extractDrugHBondAcceptorCount: Number of Hydrogen Bond Acceptors

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

Number of Hydrogen Bond Acceptors

Description

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.

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

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

2. 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.

Value

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

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')

mol = readMolFromSmi(smi, type = 'mol')
dat = extractDrugHBondAcceptorCount(mol)
head(dat)

nanxstats/Rcpi documentation built on Sept. 24, 2024, 9:36 a.m.