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Should the substructure matching work ?

 
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fision



Joined: 08 Feb 2007
Posts: 2

PostPosted: Thu Feb 08, 2007 11:35 am    Post subject: Should the substructure matching work ? Reply with quote

Hi,

I have been trying to use TCTab.SearchSubStruc, but it always returns false even if the CSmallTab is a substructure of the larger structure. Is this supposed to work ? Thanks for any hints.

Lasse Koskinen Sad
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hlohning



Joined: 08 Sep 2006
Posts: 277
Location: Austria

PostPosted: Thu Feb 08, 2007 5:53 pm    Post subject: Reply with quote

Lasse,

it should work. However, I cannot guarantee that the substructure search is free of bugs....

Could you please post the connection tables of those two structures (the big one and the small one), so that I can check it. (use the method WriteToCleartextFile to store the connection table as a text file.)

Regards,

Hans
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Hans Lohninger
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fision



Joined: 08 Feb 2007
Posts: 2

PostPosted: Fri Feb 09, 2007 3:03 pm    Post subject: Substructure matching Reply with quote

Hello Hans,

Thanks for the rapid answer. I tested the thing more throroughfully and it seems the non-cyclic compounds seem to match ok, but at least benzene, hexyl and heptyl rings do not match at all. Good example is that benzene ring does not match to phenol. When search my sample database of 2500 compounds, the Accord SDK (Accelrys) gives me 120 matches for hexyl ring and SDL suite gives zero.

Here is an example; first cyclohexene with a side chain and the second plain cyclohexane. And no match. I also noticed that if you break the ring, the corresponding aliphatic fragment matches the cyclohexyl ring.

Best regards
Lasse

MOL5EB4.tmp
Accord 0209071553

15 15 0 0 0 0 0 0 0 0 1 V2000
5.0000 10.0802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0000 9.2552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7145 8.8427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4289 9.2552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4289 10.0802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7145 10.4927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2258 9.0417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4394 8.2448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.2362 8.0312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4498 7.2344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.2467 7.0208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.4602 6.2239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2571 6.0104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.4706 5.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2675 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 1 1 0 0 0 0
7 4 1 0 0 0 0
8 7 1 0 0 0 0
9 8 1 0 0 0 0
10 9 1 0 0 0 0
11 10 1 0 0 0 0
12 11 1 0 0 0 0
13 12 1 0 0 0 0
14 13 1 0 0 0 0
15 14 1 0 0 0 0
M END


MOL5E0C.tmp
Accord 0209071521

6 6 0 0 0 0 0 0 0 0 1 V2000
5.0000 5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4125 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2375 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6500 5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2375 6.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4125 6.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 1 1 0 0 0 0
M END

[/list][/code]
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hlohning



Joined: 08 Sep 2006
Posts: 277
Location: Austria

PostPosted: Sat Feb 17, 2007 9:38 pm    Post subject: Reply with quote

Hi Lasse,

I've checked your sample structures - and, yes, the substructure search fails!! (what a shame!).

Unfortunately, a quick look at the code did not reveal the problem. Due to the recursive search algorithm fixing the bug will take some time. So I have to ask for your patience.

Regards,

Hans
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http://www.lohninger.com/
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