Calculate Molecular Descriptors Provided by OpenBabel

Usage

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

Arguments

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

Value

A data frame, each row represents one of the molecules, each column represents one descriptor. This function returns 14 columns named abonds, atoms, bonds, dbonds, HBA1, HBA2, HBD, logP, MR, MW, nF, sbonds, tbonds, TPSA:

abonds - Number of aromatic bonds
atoms - Number of atoms
bonds - Number of bonds
dbonds - Number of double bonds
HBA1 - Number of Hydrogen Bond Acceptors 1
HBA2 - Number of Hydrogen Bond Acceptors 2
HBD - Number of Hydrogen Bond Donors
logP - Octanol/Water Partition Coefficient
MR - Molar Refractivity
MW - Molecular Weight Filter
nF - Number of Fluorine Atoms
sbonds - Number of single bonds
tbonds - Number of triple bonds
TPSA - Topological Polar Surface Area

Details

This function calculates 14 types of the numerical molecular descriptors provided in OpenBabel.

Examples

mol1 = 'CC(=O)NCCC1=CNc2c1cc(OC)cc2'  # one molecule SMILE in a vector
mol2 = c('OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2',
         'CCc(c1)ccc2[n+]1ccc3c2Nc4c3cccc4',
         '[Cu+2].[O-]S(=O)(=O)[O-]')  # 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

if (FALSE) { # \dontrun{
smidesc0 = extractDrugDescOB(mol1, type = 'smile')
smidesc1 = extractDrugDescOB(mol2, type = 'smile')
sdfdesc0 = extractDrugDescOB(mol3, type = 'sdf')
sdfdesc1 = extractDrugDescOB(mol4, type = 'sdf')} # }