A Grammar for Tidying Chemical Data

Nan Xiao <https://nanx.me>

Introduction

The tidychem package offers a lightweight R interface for accessing RDKit via the RDKit Python API.

Walkthrough

library("tidychem")

mols <- "smi-multiple.smi" %>% tidychem_example %>% read_smiles

# ECFP4
mols %>% fp_morgan

# similarity
# mols %>% fp_morgan %>% sim_tanimoto

# matrix
mols %>% fp_morgan(explicit = TRUE)

df <- "logd74.tsv" %>% tidychem_example %>% read_tsv
y <- df$logD7.4
mols <- df$SMILES %>% parse_smiles
mols

# matrix of 2D/3D descriptors
x <- mols %>% desc_2d
x
x[which(is.na(x))] <- 0

library("glmnet")

cvfit = cv.glmnet(x, y)
plot(cvfit)

fit <- glmnet(x, y)
plot(fit)
head(coef(fit, s = cvfit$lambda.min, exact = TRUE), n = 30)