extractDrugShortestPath {Rcpi} | R Documentation

## Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

### Description

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`.

### Details

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

### 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.

### Author(s)

Nan Xiao <https://nanx.me>

### See Also

extractDrugShortestPathComplete

### Examples

    smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')

    mol = readMolFromSmi(smi, type = 'mol')
    fp  = extractDrugShortestPath(mol)
    head(fp)

[Package Rcpi version 1.20.1 Index]