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.

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

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.

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')
# \donttest{
mol = readMolFromSmi(smi, type = 'mol')
#> Error in parseSmiles(smi): The package "rcdk" is required to parse SMILES
dat = extractDrugWeightedPath(mol)
#> Error in evaluateDescriptor(molecules, type = "WeightedPathDescriptor",     silent = silent): The package "rcdk" is required to compute molecular descriptors
head(dat)# }
#> Error: object 'dat' not found