Subject: the most common structure

From: "水客" <[email-masked]>
Date: Mon, 8 Jul 2002 22:38:5 +0800

Sir/Miss：
    Good morning.
	Who can tell me how to pick up the most common structure from a set of compounds, and save it into a structure file? Could you indicate to me further softwares able to perform the same task? I have SYBYL software, but no DISTILL module.

      Thank you very much! 

Li Qiang

Shanghai Institute of Organic Chemistry
Chinese Academy of Sciences 

No.354 Road FengLin
ShangHai, 200032, China
Phone: 08621-64163300-2735
Fax: 08621-64166128

---

From: "Shobe, Dave" <[email-masked]>
Date: Mon, 08 Jul 2002 13:25:15 -0400

I dont' have the answer, but I will ask a clarifying question that may help
others.

If you take the phrase "most common structure" literally, it means the
(sub)structure which is present in the greatest number of compounds in the
set.  This would end up being individual atoms like C or H, if we don't make
any restrictions on what is a structure.  But if there is a restriction, for
example that a "structure" must consist of at least 5 atoms, then this would
be a meaningful question with a nontrivial answer.

However, the above interpretation relies on a fine point of English usage,
and I would not be surprised if the intended request is for the LARGEST
common structure, that is the largest substructure which is present in ALL
of the compounds of the set.  

Note that "common" can mean either "occurring frequently" as in the first
interpretation, or "occurring in all" as in the second.  

I didn't mean to turn this into an English lesson, but I hope this ensures
that the right question is answered.

--David Shobe
S黡-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  [email-masked]

Don't bother flaming me: I'm behind a firewall.

-----Original Message-----
From: [email-masked] [mailto:[email-masked]]
Sent: Monday, July 08, 2002 10:38 AM
To: [email-masked]
Subject: CCL:the most common structure

Sir/Miss：
    Good morning.
	Who can tell me how to pick up the most common structure from a set
of compounds, and save it into a structure file? Could you indicate to me
further softwares able to perform the same task? I have SYBYL software, but
no DISTILL module.

      Thank you very much! 

Li Qiang

No.354 Road FengLin
ShangHai, 200032, China

---

From: Stephen Bowlus <[email-masked]>
Date: Mon, 8 Jul 2002 12:35:00 -0700

Since you refer to the Distill module, I infer you are looking for the
"Maximal Common Substructure" (in Tripos parlance).  This will entail a lot
of trying this and trying that, but one way to attack the problem is 

0) Just to make visualization easier, delete all H from the compounds in
your database.
1) select a "representative" molecule from the database.
2) guess the largest substructure, and delete all other atoms
  - You can make a guess and run, or you can nibble away at the molecule by
deleting "trivial" functionality
3) run File > Align Database using the structure from 2 as the alignment
template
  - If the fragment is present in every molecule, the alignment will run
without any messages informing you that the structure is not present.
4) iterate steps 2 and 3 until the alignment step gives no messages.  You
can check by loading the database into Sybyl (database get * m2 retrieve);
the aligned molecules will stack up very clearly using the substructure > from
2

This does not guarantee that the fragment you find is the largest or only
large common fragment, but you can try other starting points as well.

Cheers,
Steve Bowlus

> Sent: Sunday, July 07, 2002 11:00 AM
> To: [email-masked]
> 	Who can tell me how to pick up the most common 
> structure from a set of compounds, and save it into a 
> structure file? Could you indicate to me further softwares 
> able to perform the same task? I have SYBYL software, but no 
> DISTILL module.
> 
>       Thank you very much! 
> 
> Li Qiang
>