getCompounds: Get Compounds From Database

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Get Compounds From Database

Description

Create SDF objects from the given set of compound ids. Id numbers can be found using the findCompounds function.

Usage

   getCompounds(conn,compoundIds,filename=NA, keepOrder = FALSE, allowMissing = FALSE)

Arguments

conn	A database connection object, such as is returned by initDb.
compoundIds	A vector of compound ids, as returned by loadSdf or findCompounds.
filename	If given, writes the compounds directly to the file named.
keepOrder	If true, the order of the output compound ids will be the same as the input names. This imposes a performance hit that can be significant for large datasets, thus it should be left FALSE unless needed.
allowMissing	When this is false an error will be raised when compound ids queried were not found in the database. If true, just those that are found will be returned with no error or warning.

Value

An SDFset with the requested compounds or nothing if filename was specified. A warning will be raised if not all compounds could be found.

Author(s)

Kevin Horan

See Also

loadSdf findCompounds.

Examples

   #create and initialize a new SQLite database
   conn = initDb("test3.db")

	data(sdfsample)

	#just load the data with no features or descriptors
	ids=loadSdf(conn,sdfsample)

   #returns a SDFset with 3 compounds
   getCompounds(conn, ids[1:3])

	unlink("test3.db")

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