Hi Nick,
So it is hard coded in Beam - we can change it there but I don’t think it’s
needed. Firstly the new parser will accept ‘$’ for quadruple bond as per
OpenSMILES specification.
The most portal way of encoding extra semantics with SMILES is use an auxiliary
suffix. This is basically what InChI does with AuxInfo and ChemAxon do with
extended CXSMILES It’s a good way of layering information on top the minimum
structural skeleton and keeping the parsing fast. The SMILES input order is
guaranteed and known at output - you can therefore refer to atoms by index or
explicitly use the atom classes / maps. Here’s an example of using atom maps to
indicate bond is broken.
C[CH:1]=[CH:2]C 1,2=brk
Another example to encode an aromatic fragment but will parse correctly, ‘ccc'
is not valid
o1cccc1 fragment=1,2,3
There is an example in the 1.5.4 release notes on how to add coordinates, 1.5.5
release notes have an example with atom classes / maps.
https://github.com/cdk/cdk/wiki/1.5.4-Release-Notes#wiki-smigen-outorder
You can encode and extend your encoding without having to modify the parser.
Hope that helps,
J
On 4 Feb 2014, at 10:37, Nick Vandewiele <nick.vandewi...@ugent.be> wrote:
> Hi,
>
> I am in the process of migrating some of my own code to CDK 1.5.4 from
> version 1.4.5.
>
> In the past, I modified SMILESParser by allowing the parsing of my custom
> symbols (eg ‘$’) that were not part of the original syntax of SMILES. I used
> them to represent transitioning bond orders in reactions for example.
> That was easy in v1.4.5 because you could just hard code these extra rules at
> the location where other bond order symbols such as ‘=’ and ‘#’ were parsed.
>
> I see that in v1.5.4 the job is taken over by BEAM, and this hard coded part
> of symbol parsing is not part of CDK anymore.
>
> Do you see how I can extend the SMILESParser with my own custom symbols?
>
> Regards,
> Nick
>
>
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