On Fri, Feb 21, 2014 at 5:45 PM, Jan Holst Jensen <[email protected]>wrote:
> Hi Greg,
>
> It would be great to gain the experience. I am working on a registration
> project where we will likely need to surface additional functions in the
> cartridge, just to try them out. So, knowing how to do that in a way where
> things that turn out useful can be contributed back cleanly would be great.
>
>
Sounds good.
>
> > if structures don't have conformers
>
> Ah, yes; good question. Decisions, decisions... I'll dodge the question
> :-) and say it sounds like a perfect fit for an optional parameter, e.g.
>
> mol_to_ctab(m mol, add_depiction_if_missing bool default true)
>
> I would go for default true because I believe that is the general
> preference.
>
>
Having the optional argument that defaults to true make sense to me.
Here's an attempt to briefly summarize what needs to be changed in order to
add the new functionality:
- Add mol_to_ctab to rdkit_io.c
- Add molToCtabText (or some such thing) to adapter.cpp and rdkit.h
- Add mol_to_ctab() definitions to rdkit.sql91.in and, if you want to
support older versions of postgres, rdkit.sql.in
- Update link dependencies in Makefile if necessary (will be necessary if
you add depictions)
- Add tests to one of the files in sql/ (the most logical place is probably
rdkit-91.sql and rdkit-pre91.sql if you are supporting older versions) and
the corresponding output file in expected/
I think that's it.
-greg
> Cheers
> -- Jan
>
>
> On 2014-02-21 16:47, Greg Landrum wrote:
>
> Hi Jan,
>
> Great idea. I'd be happy to add it, but I can also "talk" you through it
> if you want to gain the experience.
>
> One important question: if structures don't have conformers (if they are
> loaded from SMILES, for example), should ctabs with all zero coordinates be
> generated or should depictions be generated?
>
> -greg
>
>
>
> On Fri, Feb 21, 2014 at 2:23 PM, Jan Holst Jensen
> <[email protected]>wrote:
>
>> Hi Greg,
>>
>> Are there any plans for a mol_*to*_ctab() function in the PG cartridge ?
>> Would make SD file export from the database a bit easier.
>>
>> If there are no immediate plans, I can take a stab at adding it myself.
>>
>> * Looks like rdkit_io.c is the place to add it ?
>> * Should I manually define the new SQL function in rdkit.sql.in, or is
>> there some higher-level place I should add it instead ?
>>
>> Cheers
>> -- Jan
>>
>>
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