extrDrugAP: Calculate the Atom Pair Fingerprints

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Description

Calculate the Atom Pair Fingerprints

Usage

extrDrugAP(x, descnames = 1024)

Arguments

x	Object of classe APset or list of vectors
descnames	Descriptor set to consider for fingerprint encoding. If a single value from 1-4096 is provided then the function uses the corresponding number of the most frequent atom pairs stored in the apfp data set provided by the package. Alternatively, one can provide here any custom atom pair selection in form of a character vector.

Details

Generates fingerprints from descriptor vectors such as atom pairs stored in APset or list containers. The obtained fingerprints can be used for structure similarity comparisons, searching and clustering. Due to their compact size, computations on fingerprints are often more time and memory efficient than on their much more complex atom pair counterparts.

Value

matrix or character vectors

Author(s)

Min-feng Zhu <[e-mail]>,

Examples

data(sdfbcl)

apbcl <- convSDFtoAP(sdfbcl)
mol <- extrDrugAP(x = apbcl, descnames = 1024)

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.