Markush search very slow

Hi all,

I am trying to create a database of markush structures
and then query it to determine if a specific chemical is a match
against a markush structure in the database. I created the Markush
library in IJC 2.5.1 using Markush library table contents option when creating
JChem table in IJC. The problem I am having is that search is "never"
completed or at least it doesn't complete in the period I waited for it
to complete ~ 20 min. The query structure I am using is: "CC1=C(C)C2=C(NC(=O)NC2=O)S1" and the database contains only 3 Markush structures, see attachments.

 

OS: Windows XP SP2

Java 1.6.13

IJC 2.5.1

 

Oleg.

Hi Oleg,

Thank you for the structures. I could reproduce the problem.

We will investigate and get back here.

 

Best regards,

Szabolcs

Hi Oleg,

This slow (infinite) search is caused by a combinatorial explosion during searching. This occurs because the targets are searched with aromatic rings, and the targets rings' aromaticity change with the selected markush features. In this case we have to check each possibility.

http://chemaxon.com/jchem/doc/user/query_combinatorial_markush.html#combinatorialMarkushArom

We will consider how we can improve the markush aromaticity handling but this will be schedulled after the comming major release (5.3). 

You can regulate markush aromaticity by the following function:

http://chemaxon.com/jchem/doc/api/chemaxon/sss/search/MolSearchOptions.html#setMarkushArom(int)

 

Bye,

Robert

Hi Robert,

 

I looked in Instant JChem and I didn't see equivalent option in search panel. I will test it from a Java program to see how it can improve speed, but it would be desirable to have this option in the IJC GUI.

 

Oleg.

Hi Oleg,

You are right, this option is not available in the Instant JChem panel. I will discuss with Tim how to make it possible to specify advanced search options.

 

Best regards,

Szabolcs