extractDrugShortestPath: Calculate the Shortest Path Molecular Fingerprints (in...

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

Usage

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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 <http://nanx.me>

See Also

extractDrugShortestPathComplete

Examples

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

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


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