Many thanks Jan, that's very helpful.
Cheers,
George
On 20 February 2014 21:32, Jan Holst Jensen <j...@biochemfusion.com> wrote:
> Hi George et al,
>
> flexmatch(... 'all') is the most strict exact match that the
> Symyx/Accelrys cartridge has. You can relax the matching behavior to
> varying degrees by passing it different options, e.g. using 'tau' instead
> of 'all' will make the identity check tautomer-agnostic (to the extent that
> the cartridge will perceive tautomers "correctly" - an interesting
> discussion topic in itself).
>
> The various options to flexmatch() are well documented in the Accelrys
> documentation for the cartridge, but I don't know if that is publicly
> available.
>
> The short answer in my opinion: Yes, @= should be the equivalent of
> flexmatch(m1, m2, 'all'). To emulate flexmatch(..., 'all') with rdkit, I
> find a small gotcha with regards to chiral matching:
>
> -- Clearly not identical.
> postgres=# select mol('CCC') @= mol('CCF');
> ?column?
> ----------
> f
> (1 row)
>
> -- Clearly identical.
> postgres=# select mol('CCC') @= mol('CCC');
> ?column?
> ----------
> t
> (1 row)
>
> -- Ala versus dAla - should *not* be identical ?
> postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@@H](N)C(=O)O');
> ?column?
> ----------
> t
> (1 row)
>
> To get the expected behavior of @= you need to turn on chiral matching.
> Even though the parameter says that is controls SSS behavior it apparently
> also has an effect on exact matching:
>
> postgres=# set rdkit.do_chiral_sss=true;
> SET
> -- Ala versus dAla - no longer identical.
> postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@@H](N)C(=O)O');
> ?column?
> ----------
> f
> (1 row)
>
> -- Ala versus Ala - phew, identical.
> postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@H](N)C(=O)O');
> ?column?
> ----------
> t
> (1 row)
>
> Cheers
> -- Jan
>
>
>
> On 2014-02-20 13:46, George Papadatos wrote:
>
> Hi there,
> Wouldn't that be (at least partly) possible with an exact structure search?
>
> - @= : returns whether or not two molecules are the same.
>
> Cheers,
> George
>
>
> On 20 February 2014 11:59, Greg Landrum <greg.land...@gmail.com> wrote:
>
>> Sounds interesting. Can anyone provide a pointer to a doc with more
>> specific info about what this actually does?
>>
>>
>> On Thursday, February 20, 2014, Michał Nowotka <mmm...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> Symix cartridge defines something called flexmatch - "Finds records
>>> that are an exact match of the 2D or 3D structure that you specify in the
>>> query."
>>> Is there anything similar in RDKit cartridge? I looked into
>>> documentation and couldn't find this feature.
>>>
>>> Regards,
>>> Michal Nowotka
>>>
>>
>>
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