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

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

Usage

extrDrugShortestPath(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)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

See Also

extrDrugShortestPathComplete

Examples

smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
fp  = extrDrugShortestPath(mol)
head(fp)

BioMedR documentation built on July 5, 2019, 9:03 a.m.