extractDrugGraphComplete: Calculate the Graph Molecular Fingerprints (in Complete...

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

Description

Calculate the Graph Molecular Fingerprints (in Complete Format)

Usage

extractDrugGraphComplete(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

An integer vector or a matrix. Each row represents one molecule, the columns represent the fingerprints.

Author(s)

Nan Xiao <https://nanx.me>

See Also

extractDrugGraph

Examples

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

mol = readMolFromSmi(smi, type = 'mol')
fp  = extractDrugGraphComplete(mol)
dim(fp)

Example output

OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed
[1]  796 1024

Rcpi documentation built on Nov. 8, 2020, 8:23 p.m.