Calculate Atom Additive logP and Molar Refractivity Values Descriptor

Usage

extractDrugALOGP(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 three columns named ALogP, ALogp2 and AMR.

Details

Calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity as described by Ghose, A.K. and Crippen, G.M. Note the underlying code in CDK assumes that aromaticity has been detected before evaluating this descriptor. The code also expects that the molecule will have hydrogens explicitly set. For SD files, this is usually not a problem since hydrogens are explicit. But for the case of molecules obtained from SMILES, hydrogens must be made explicit.

References

Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity, Journal of Computational Chemistry, 1986, 7:565-577.

Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions, Journal of Chemical Information and Computer Science, 1987, 27:21-35.

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 = extractDrugALOGP(mol)
#> Error in evaluateDescriptor(molecules, type = "ALOGPDescriptor", silent = silent): The package "rcdk" is required to compute molecular descriptors
head(dat)# }
#> Error: object 'dat' not found