Descriptor that Calculates the Number of Hydrogen Bond Acceptors

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Description

Descriptor that Calculates the Number of Hydrogen Bond Acceptors

Usage

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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 <http://nanx.me>

Examples

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

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

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