convertFormat: Convert Formats

Description

Converts compound data from one format to another.

Usage

convertFormat(from, to, source,options=data.frame(names="gen2D",args=""))

Arguments

from

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

The format to convert source to.

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.

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 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 Fill the unit cell (strict or keepconnect) gen2D Generate 2D coordinates gen3D Generate 3D coordinates minimize ForceField Energy Minimization (not displayed in GUI) partialcharge 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 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)

Value

Returns the compound given in source in the format specified by to.

References

OpenBabel http://openbabel.org

Examples

Run this code

   #create an SDF from a SMILES string and put the atoms in the canonical order
	sdfStr = convertFormat("SMI","SDF","CC(=O)OC1=CC=CC=C1C(=O)O\ttest_name",
                          options=data.frame(names="canonical",args=""))