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smartsquery [2012/10/13 17:49] – [Results] sanmarksmartsquery [2013/10/10 16:06] (current) flack
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 ====== SMARTS query filter ====== ====== SMARTS query filter ======
  
 +{{:smarts.png?700|}}
  
-The SMARTS language (ref1) is designed to describe substructure patterns in molecules, and to overcome the limitations of simple substructure matching. The SMARTS query filter at mcule.com provides nearly full SMARTS language support, based on the Indigo (ref2) implementation of SMARTS.+The [[http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html|SMARTS]] language is designed to describe substructure patterns in molecules, and to overcome the limitations of simple substructure matching. The SMARTS query filter at [[https://mcule.com/|mcule.com]] provides nearly full SMARTS language support, based on the [[http://ggasoftware.com/opensource/indigo|Indigo]] implementation of SMARTS.
  
 Using the SMARTS query filter you can select or eliminate molecules containing specific SMARTS patterns. The filter allows multiple SMARTS queries. Molecules matching with ALL or ANY of the queries can be either included to or excluded from the result collection. Using the SMARTS query filter you can select or eliminate molecules containing specific SMARTS patterns. The filter allows multiple SMARTS queries. Molecules matching with ALL or ANY of the queries can be either included to or excluded from the result collection.
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-SMARTS query filter is a powerful and flexible tool to perform complex structural queries impossible to describe with a simple Substructure search (link). For example, if you are seeking for molecules containing a phenol substituted with any halogen atoms at para position, you can easily define the corresponding SMARTS pattern, and do the search.+SMARTS query filter is a powerful and flexible tool to perform complex structural queries impossible to describe with a simple [[substructuresearch|Substructure search]]. For example, if you are seeking for molecules containing a phenol substituted with any halogen atoms at para position, you can easily define the corresponding SMARTS pattern, and do the search.
  
-Things become more interesting if you consider the batch functionalities. Using proper lists of SMARTS queries you can effectively eliminate problematic (non-druglike, toxic, reactive) molecules from a collection; thus you can use the SMARTS filter to build up your own REOS (Rapid Elimination of Swill) filter (link to reos filter) (ref3). Another use case is to generate a collection of specific structures, for example, strong acids or bases, using specific SMARTS. All you need is a list of SMARTS queries and to apply the appropriate settings.+Things become more interesting if you consider the batch functionalities. Using proper lists of SMARTS queries you can effectively eliminate problematic (non-druglike, toxic, reactive) molecules from a collection; thus you can use the SMARTS filter to build up your own [[REOS|REOS]] (Rapid Elimination of Swill) filter. Another use case is to generate a collection of specific structures, for example, strong acids or bases, using specific SMARTS. All you need is a list of SMARTS queries and to apply the appropriate settings.
  
 ===== How to use ===== ===== How to use =====
  
  
-To create a SMARTS query, you can either go through the Daylight documentation (ref4), or use a molecule sketcher supporting the export of the SMARTS format (e.g. MarvinSketch from ChemAxon (ref5)).+To create a SMARTS query, you can either go through the [[http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html|Daylight documentation]], or use a molecule sketcher supporting the export of the SMARTS format (e.g. [[http://www.chemaxon.com/products/marvin/marvinsketch|MarvinSketch from ChemAxon]]).
  
 ==== Options ==== ==== Options ====
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 INCLUDE molecules matching ANY of the SMARTS queries (default) INCLUDE molecules matching ANY of the SMARTS queries (default)
 +
 INCLUDE molecules matching ALL of the SMARTS queries INCLUDE molecules matching ALL of the SMARTS queries
 +
 EXCLUDE molecules matching ANY of the SMARTS queries EXCLUDE molecules matching ANY of the SMARTS queries
 +
 EXCLUDE molecules matching ALL of the SMARTS queries EXCLUDE molecules matching ALL of the SMARTS queries
  
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 ===== Limits ===== ===== Limits =====
  
-SMARTS filter available in the Free package (link) has the following limitations:+SMARTS filter available in the [[freepackage|Free package]] has the following limitations:
 - max 5 queries per filter - max 5 queries per filter
 - max 1 filter per workflow - max 1 filter per workflow
-To get access to unlimited SMARTS query filter, subscribe to our Library Design (link) package.+To get access to unlimited SMARTS query filter, [[subscriptionpackages|subscribe]] to our Library Design package.
  
 ===== SMARTS language limitations ===== ===== SMARTS language limitations =====
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 ===== Further information ===== ===== Further information =====
  
-If you would like to get further information on SMARTS format, visit the following web pages by Daylight (developer of the SMARTS language) 6): +If you would like to get further information on SMARTS format, visit the following web pages by [[http://www.daylight.com|Daylight]] (developer of the SMARTS language):
- +
-SMARTS - A language describing molecular patterns+
  
-SMARTS Tutorial+[[http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html|SMARTS - A language describing molecular patterns]]
  
-SMARTS Examples+[[http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html|SMARTS Tutorial]]
  
-Additional information about the Indigo 7) implementation of SMARTS:+[[http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html|SMARTS Examples]]
  
-Indigo concepts - Daylight Formats+[[http://ggasoftware.com/opensource/indigo/concepts#substructure-and-smarts-matching|Additional information about the Indigo implementation of SMARTS]]
  
-Difference between SMILES and SMARTS matching in Indigo+[[http://ggasoftware.com/opensource/indigo/concepts#daylight-formats-with-chemaxon-and-curlysmiles-extensions|Indigo concepts - Daylight Formats]]
  
-1) , 4) http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html +[[http://ggasoftware.com/opensource/indigo/concepts#differences-between-smarts-and-query-smiles|Difference between SMILES and SMARTS matching in Indigo]]
-2) , 7) http://ggasoftware.com/opensource/indigo +
-3) http://www.sciencedirect.com/science/article/pii/S135964469701163X +
-5) http://www.chemaxon.com/products/marvin/marvinsketch/ +
-6) http://www.daylight.com+
smartsquery.1350150583.txt.gz · Last modified: 2012/10/13 17:49 by sanmark