extractDrugStandardComplete: Calculate the Standard Molecular Fingerprints (in Complete...

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

Description

Calculate the Standard Molecular Fingerprints (in Complete Format)

Usage

extractDrugStandardComplete(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 standard molecular fingerprints. Considers paths of a given length. 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

extractDrugStandard

Examples

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

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

Example output

OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file:
   4069139
Try using the -Djava.io.tmpdir= option to select an alternate temp location.

[1]  796 1024

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