extrDrugGraph: Calculate the Graph Molecular Fingerprints (in Compact...

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

Description

Calculate the Graph Molecular Fingerprints (in Compact Format)

Usage

extrDrugGraph(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 graph molecular fingerprints. Similar to the standard type by simply considers connectivity. This is hashed fingerprints, with a default length of 1024.

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

extrDrugGraphComplete

Examples

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

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.