Trouble with Standardizer

Hi,

 

I'm using jchem 5.8.3 API

 

I'm trying to standardize the following molecule:

 

[O-][N+]1=CC=CC=C1  =>  O=N1=CC=CC=C1

 

The following command does not standardize it:

 

Standardizer standardizer = new Standardizer("[!#1:1]-[N+:2](-[O-:3])=[*:4]>>[!#1:1]-[N:2](=[O:3])=[*:4]");

 

However, this command does:

 

Standardizer standardizer = new Standardizer("[N+:1]-[O-:2]>>[N:1]=[O:2]");

(but this command is too general, I would like to use the previous one)

 

Can you tell me what I'm doing wrong in the first standardizer command?

 

Thanks.

 

Andrew 

 

In case it is useful, the following search finds a match in the molecule as desired:

 

Molecule mol = MolImporter.importMol("[O-][N+]1=CC=CC=C1");

MolHandler mhl = new MolHandler("[!#1]-[N+]([O-])=*", true); // if true, import SMILES string as SMARTS

        Molecule query = mhl.getMolecule();

 

MolSearch s = new MolSearch();

         MolSearchOptions so = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);

         so.setQueryAbsoluteStereo(true);

         so.setChargeMatching(SearchConstants.CHARGE_MATCHING_EXACT);

         so.setImplicitHMatching(SearchConstants.IMPLICIT_H_MATCHING_IGNORE); // we won't match H's at all here

         so.setDoubleBondStereoMatchingMode(StereoConstants.DBS_ALL);

         so.setExactBondMatching(true);

         so.setStereoSearchType(SearchConstants.STEREO_EXACT);

         so.setTautomerSearch(SearchConstants.TAUTOMER_SEARCH_OFF);

         s.setSearchOptions(so);

s.setTarget(mol);

         s.setQuery(query);

         SearchHit[] sh = s.findAllHits();

if (sh!=null) {

 

// match found

 

}

 

 

Standardizer standardizer = new Standardizer("[!#1:1]-[N+:2](-[O-:3])=[*:4]>>[!#1:1]-[N:2](=[O:3])=[*:4]");

However, this command does:

	Standardizer standardizer = new Standardizer("[N+:1]-[O-:2]>>[N:1]=[O:2]");
(but this command is too general, I would like to use the previous one)

Can you tell me what I'm doing wrong in the first standardizer command?

In first command the nitrogen is connected with double bond to the any atom and with single bond to the list atom, while in your input molecule ("[O-][N+]1=CC=CC=C1") these bonds are aromatic in reality.

These double and single bonds should be changed to aromatic or any bonds. These will work in Standardizer:

C:\>standardize -c "[!#1:1]-,:[#7+:2]([*:4])[O-:3]>>[!#1:1]-,:[#7:2]([*:4])=[O:3]" "[O-][N+]1=CC=CC=C1"
O=N1=CC=CC=C1

C:\> standardize -c "[!#1:1]~[N+:2](~[*:4])[O-:3]>>[!#1:1]~[N:2](~[*:4])=[O:3]" "[O-][N+]1=CC=CC=C1"
O=N1=CC=CC=C1

In first example I connected nitrogen to any atom and to list atom with "single or aromatic" bond, in second example I used any bonds.

Sorry for the late answer.

Zsolt

Thank you for reply.  Very helpful.

I had also tried to match using this:  a:[n+]([O-]):a   .. but it did not find match to [O-][N+]1=CC=CC=C1

Can you tell me why that one doesn't find a match?

Thanks.

awrk wrote:

I had also tried to match using this:  a:[n+]([O-]):a   .. but it did not find match to [O-][N+]1=CC=CC=C1 Can you tell me why that one doesn't find a match?

It works for me.

C:\>standardize -c "a:[n+]([O-]):a>>a:n(:a)=O" "[O-][N+]1=CC=CC=C1"
O=N1=CC=CC=C1

Zsolt

Thank you for quick response.  When I try below in API, I get null search hits.  Do you also get null?

Molecule mol = MolImporter.importMol("[O-][N+]1=CC=CC=C1");

MolHandler mhl = new MolHandler("a:[n+]([O-]):a", true);

Molecule query = mhl.getMolecule();

MolSearch s = new MolSearch();

MolSearchOptions so = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);

You have to use StandardizedMolSearch instead of MolSearch to make your code work. MolSearch does not handle aromatization by default, so the query having aromatic bonds will not be found in a target which has only single and double bonds. Standardizer uses StandardizedMolSearch internally as well.

Zsolt

Thanks for the clarification, I will look at that class!