Hi Rajarshi,

Thanks for the pointer.

I was also wondering if matches() can work in two modes isSubgraph() and getSubgraphs(Molecule) .

isSubgraph() just looks for firstMap whereas  getSubgraphs(Molecule) is an exhaustive search for all maps.


I was going thru the pubchem fp in the CDK and If I understand the  
code correctly, it calls SMARTQueryTool n-number of times for find  
Each call to SMARTQueryTool leads to the processing of the SAME  
atomcontainer again and again (i.e All ring finder, perceive atoms  
etc ).
I think in such a situation where only query changes but the target  
container doesn't, we need a code which skips reprocessing of the  
target .

A quick check indictates that one can avoid reinitialization via the  
matches() method

Rajarshi Guha        | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
Heisenberg may have slept here...

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