extractDrugHBondAcceptorCount: Number of Hydrogen Bond Acceptors

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

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.

Author(s)

Nan Xiao <https://nanx.me>

Examples

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

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

Example output

OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed
                                                        nHBAcc
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O      2
c1(ccc(cc1)O)NC(=O)C                                         2
c1ccccc1NC(=O)C                                              2
n1nc(S(=O)(=O)N)sc1NC(=O)C                                   7
O=S(=O)(c1ccc(cc1)C(=O)C)NC(=O)NC1CCCCC1                     6
CC(=O)NO                                                     1

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