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

In nanxstats/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

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.

See Also

extractDrugShortestPathComplete

Examples

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

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

nanxstats/Rcpi documentation built on Sept. 24, 2024, 9:36 a.m.