extractDrugOBFP2: Calculate the FP2 Molecular Fingerprints

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Description

Calculate the FP2 Molecular Fingerprints

Usage

extractDrugOBFP2(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)

Nan Xiao <https://nanx.me>

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
mol3 = readChar(system.file('compseq/DB00860.sdf', package = 'Rcpi'),
                nchars = 1e+6)  # single molecule in a sdf file
mol4 = readChar(system.file('sysdata/OptAA3d.sdf', package = 'Rcpi'),
                nchars = 1e+6)  # multiple molecules in a sdf file


smifp0 = extractDrugOBFP2(mol1, type = 'smile')
smifp1 = extractDrugOBFP2(mol2, type = 'smile')
sdffp0 = extractDrugOBFP2(mol3, type = 'sdf')
sdffp1 = extractDrugOBFP2(mol4, type = 'sdf')

Example output

OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed

Rcpi documentation built on Nov. 8, 2020, 8:23 p.m.