SMARTS expression test set

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SMARTS expression test set

Christian E
Hello everyone,

I am looking for a large set of SMARTS expressions in order to test my
SMARTS parser. Any valid SMARTS expression will do and the more the
better.

Thanks in advance from the University of Hamburg, Germany
Christian


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Re: SMARTS expression test set

Noel O'Boyle
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See my test set and also Joerg's comment at
http://baoilleach.blogspot.com/2008/05/cheminformatics-toolkit-face-off-smarts.html
- Noel

2008/11/6 Christian Ehrlich <[hidden email]>:

> Hello everyone,
>
> I am looking for a large set of SMARTS expressions in order to test my
> SMARTS parser. Any valid SMARTS expression will do and the more the
> better.
>
> Thanks in advance from the University of Hamburg, Germany
> Christian
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
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Re: SMARTS expression test set

Noel O'Boyle
Administrator
Sorry - in my previous email that should be "see Rajarshi's test set".
It's a test set he put together to test the CDK.

2008/11/11 Noel O'Boyle <[hidden email]>:

> See my test set and also Joerg's comment at
> http://baoilleach.blogspot.com/2008/05/cheminformatics-toolkit-face-off-smarts.html
> - Noel
>
> 2008/11/6 Christian Ehrlich <[hidden email]>:
>> Hello everyone,
>>
>> I am looking for a large set of SMARTS expressions in order to test my
>> SMARTS parser. Any valid SMARTS expression will do and the more the
>> better.
>>
>> Thanks in advance from the University of Hamburg, Germany
>> Christian
>>
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
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>> _______________________________________________
>> OpenBabel-discuss mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>

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Re: SMARTS expression test set

Andrew Dalke
In reply to this post by Christian E
On Nov 6, 2008, at 12:08 PM, Christian Ehrlich wrote:
> I am looking for a large set of SMARTS expressions in order to test my
> SMARTS parser. Any valid SMARTS expression will do and the more the
> better.

In addition to Noel's pointers, see:
   http://www.daylight.com/dayhtml_tutorials/languages/smarts/ 
smarts_examples.html
   ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/
pubchem_fingerprints.txt

You might also be interested in my SMARTS parser,
which is part of FROWNS:
   http://frowns.sourceforge.net/

FROWNS is no longer being maintained, and I wouldn't really
advise you to use the package for your work, but as I wrote
those parser's, I'm rather fond of them. I say that they are
some of the clearest examples of parsing SMILES and SMARTS
that you'll find. (The SMILES one more than SMARTS.)

SMILES:
http://frowns.cvs.sourceforge.net/viewvc/frowns/frowns/smiles_parsers/ 
Smiles.py

SMARTS:
http://frowns.cvs.sourceforge.net/viewvc/frowns/frowns/smiles_parsers/ 
Smarts.py

The SMILES and SMARTS parsers in RDKit are based on
lex and yacc, if you're interested in another approach.

                                Andrew
                                [hidden email]



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Re: SMARTS expression test set

Christian E

Hi Everone,

some time has passed and a bison/flex parser and a matcher emerged.

Now I am looking for a SMARTS matching test set. It should contain SMARTS
and corresponding SMILES in which the SMARTS expression should be contained.

Some here, the more the better.

Christian

ps: Anyone interested in my SMARTS collection feel free to contact me.

 

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Re: SMARTS expression test set

Christian E
In reply to this post by Andrew Dalke
Hi Everyone,

some time has passed and a bison/flex parser and a matcher emerged.

Now I am looking for a SMARTS matching test set. It should contain SMARTS and corresponding SMILES in which the SMARTS expression should be contained.

Some here, the more the better.

Christian

ps: Anyone interested in my SMARTS collection feel free to contact me.

 
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Re: SMARTS expression test set

Andrew Dalke
On Oct 13, 2009, at 3:10 PM, Christian E wrote:
> some time has passed and a bison/flex parser and a matcher emerged.

Nice! There aren't many of those for SMARTS. Have you seen the one in  
RDKit?

> Now I am looking for a SMARTS matching test set. It should contain  
> SMARTS
> and corresponding SMILES in which the SMARTS expression should be  
> contained.

You should also have some which are close but exclude the molecule
.

Since I mentioned RDKit, its test cases are in C++ code in:

   rdkit/Code/GraphMol/SmilesParse/smatest.cpp
and many are in the form of this snippet

   // Issue 71
   _checkMatches("CCC", "CCC", 1, 3);
   _checkMatches("CCC", "C1CC1", 1, 3);

   // this pattern caused crashes at one point
   _checkNoMatches("[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]", "N#CCC#N");


There's also Noel O'Boyle's regression code for all the cross-
comparisons that he's done, but it's not part of his Cinfony code.

> ps: Anyone interested in my SMARTS collection feel free to contact me.

I would, for general principles, but I haven't done SMARTS parsing  
for some years.


                                Andrew
                                [hidden email]



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