TJ,
Thanks for letting us know about this work. I haven't had a chance to look
at it in detail yet, but after the skim that I did, it certainly looks
interesting. What are your future plans w.r.t. openchord?
-greg
On Mon, Feb 24, 2014 at 9:41 PM, TJ O'Donnell <[email protected]> wrote:
> 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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