Hi All
I would like to announce the availability of a somewhat different
rdkit-based
postgresql extension. This uses rdkit for all the basic cheminformatics
functions (canonical smiles, molfile handling, smarts matching,
fingerprints, etc.)
but is based on the use of postgres' plpython language.
This does not use the existing rdkit postgres cartridge, although I have
demonstrated that the two can be used side-by-side (via the use of
rdkit pickled mol objects).
I hope this use of python might make it easier to extend postgres even
further with
additional functions based on rdkit. The code can be checked out from
sourceforge using this:
svn checkout svn://svn.code.sf.net/p/sci3d/code/trunk/openchord/src/rdkitchord
This is a work in progress, so I would appreciate any feedback. There are
still
some wrinkles that need to be ironed out. I plan to document
the installation and useage better, probably using github.
TJ O'Donnell
On Sat, Feb 22, 2014 at 10:53 PM, Greg Landrum <[email protected]>wrote:
>
> 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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>
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