iload.molecules: Load molecules using an iterator.

Description

The CDK can read a variety of molecular structure formats. Some file formats support multiple molecules in a single file. If read using load.molecules, all are read into memory. For very large structure files, this can lead to out of memory errors. Instead it is recommended to use the iterating version of the loader so that only a single molecule is read at a time.

Usage

iload.molecules(
  molfile,
  type = "smi",
  aromaticity = TRUE,
  typing = TRUE,
  isotopes = TRUE,
  skip = TRUE
)

Arguments

molfile: A string containing the filename to load. Must be a local file
type: Indicates whether the input file is SMILES or SDF. Valid values are `"smi"` or `"sdf"`
aromaticity: If `TRUE` then aromaticity detection is performed on all loaded molecules. If this fails for a given molecule, then the molecule is set to `NA` in the return list
typing: If `TRUE` then atom typing is performed on all loaded molecules. The assigned types will be CDK internal types. If this fails for a given molecule, then the molecule is set to `NA` in the return list
isotopes: If `TRUE` then atoms are configured with isotopic masses
skip: If `TRUE`, then the reader will continue reading even when faced with an invalid molecule. If `FALSE`, the reader will stop at the fist invalid molecule

Author

Rajarshi Guha (rajarshi.guha@gmail.com)

Details

Note that the iterating loader only supports SDF and SMILES file formats.

Examples

Run this code

if (FALSE) {
moliter <- iload.molecules("big.sdf", type="sdf")
while(hasNext(moliter)) {
mol <- nextElem(moliter)
  print(get.property(mol, "cdk:Title"))
}
}