load.molecules {rcdk}R Documentation

Load Molecular Structure From Disk

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

Usage

load.molecules(molfiles=NA, aromaticity = TRUE, typing = 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
verbose If TRUE, output (such as file download progress) will be bountiful

Value

A list of CDK Molecule objects, which can be used in other rcdk functions

Author(s)

Rajarshi Guha (rguha@indiana.edu)

See Also

view.molecule.2d


[Package rcdk version 2.9.2 Index]