Hi,
Here are all the cases I found:
Testing: [C-4].[Si+4]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[C-4] not found in [CH4-4].[SiH4+4]
Testing: [C-4].[Co].[W+4]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[C-4] not found in [CH4-4].[Co].[W+4]
Testing: [C-4].[W+4]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[C-4] not found in [CH4-4].[W+4]
Testing: [C-4].[Hf+4]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[C-4] not found in [CH4-4].[Hf+4]
Testing: [C-4].[Zr+4]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[C-4] not found in [CH4-4].[Zr+4]
Testing: [C-4].[Ti+4]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[C-4] not found in [CH4-4].[Ti+4]
Testing: [Al+3].[Al+3]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[Al+3] not found in [AlH3+3].[AlH3+3]
Testing: [Ga+3].[Ga+3]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[Ga+3] not found in [GaH3+3].[GaH3+3]
Tim
On Mon, Mar 17, 2014 at 3:49 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > While implementing a test described by Craig for multi-fragment SMILES
> canonicalization, I found this strange bug:
> ...
> > 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.
>
> I still don't even know where to start on this one. Can you give me a few
> other strings? My guess is that it's an implicit valence perception issue.
>
> -Geoff
>
>
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