load.molecules: Load molecular structures from disk or URL

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/io.R

Description

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

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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

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.

Value

A 'list' of CDK 'IAtomContainer' objects, represented as 'jobjRef' objects in R, which can be used in other 'rcdk' functions

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

write.molecules, parse.smiles, iload.molecules

Examples

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## Not run: 
sdffile <- system.file("molfiles/dhfr00008.sdf", package="rcdk")
mols <- load.molecules(c('mol1.sdf', 'mol2.smi', sdfile))

## End(Not run)

rcdk documentation built on March 13, 2020, 1:30 a.m.