3.2 to canonicalize some SMILES strings.

I thought that each fragment of a disconnected SMILES would be canonicalized separately (which I believe agrees what what is explained in http://openbabel.org/dev-api/canonical_code_algorithm.shtml)

However, that is not the case in the below example, adding a fragment causes the first fragment to canonicalize differently:

echo 'OC(=O)C@@HO)O.CNCC@@HO)O' | obabel -ismi -ocan
OC(=O)C@@HO)O.CNCC@@HO)O
1 molecule converted

echo 'OC(=O)C@@HO)O' | obabel -ismi -ocan
OC@HO)C(=O)O
1 molecule converted

[Jeff Janes]

The formatting on this ticket get mangled. Let me try again with correct formatting.

echo 'OC(=O)[C@@H]([C@H](C(=O)O)O)O.CNC[C@@H](c1ccc(c(c1)O)O)O' | obabel -ismi -ocan
OC(=O)[C@@H]([C@H](C(=O)O)O)O.CNC[C@@H](c1ccc(c(c1)O)O)O

echo 'OC(=O)[C@@H]([C@H](C(=O)O)O)O' | obabel -ismi -ocan
O[C@H]([C@H](C(=O)O)O)C(=O)O

[Geoff Hutchison]

Thanks for the bug and the follow-up. This is now fixed in git master, so I'm closing the bug. Thanks!