extractDrugALOGP: Calculate Atom Additive logP and Molar Refractivity Values...

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

Description

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.

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.

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.

Author(s)

Nan Xiao <https://nanx.me>

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')

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

Example output

OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed
                                                          ALogP    ALogp2
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O  3.1617 9.9963469
c1(ccc(cc1)O)NC(=O)C                                     0.6830 0.4664890
c1ccccc1NC(=O)C                                          0.9504 0.9032602
n1nc(S(=O)(=O)N)sc1NC(=O)C                              -1.3288 1.7657094
O=S(=O)(c1ccc(cc1)C(=O)C)NC(=O)NC1CCCCC1                 2.1193 4.4914325
CC(=O)NO                                                -1.1888 1.4132454
                                                            AMR
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 93.0381
c1(ccc(cc1)O)NC(=O)C                                    40.8343
c1ccccc1NC(=O)C                                         39.1402
n1nc(S(=O)(=O)N)sc1NC(=O)C                              47.6136
O=S(=O)(c1ccc(cc1)C(=O)C)NC(=O)NC1CCCCC1                82.7714
CC(=O)NO                                                16.2305

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