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Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

Source: R/379-extractDrugShortestPath.R
extractDrugShortestPath.Rd

Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

Usage

extractDrugShortestPath(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

A list, each component represents one of the molecules, each element in the component represents the index of which element in the fingerprint is 1. Each component's name is the length of 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

extractDrugShortestPathComplete

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  = extractDrugShortestPath(mol)
#> Error: object 'mol' not found
head(fp)# }
#> Error: object 'fp' not found