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