fmcsR (version 1.14.2)

fmcsBatch: FMCS Search Function

Description

Compound search function that runs the FMCS algorithm for a query compound against a set of molecules stored in an SDFset container.

Usage

fmcsBatch(querySdf, sdfset, al = 0, au = 0, bl = 0, bu = 0,
matching.mode = "static",timeout=60000,numParallel=1)

Arguments

querySdf

Input query SDF object or SDFset object of length one.

sdfset

Input target SDFset object.

al

Lower bound for the number of atom mismatches.

au

Upper bound for the number of atom mismatches.

bl

Lower bound for the number of bond mismatches.

bu

Upper bound for the number of bond mismatches.

matching.mode

Three matching mode are supported, "static", "aromatic", and "ring".

timeout

The maximum amount of time to spend on each pair of comparisons, in milliseconds. A value of 0 indicates no timeout.

numParallel

The number of comparisons to run in parallel, using local cores.

Value

• Returns a matrix with compound IDs as row names and the following columns: Query_Size, Target_Size, MCS_Size, Tanimoto_Coefficient and Overlap_Coefficient. For details see vignette of this package.

Details

This function runs the FMCS algorithm in fast computing mode. Thus, it will only return the similarity scores and size information about the source structures and their MCSs, while omitting all structural information.

See Also

plotMCS, fmcs, ?"MCS-class"

Examples

library(fmcsR)
data(sdfsample)
sdfset <- sdfsample
fmcsBatch(sdfset[[1]], sdfset[1:3])
fmcsBatch(sdfset[[1]], sdfset[1:3], au=2)
fmcsBatch(sdfset[[1]], sdfset[1:3], bu=1)
fmcsBatch(sdfset[[1]], sdfset[1:3], matching.mode="aromatic", au=1, bu=1)