SMARTS to SMILES

[Vinay M-2]

Hi
   Can anyone help to know, how to convert from SMARTS to SMILES.

Thanks 
With Warm Regards
Vinay

[Craig A. James-3]

Vinay M wrote:
>  Can anyone help to know, how to convert from SMARTS to SMILES.

You can't. SMARTS is a superset of SMILES, and most SMARTS are not valid SMILES.

Perhaps if you explain why you need to do this, we might be able to suggest a solution.

Craig

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Vinay M-2]

Hi
    Craig,
              Thanks for your reply, i was using smiles to view the structure, so few are in smarts. I just wanted to convert smiles to smarts and smarts to smiles.
Thanks
Kindly help
 With Warm regards
Vinay
  
--- On Tue, 11/10/09, Craig A. James <[hidden email]> wrote:

From: Craig A. James <[hidden email]>
Subject: Re: [Open Babel] SMARTS to SMILES
To: "Vinay M" <[hidden email]>, [hidden email]
Received: Tuesday, November 10, 2009, 7:29 PM

Vinay M wrote:
>  Can anyone help to know, how to convert from SMARTS to SMILES.

You can't. SMARTS is a superset of SMILES, and most SMARTS are not valid SMILES.

Perhaps if you explain why you need to do this, we might be able to suggest a solution.

Craig

---

Make your browsing faster, safer, and easier with the new Internet Explorer® 8. Optimized for Yahoo! Get it Now for Free!
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Geoffrey Hutchison-2]

>               Thanks for your reply, i was using smiles to view the structure, so few are in smarts. I just wanted to convert smiles to smarts and smarts to smiles.

SMILES is a subset of SMARTS, so any SMILES string can be used as a SMARTS. The reverse is not true. I can design many SMARTS, which are not valid SMILES. For example [*] matches any atom.

So no, as Craig said, you cannot interconvert them.
-Geoff
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Vinay M-2]

Hi
   Thanks a lot for your reply. I then use smiles for SMARTS.

Vinay

--- On Tue, 11/10/09, Geoffrey Hutchison <[hidden email]> wrote:

From: Geoffrey Hutchison <[hidden email]>
Subject: Re: [Open Babel] SMARTS to SMILES
To: "Vinay M" <[hidden email]>
Cc: "babel" <[hidden email]>
Received: Tuesday, November 10, 2009, 8:55 PM

>               Thanks for your reply, i was using smiles to view the structure, so few are in smarts. I just wanted to convert smiles to smarts and smarts to smiles.

SMILES is a subset of SMARTS, so any SMILES string can be used as a SMARTS. The reverse is not true. I can design many SMARTS, which are not valid SMILES. For example [*] matches any atom.

So no, as Craig said, you cannot interconvert them.
-Geoff

---

All new Yahoo! Mail - Get a sneak peak at messages with a handy reading pane.
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Craig A. James-3]

Vinay,

>               Thanks for your reply, i was using smiles to view the
> structure, so few are in smarts. I just wanted to convert smiles to
> smarts and smarts to smiles.

Ok, now that I know what you're doing, I can suggest a possible way to do it, but it's not easy.  Attached is a little Perl program that might work for 95% of the SMARTS you will encounter.  With a bit of work, you might be able to improve it even more.  (If you need this in C or C++, it's a lot harder.)  You should be able to modify this example to suit your needs.

This will parse a SMARTS, and also knows what symbols are valid for SMILES atoms and bonds.  Any time it encounters a SMARTS atom that's not a valid SMILES atom, it is replaced it with '*'.

  C1[C,N]CCCC1  ==> C1*CCCC1

  CC-=CC  ==> CC-CC

It's made more difficult by aromatic structures, for example, c1[n,c]cccc1 becomes c1*cccc1, which in theory is a valid aromatic SMILES, but in practice some interpreters don't consider it aromatic.

It doesn't try to deal with bonds, and there are probably SMARTS that it doesn't get right, I just spent a few minutes on it.

Craig


------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Vinay M-2]

Hi Craig,
             Thanks a lot, could you please send me the C or C++ code, since it deal with it a lot. I will follow those in perl and try. Thanks a lot.

---

Instant message from any web browser! Try the new Yahoo! Canada Messenger for the Web BETA
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Craig A. James-3]

Vinay,

>              Thanks a lot, could you please send me the C or C++ code,
> since it deal with it a lot. I will follow those in perl and try. Thanks
> a lot.

You're welcome, but I can't do it in C or C++.  It would take days to do the same thing.  Perl has very powerful string-handling functions, which is the only reason I could write the program so quickly.  That's why we use Perl so much.  You should try to find a way to incorporate a Perl program into your system. If you rewrite this in C or C++, it will be very difficult.

Craig

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss