findCompounds: Find Compounds in Database

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Find Compounds in Database

Description

Searches the SQL database using features computed at load time. Each feature used should be specified in the featureNames parameter. Then a set of filters can be given to search for specific compounds.

Usage

findCompounds(conn, featureNames, tests)

Arguments

conn	A database connection object, such as is returned by initDb.
featureNames	A list of all feature names used in any test.
tests	A vector of filters that must all be true for a compound to be returned. For example: c("MW <= 400","RINGS > 3") would return all compounds with a molecular weight of 400 or less and a more than 3 rings, assuming these features exist in the database. The syntax for each test is "<feature name> <SQL operator> <value>". These tests will simply be concatenated together with " AND " in-between them and tacked on the end of a WHERE clause of an SQL statement. So any SQL that will work in that context is fine.

Value

Returns a list of compound ids. The actual compounds can be fetched with getCompounds.

Author(s)

Kevin Horan

See Also

getCompounds

Examples

   #create and initialize a new SQLite database
   conn = initDb("test1.db")

	data(sdfsample)

	#load data and compute 3 features: molecular weight, with the MW function, 
	# and counts for RINGS and AROMATIC, as computed by rings, which returns a data frame itself.
	ids=loadSdf(conn,sdfsample,
			  function(sdfset) 
					data.frame(MW = MW(sdfset),  rings(sdfset,type="count",upper=6, arom=TRUE))
			 )
   #search for compounds with molecular weight less than 200
   lightIds = findCompounds(conn,"MW",c("MW < 200"))
   MW(getCompounds(conn,lightIds)) # should find one compound with weight 140
	unlink("test1.db")

girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.