[Cdk-devel] [ cdk-Patches-3052052 ] SMARTSQueryTool Patch based on the SMSD

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Patches item #3052052, was opened at 2010-08-24 07:26
Message generated for change (Comment added) made by asadrahman
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Category: master
>Group: None
>Status: Closed
>Resolution: Out of Date
Priority: 5
Private: Yes
Submitted By: Asad (asadrahman)
Assigned to: Nobody/Anonymous (nobody)
Summary: SMARTSQueryTool Patch based on the SMSD

Initial Comment:
a) SMARTSQueryTool uses SMSD based substructure package. It will be much
faster in case of bigger mols, worst case is as good as UIT (in case if
smaller mols) and better than UIT in case of larger mols (as it switches to
VF lib)
b) RecursiveSmartsAtom uses UIT from the SMSD package for the sake of
consistency in the code.

I was debating if I can replace AllRingFInder in the SMARTSQueryTool to
Hanser Ring finder as implemented in the SMSD package.

Best,
Asad

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>Comment By: Asad (asadrahman)
Date: 2010-08-29 23:48

Message:
This patch needs to be discussed on the mailing list as this will lead to
major changes in the smartquerytoool class.

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Comment By: Rajarshi Guha (rajarshi)
Date: 2010-08-29 21:33

Message:
Some issues wrt 0007

You have


+            if (smsd.isSubgraph()) {
+                List<Map<Integer, Integer>> maps = smsd.getAllMapping();
+                for (Map<Integer, Integer> map : maps) {
+                    matchingAtoms.add(new
ArrayList<Integer>(map.values()));
+                }
+                return true;
+            }

Shouldn;t false be returned if smsd.isSubgraph() is false?

In 0007, please remove the comment out code blocks (Old Code Block etc) -
we can always go back to old code via git

0008 looks OK to me

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Comment By: Asad (asadrahman)
Date: 2010-08-24 07:29

Message:
Note: This patch depends on the SMSD patch 3037137

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