Get Chemical Descriptors for a list of molecules

Calculate Chemical Descriptors (CDs) for a list of molecules. Molecules can appear multiple times in the list.

Usage

getCDs(df, verbose = 1, nw = 1, keepdf = TRUE, cache = TRUE)

Arguments

df

dataframe with two mandatory columns: "NAME" and "SMILES"

verbose

0: no output, 1: progress, 2: more progress and warnings

nw

number of workers for parallel processing

keepdf

If TRUE, cbind(df, CDs) is returned. Else CDs.

cache

If TRUE (default), descriptors are cached on disk (an SQLite database under tools::R_user_dir("FastRet", "cache")): already-known descriptors are read from the cache and newly computed ones are written back, so repeated calls on the same molecules are fast and the cache is shared across processes. If FALSE, the cache is bypassed entirely and every descriptor is (re)computed via rCDK – useful for benchmarking the uncached runtime.

Value

A dataframe with all input columns (if keepdf is TRUE) and chemical descriptors as remaining columns.

Examples

cds <- getCDs(head(RP, 3), verbose = 1, nw = 1)
#> 2026-07-05 18:22:42.87 Obtaining chemical descriptors for 3 molecules
#> 2026-07-05 18:22:42.89 Finished obtaining chemical descriptors in 0.01s