findCompounds {ChemmineR} | R Documentation

## 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")

[Package ChemmineR version 3.36.0 Index]