extrDrugOBFP2: Calculate the FP2 Molecular Fingerprints

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Calculate the FP2 Molecular Fingerprints

Usage

extrDrugOBFP2(molecules, type = c("smile", "sdf"))

Arguments

molecules	R character string object containing the molecules. See the example section for details.
type	'smile' or 'sdf'.

Details

Calculate the 1024 bit FP2 fingerprints provided by OpenBabel.

Value

A matrix. Each row represents one molecule, the columns represent the fingerprints.

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

Examples

mol1 = 'C1CCC1CC(CN(C)(C))CC(=O)CC'  # one molecule SMILE in a vector
mol2 = c('CCC', 'CCN', 'CCN(C)(C)', 'c1ccccc1Cc1ccccc1',
         'C1CCC1CC(CN(C)(C))CC(=O)CC')  # multiple SMILEs in a vector

smifp0 = extrDrugOBFP2(mol1, type = 'smile')
smifp1 = extrDrugOBFP2(mol2, type = 'smile')

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.