fmcsBatch: FMCS Search Function

In girke-lab/fmcsR: Mismatch Tolerant Maximum Common Substructure Searching

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.

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.

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.

Author(s)

Yan Wang, Thomas Girke

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)

girke-lab/fmcsR documentation built on May 17, 2019, 5:27 a.m.