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SMARTS Substructure searches
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James

Joined: 08 Feb 2013
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Link to postPosted: Mon Apr 18, 2016 9:14 pmPost subject: SMARTS Substructure searches Reply with quote

In Excel,† Iím using =JCSubstructureMatchCount(J$2,$B31) to look for specific substructures in SMILES structures. †

I have two specific questions.†

I have used a number of SMARTS like

CH (aromatic) † †

[cH1]

-C (aromatic) † †

[cH0]

N (aromatic) † †

n

Where the small letter c or n should mean carbon or nitrogen in an aromatic context,† but the JCSubstructureMatchCount is finding them in any context. †

Secondly, I would like to find, for example, a primary alchohol, but not in a carboxylic acid.† ([Cv4][OH1]) finds primary alcohols in any context.

†I†would think that ††([Cv4][OH1])!([CX3](=O)[OX2H1])† would work. But it doesnít.† Can you suggest a solution?

Krisztina
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Joined: 27 May 2011
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Link to postPosted: Wed Apr 20, 2016 10:10 amPost subject: Reply with quote

Hi James,

Regarding your second question, as a first idea we recommend to apply the following SMARTS expression:

[$([CX4]O)]

The following pages might also help you to create the appropriate SMARTS:

http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html (see the Recursive SMARTS section)

http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html

Best regards,

Krisztina

Anna
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Link to postPosted: Wed Apr 20, 2016 11:22 amPost subject: Reply with quote

Hi James,

The issue is, that [n] is recognized as a simple N is SMILES and SMARTS. Please, use [n;a] or [#7;a] instead, see in attached example file.

You can check if your SMARTS is correct in MarvinSketch, if you draw the structure and select Edit/Source/View: SMARTS, SMARTS.

Let me know, if this helps.

Regards,

Anna




 Filename: SMARTS_Queries_SubstructureMatchCount.xlsx    Filesize: 15.6 KB    Downloaded: 77 Time(s)
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James

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Link to postPosted: Wed Apr 20, 2016 4:04 pmPost subject: SMARTS Substructure searches Reply with quote

aforro wrote:

Hi James,

The issue is, that [n] is recognized as a simple N is SMILES and SMARTS. Please, use [n;a] or [#7;a] instead, see in attached example file.

You can check if your SMARTS is correct in MarvinSketch, if you draw the structure and select Edit/Source/View: SMARTS, SMARTS.

Let me know, if this helps.

Regards,

Anna

Hi Anna,†

Thanks!†

This absolutely solved the problem! †I have referred to the Daylight documentation and I never saw the "a" functionality. †Is this a standard SMARTS nomenclature?

James

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Link to postPosted: Wed Apr 20, 2016 4:07 pmPost subject: SMARTS Substructure searches Reply with quote

Thanks,†Krisztina

That solved the problem.†

Can you explain what the function of $ is in this context?

James

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Link to postPosted: Wed Apr 20, 2016 4:20 pmPost subject: SMARTS Substructure searches Reply with quote

Anna and†Krisztina,†

As follow up questions.†

1. Similar to the alcohol but not carboxyllic acid, how do I specific and amine but not amide? I used [NX3;H2], but this also hits amides.†

2. How can I specify a primary secondary and tertiary alcohol eg CX3-OH, CX2H-OH, CXH2-OH?

Thanks

Alex†

Krisztina
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Link to postPosted: Thu Apr 21, 2016 1:52 pmPost subject: Reply with quote

Hi Alex,

I think the answers are found on the pages I linked in my previous post† -† I could not answer better.

On that page, please look for:

Recursive SMARTS

amine, not amide

If you need more detailed support we can assist within the frame of a consultancy project.

Best regards,

Krisztina

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