LogS: Small Molecule Solubility (LogS) Data

In conformal: Conformal Prediction for Regression and Classification

Description

Aqueous solubility datas for 1,606 small molecules. PaDEL descriptors have been computed for these molecules. The data has been split into a training (70%) and a test (30%) set.

Details

This dataset comprises the aqueous solubility (S) values at a temperature of 20-25 Celsius degrees in mol/L, expressed as logS, for 1,708 small molecules reported by Wang et al. Compound structures were standardized with the function StandardiseMolecules from the R package camb using the default parameters: (i) all molecules were kept irrespective of the numbers of fluorines, iodines, chlorine, and bromines present in their strucuture, or (ii) of their molecular mass. 905 one-dimensional topological and physicochemical descriptors were calculated with the function GeneratePadelDescriptors from the R package camb which invokes the PaDEL-Descriptor Java library. Near zero variance and highly-correlated descriptors were removed with the functions (i) RemoveNearZeroVarianceFeatures (cut-off value of 30/1), and (ii) RemoveHighlyCorrelatedFeatures (cut-off value of 0.95) After applying these steps the dataset consists of 1,606 molecules encoded with 211 descriptors.

Using data(LogS) exposes 4 objects:

(i) LogSDescsTrain is a data frame with PaDEL descriptors for the datapoints in the training set (70% of the data). (ii) LogSTrain is a numeric vector containing the data solubility values for the datapoints in the training set. (iii) LogSDescsTest is a data frame with PaDEL descriptors for the datapoints in the test set (30% of the data). (iv) LogSTest is a numeric vector containing the data solubility values for the datapoints in the test set.

References

Wang et al. J. Chem. Inf. Model., 2007, 47 (4), pp 1395-1404 DOI: 10.1021/ci700096r http://pubs.acs.org/doi/abs/10.1021/ci700096r

Examples

# To use the data
data(LogS)

Example output

Loading required package: caret
Loading required package: lattice
Loading required package: ggplot2
Loading required package: e1071
Loading required package: grid
No methods found in "randomForest" for requests: predict.randomForest
No methods found in "randomForest" for requests: plot.randomForest

conformal documentation built on May 30, 2017, 6:49 a.m.