Number of Hydrogen Bond Acceptors

Usage

extractDrugHBondAcceptorCount(molecules, silent = TRUE)

Arguments

molecules: Parsed molucule object.
silent: Logical. Whether the calculating process should be shown or not, default is TRUE.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns one column named nHBAcc.

Details

This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types. The following groups are counted as hydrogen bond acceptors: any oxygen where the formal charge of the oxygen is non-positive (i.e. formal charge <= 0) except

an aromatic ether oxygen (i.e. an ether oxygen that is adjacent to at least one aromatic carbon)
an oxygen that is adjacent to a nitrogen

and any nitrogen where the formal charge of the nitrogen is non-positive (i.e. formal charge <= 0) except a nitrogen that is adjacent to an oxygen.

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
# \donttest{
mol = readMolFromSmi(smi, type = 'mol')
#> Error in parseSmiles(smi): The package "rcdk" is required to parse SMILES
dat = extractDrugHBondAcceptorCount(mol)
#> Error in evaluateDescriptor(molecules, type = "HBondAcceptorCountDescriptor",     silent = silent): The package "rcdk" is required to compute molecular descriptors
head(dat)# }
#> Error: object 'dat' not found