Compute Morgan fingerprints (circular fingerprints).
Arguments
- mols
A
tidymol
object.- radius
The radius parameter for Morgan fingerprints.
radius = 2
is roughly equivalent to ECFP4 and FCFP4.- use_features
Should we use the feature-based invariants, similar to those used for the FCFP fingerprints? Defaults to
FALSE
. This means only apply the default atom invariants, which use the connectivity information similar to those used for the ECFP fingerprints.- explicit
Return the fingerprints as a vector or matrix? Default is
FALSE
.
Examples
if (FALSE) { # is_installed_rdkit()
mol <- parse_smiles("Cc1ccccc1")
mols <- read_smiles(tidychem_example("smi-multiple.smi"))
# ECFP4
fp_morgan(mol)
fp_morgan(mols)
# get fingerprints matrix
fp_morgan(mol, explicit = TRUE)
fp_morgan(mols, explicit = TRUE)
# FCFP2
fp_morgan(mol, radius = 1L, use_features = TRUE)
fp_morgan(mols, radius = 1L, use_features = TRUE)
# get fingerprints matrix
fp_morgan(mol, radius = 1L, use_features = TRUE, explicit = TRUE)
fp_morgan(mols, radius = 1L, use_features = TRUE, explicit = TRUE)
}