extrDrugKappaShapeIndices: Descriptor that Calculates Kier and Hall Kappa Molecular...

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Description

Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices

Usage

extrDrugKappaShapeIndices(molecules, silent = TRUE)

Arguments

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

Details

Kier and Hall Kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; see http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH for details: "they are intended to capture different aspects of molecular shape. Note that hydrogens are ignored. In the following description, n denotes the number of atoms in the hydrogen suppressed graph, m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2 and let p3 denote the number of paths of length 3".

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 3 columns named Kier1, Kier2 and Kier3:

• Kier1 - First kappa shape index

• Kier2 - Second kappa shape index

• Kier3 - Third kappa shape index

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

Examples

smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugKappaShapeIndices(mol)
head(dat)

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.