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Power Up: Using Match Level to broaden or narrow structure search results in MARPAT

Background and introduction

Markush structures can include:

• Specific atoms, e.g., C, N, Cl
• Generic nodes, e.g., Ak (any carbon chain), Hy (any cyclic group with one or more non-carbon atoms), Cb (any cyclic group with all carbons), Cy (any cyclic group), R (any non-hydrogen group)  

Have you ever wanted to control whether you retrieve (1) only specific atoms or (2) both specific atoms and generic nodes at a particular node or structure fragment of your query structure?   

By assigning Match Level to a part or the entire query structure, you can change the degree to which the nodes of your query structure match the nodes in the MARPAT answers, thereby increasing or decreasing the number of answers retrieved.

This article highlights the differences between Match Level ATOM and Match Level CLASS.

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Match Level ATOM vs. Match Level CLASS

Match Level ATOM is the more restrictive Match Level and retrieves a smaller, more precise set of answers.

• Specific atoms in the query structure match only specific atoms in MARPAT answers.
• Generic nodes in the query structure match only specific atoms in MARPAT answers.

Match Level CLASS is likely to result in more answers retrieved than with Match Level ATOM.

• Specific atoms in the query structure match not only specific atoms but also generic nodes in MARPAT answers.
• Generic nodes in the query structure match specific atoms as well as generic nodes in MARPAT answers.

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Default Match Level assignment

For structures built in STN Express or STN on the Web^SM, Match Level is assigned automatically when searching MARPAT.

The default settings for Match Level are:

• ATOM for specific ring atoms and the ring generic groups Cy, Cb, and Hy
• CLASS for specific or generic chain nodes and the chain generic group Ak

Comparison of retrievals with Match Level ATOM vs. Match Level CLASS.

Query structure node	MARPAT answer node	Retrieve with Match Level ATOM	Retrieve with Match Level CLASS	Retrieve with default Match Level
F	F	Yes	Yes	Yes
F	Cl	No	No	No
F	X	No	Yes	Yes
X	F or Cl or Br or I or At	Yes	Yes	Yes
X	X	No	Yes	Yes
Ak	CH3, CH2CH3, etc.	Yes	Yes	Yes
Ak	Ak	No	Yes	Yes

 

Query structure ring	MARPAT answer ring	Retrieve with Match Level ATOM	Retrieve with Match Level CLASS	Retrieve with default Match Level
		Yes	Yes	Yes
		No	No	No
	Hy	No	Yes	No
Hy		Yes	Yes	Yes
Hy	Hy	No	Yes	No

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Changing the default Match Level

To change the Match Level in a structure:

1. Highlight a node or a structure fragment with the Selection Tool ( ). 
2. Select Markush Attributes from the QueryDef menu.  The radio button indicates the default Match Level.
3. Select another Match Level and click OK.

This is shown in two examples.

 

 

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Additional resources

For more information about using Match Level, refer to the MARPAT User Guide, attend an STN training session, or consult with the STN Help Desk.