Hi there,
Thanks for including me in the developer discussion, the bug report must have
come from somebody else because I didn't submit one.
I'm actually looking at a bunch of chemical reactions, but I'm not using the
OpenBabel functionality for reactions because I had issues with it - just the
individual reactants and products.
Here is a bunch of complexes generated by OpenBabel canonical SMILES that have
formaldehyde occurring in different orderings. My temporary workaround is to
split the complex by ".", canonicalize each one, and sort alphabetically. It
would be great to have the fix implemented though.
Thanks,
- Lee-Ping
O=[CH2].[NH3].[NH4]
[CH2]=O
[NH2][C@@H]1[NH]O1.[CH2]=O
O=[CH2].[NH3].[NH3]
[CH2]=O.[NH3]
[CH2]=O.[OH2].[NH3]
[CH2]=O.[OH2]
O=[CH2].[OH2].[OH2]
[CH2]=O.[OH2].[NH3]
[CH2]=O.[NH3]
[CH2]=O.[OH2].[NH3]
[CH3][CH2][NH2].[CH2]=O
O=[CH2].[NH3].[H][H]
O=[CH2].[NH3].[NH4]
[CH2]=O.[OH2]
[CH2]=O.[NH3]
[CH2]=O.[OH2].[NH3]
[CH2]=O.[NH2]
[CH2]=O
O=[CH2].O=[C]
O=[CH2].O=[C]
[CH2]=O.[CH2]
[CH2]=O.[OH2]
[CH2]=O.[NH]
[CH2][C][O].[CH2]=O
[OH]N=[CH2].[CH2]=O.[OH2]
[NH][CH][OH].[CH2]=O.[OH2]
[NH][CH]O[CH2]OC(=O)[OH].[CH2]=O
[NH][CH]O[CH2]OC(=O)[OH].[CH2]=O
[OH][CH2]OC(=O)[OH].[CH2]=O.[C][NH]
[CH2]=O.[OH2]
O=[CH2].[H][H]
[CH2]=O.[OH2]
[CH2]=O.[OH2].[NH3]
[CH2]=O.[OH2]
[CH2]=O.[CH3][NH2].[NH3]
[CH2]=O.[NH3]
[CH2]=O
O1O[CH]1.O=[CH2]
O=[CH2].[CH3][CH]
[CH2]=O.[O]
On Feb 17, 2014, at 11:10 AM, Tim Vandermeersch <tim.vandermeer...@gmail.com>
wrote:
> Hi,
>
> I found the examples in the bug report. The code in canon.h handles
> disconnected fragments correctly. However, in smilesformat.cpp the symmetry
> classes are computed for the molecule as a whole. This is not what the
> canonical coding algorithm expects and the resulting smiles may be different
> when canonicalized separately or as part of a complex.
>
> I have a simple patch to fix this here:
> http://moldb.net/timvdm/multi_mol_smiles.patch
>
> With this patch I get the correct results:
>
> $ echo 'OC(=O)[C@@H]([C@H](C(=O)O)O)O.CNC[C@@H](c1ccc(c(c1)O)O)O' | obabel
> -ismi -ocan
> O[C@H]([C@H](C(=O)O)O)C(=O)O.CNC[C@@H](c1ccc(c(c1)O)O)O
> 1 molecule converted
> $ 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
> 1 molecule converted
>
> This patch should only affect multi-molecule smiles. Single fragment smiles
> are not affected. I can run this patch on a few million molecules and compare
> the results to get a better view (with more confidence) of what would
> actually change.
>
> Tim
>
>
> On Mon, Feb 17, 2014 at 6:41 PM, Tim Vandermeersch
> <tim.vandermeer...@gmail.com> wrote:
> Hi,
>
> Are there any examples of disconnected SMILES that have this problem? IIRC, a
> canonical code is created for each fragment individually and these are later
> sorted to create the entire canonical order. A quick look at the code
> confirms this but I'll try to test some cases tonight to see if this is still
> the case.
>
> Tim
>
>
> On Mon, Feb 17, 2014 at 4:50 PM, Geoffrey Hutchison
> <geoff.hutchi...@gmail.com> wrote:
> > This is actually a pretty bad thing. But it may not be that easy to fix,
> > and would result in a major change to the SMILES that OpenBabel produces
> > (very unfortunate, as it requires large databases to be completely
> > re-canonicalized).
>
> As far as I can tell, the code is still there.. As far as the different
> canonicalization, we had a variety of bugs in the canonicalization going from
> 2.2 -> 2.3. I agree, it's not present, but I think it's an important bug to
> fix soon and will be part of the 2.4.0 release.
>
> -Geoff
>
>
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