The CDK can read a variety of molecular structure formats. This function encapsulates the calls to the CDK API to load a structure given its filename or a URL to a structure file.
Usage
load.molecules(
molfiles = NA,
aromaticity = TRUE,
typing = TRUE,
isotopes = TRUE,
verbose = FALSE
)Arguments
- molfiles
A `character` vector of filenames. Note that the full path to the files should be provided. URL's can also be used as paths. In such a case, the URL should start with "http://"
- 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
- verbose
If `TRUE`, output (such as file download progress) will be bountiful
Value
A `list` of CDK `IAtomContainer` objects, represented as `jobjRef` objects in R, which can be used in other `rcdk` functions
Details
Note that this method will load all molecules into memory. For files containing tens of thousands of molecules this may lead to out of memory errors. In such situations consider using the iterating file readers.
Note that if molecules are read in from formats that do not have rules for
handling implicit hydrogens (such as MDL MOL), the molecule will not have
implicit or explicit hydrogens. To add explicit hydrogens, make sure that the molecule
has been typed (this is `TRUE` by default for this function) and then call
convert.implicit.to.explicit. On the other hand for a format
such as SMILES, implicit or explicit hydrogens will be present.
Author
Rajarshi Guha (rajarshi.guha@gmail.com)
Examples
if (FALSE) {
sdffile <- system.file("molfiles/dhfr00008.sdf", package="rcdk")
mols <- load.molecules(c('mol1.sdf', 'mol2.smi', sdfile))
}