extractDrugWeightedPath: Descriptor that Calculates the Weighted Path (Molecular ID)

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

Description

Descriptor that Calculates the Weighted Path (Molecular ID)

Usage

extractDrugWeightedPath(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 weighted path (molecular ID) described by Randic, characterizing molecular branching. Five descriptors are calculated, based on the implementation in the ADAPT software package. Note that the descriptor is based on identifying all paths between pairs of atoms and so is NP-hard. This means that it can take some time for large, complex molecules.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 5 columns named WTPT.1, WTPT.2, WTPT.3, WTPT.4, WTPT.5:

• WTPT.1 - molecular ID

• WTPT.2 - molecular ID / number of atoms

• WTPT.3 - sum of path lengths starting from heteroatoms

• WTPT.4 - sum of path lengths starting from oxygens

• WTPT.5 - sum of path lengths starting from nitrogens

Author(s)

Nan Xiao <https://nanx.me>

References

Randic, M., On molecular identification numbers (1984). Journal of Chemical Information and Computer Science, 24:164-175.

Examples

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

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

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