Difference between revisions of "SMARTS"

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(Added note on 2.1 cis/trans notation)
(removed items that are already fixed)
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* Use of non-tetrahedral chirality [http://sourceforge.net/tracker/index.php?func=detail&aid=1465334&group_id=40728&atid=428743 Feature Request]
 
* Use of non-tetrahedral chirality [http://sourceforge.net/tracker/index.php?func=detail&aid=1465334&group_id=40728&atid=428743 Feature Request]
 
* Unspecified chirality (i.e., "@?") [http://sourceforge.net/tracker/index.php?func=detail&aid=1364638&group_id=40728&atid=428740 Bug Report]
 
* Unspecified chirality (i.e., "@?") [http://sourceforge.net/tracker/index.php?func=detail&aid=1364638&group_id=40728&atid=428740 Bug Report]
* New v4.9 primitive "x#" for number of ring connections [http://sourceforge.net/tracker/index.php?func=detail&aid=1504845&group_id=40728&atid=428743 Feature Request]
 
* [H] does not match explicit hydrogen atoms [http://sourceforge.net/tracker/index.php?func=detail&aid=1463791&group_id=40728&atid=428740 Bug Report]
 
** A workaround for this exists -- [#1] should be equivalent to [H] in this respect (i.e., element number 1).
 
  
 
This list may not be complete. Please e-mail the [mailto:[email protected] openbabel-discuss] mailing list if you have questions about the SMARTS support in Open Babel.
 
This list may not be complete. Please e-mail the [mailto:[email protected] openbabel-discuss] mailing list if you have questions about the SMARTS support in Open Babel.

Revision as of 07:50, 10 July 2008

The SMARTS format is a language for matching substructures of chemical files and was created by Daylight Chemical Information Systems, Inc. alongside the SMILES format.

Specification URL http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
Examples http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html

Limitations of the Open Babel SMARTS Implementation

The Open Babel implementation of SMARTS is not bug-free, nor does it support everything in the Daylight Toolkit. In particular, it is known to not currently support:

  • Cis/trans double bond stereochemistry. Feature Request
    • Note: The SMARTS '/' and '\' notation will be accepted, but will not restrict to cis/trans functionality. Instead these bond notations are treated equivalently to a single bond.
  • Component-level grouping (i.e., "(C).(C)") Feature Request
  • Use of non-tetrahedral chirality Feature Request
  • Unspecified chirality (i.e., "@?") Bug Report

This list may not be complete. Please e-mail the openbabel-discuss mailing list if you have questions about the SMARTS support in Open Babel.

Open Babel Extensions to SMARTS Syntax

In addition to the Daylight Toolkit syntax, Open Babel also offers the following extensions to SMARTS which are not currently supported by Daylight:

  • Atom hybridization matching "^". For example [#6^3] matches a carbon atom (atomic number 6) with sp3 hybridization. Accepted hybridizations include:
    • 1 - sp e.g., [#6^1][#7]
    • 2 - sp2 e.g., [#6^2][#6^2]
    • 3 - sp3 e.g., [#8^3]