bachi55/rcdkTools

Wrapper functions for the rcdk-library.

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
  • The original rcdk only supports ECFP6
  • My extension provides access to the all types provided 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.