extractDrugOBFP3 {Rcpi} | R Documentation

## Calculate the FP3 Molecular Fingerprints

### Description

Calculate the FP3 Molecular Fingerprints

### Usage

    extractDrugOBFP3(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 64 bit FP3 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 = extractDrugOBFP3(mol1, type = 'smile')
    smifp1 = extractDrugOBFP3(mol2, type = 'smile')
    sdffp0 = extractDrugOBFP3(mol3, type = 'sdf')
    sdffp1 = extractDrugOBFP3(mol4, type = 'sdf')

[Package Rcpi version 1.20.1 Index]