/rcdkTools

Wrapper functions for the rcdk-library.

Primary LanguageRMIT LicenseMIT

The rcdkTools package

This package provides some functions to simplify the fingerprint calculation for larger sets of molecules. It is mainly indeted to be a wrapper around the rcdk-package.

TODO:

  • Add convenient functions to handle counting fps
    • store counting fps matrices
    • store counting fps hashed lists
  • Add tools to handle molecular descriptors
  • Add parallel calculation of fingerprints and descriptors

My modified rcdk-package

Currently not support by the original package:

  • substructure fingerprint provided by CDK
    • In this way the MACCS counting fingerprints can be used.
    • For that the corresponding SMARTS pattern must be downloaded.
  • additional circular fingerprint type as supported by CDK

Installation

Open a R terminal:

library(devtools)
install_github("bachi55/cdkr", subdir="rcdklibs", ref="support_cdk_substructure_fps")
install_github("bachi55/cdkr", subdir="rcdk", ref="support_cdk_substructure_fps")

Please note: This overwrites the possible already existing installations.