Calculate the Shortest Path Molecular Fingerprints (in Complete Format) — extractDrugShortestPathComplete • Rcpi

Calculate the Shortest Path Molecular Fingerprints (in Complete Format)

Usage

extractDrugShortestPathComplete(
  molecules,
  depth = 6,
  size = 1024,
  silent = TRUE
)

Arguments

molecules: Parsed molucule object.
depth: The search depth. Default is 6.
size: The length of the fingerprint bit string. Default is 1024.
silent: Logical. Whether the calculating process should be shown or not, default is TRUE.

Value

An integer vector or a matrix. Each row represents one molecule, the columns represent the fingerprints.

Details

Calculate the fingerprint based on the shortest paths between pairs of atoms and takes into account ring systems, charges etc.

See also

extractDrugShortestPath

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
# \donttest{
mol = readMolFromSmi(smi, type = 'mol')
#> Error in parseSmiles(smi): The package "rcdk" is required to parse SMILES
fp  = extractDrugShortestPathComplete(mol)
#> Error in eval(expr, envir, enclos): object 'mol' not found
dim(fp)# }
#> Error in eval(expr, envir, enclos): object 'fp' not found