BAZOO

So much to do, so little time

Trying to squeeze sense out of chemical data

New Version of rcdk

without comments

Based on feedback from the recent R workshop at the EBI, I’ve updated the rcdk package to include more methods operating on atoms, a modification to parse.smiles to allow it to handle a vector of SMILES strings, which makes it more R-like (thanks to Tobias Verbeke for the patch). In addition, one can now load very large SMILES or SDF files using the iterating readers from the CDK. This feature makes use of the iterators package and lets you write code such as

1
2
3
4
5
iter <- iload.molecules('big.smi', type='smi')
while(hasNext(iter)) {
  mol <- nextElem(iter)
  print(get.property(mol, "cdk:Title")
}

As a result, only one molecule is loaded at a time, allowing one to process arbitrarily large files. Version 2.9.23 has been uploaded to CRAN and should be available in a day or two

Written by Rajarshi Guha

May 21st, 2010 at 11:43 pm

Posted in software

Tagged with ,

Leave a Reply