convertToImage: Convert To Image

Description Usage Arguments Value Author(s) References Examples

View source: R/wrappers.R

Description

Converts compound data to an image format

Usage

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convertToImage(from,to,source,toFile,options=data.frame(names="gen2D",args=""),
									out_options=data.frame(names=c("p"),args=c(300)))

Arguments

from

The format that source is in. This should be a string supported by OpenBabel.

to

The image format to convert source to. This should be either "PNG", "POV", or "SVG".

source

The initial compound format, as a string. The format of the string should be identical to the file format of the same name. Tabs and newlines may be represented with \t and \n, repsectivly.

toFile

The name of the output file.

options

This is a data frame listing OpenBabel Options that should be applied while converting each compound. The "names" column should be the name of each option and the "args" column sould be the arguments to the corresponding option. For example, the default value shown above will cause 2D coordinates to be generated from the input compound and saved in the output compound, assuming the ouptut format supports it.

A full list of available options can be found by executing "obabel -L ops" at the command line. The current list is:

0xout <file.xxx> Additional file output AddInIndex Append input index to title AddPolarH Adds hydrogen to polar atoms only canonical Canonicalize the atom order energy ForceField Energy Evaluation (not displayed in GUI) fillUC <param> Fill the unit cell (strict or keepconnect) gen2D Generate 2D coordinates gen3D Generate 3D coordinates minimize ForceField Energy Minimization (not displayed in GUI) partialcharge <method> Calculate partial charges by specified method readconformer Adjacent conformers combined into a single molecule s Isomorphism filter(-s, -v options replacement)(not displayed in GUI) sort <desc> Sort by descriptor(~desc for reverse) unique [param] remove duplicates by descriptor;default inchi v Isomorphism filter(-s, -v options replacement)(not displayed in GUI)

out_options

Similar to the options argument, but these options apply to the output format.

For the "PNG" format, possible options are:

"p" for the number of pixels on the square output file.

For the "SVG" format, see the OpenBabel docs for a full list (https://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html).

Value

Generates a square image with the given compounds arranged in a grid format. The width (and height, which must be the same) can be given using the out_options with argument "p". Writes the resulting image to a file specified by to_file.

Author(s)

Kevin Horan

References

OpenBabel http://openbabel.org

Examples

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   # Convert the given smiles string to a PNG image with size 500x500.
	sdfStr = convertToImage("SMI","PNG","CC(=O)OC1=CC=CC=C1C(=O)O\ttest_name","out_iamge.png",
                          out_options=data.frame(names="p",args="500"))

ChemmineOB documentation built on Nov. 1, 2018, 2:06 a.m.