org.openscience.cdk.graph.invariant

Class InChINumbersTools

java.lang.Object

org.openscience.cdk.graph.invariant.InChINumbersTools

public class InChINumbersTools
extends Object

Tool for calculating atom numbers using the InChI algorithm.

Source code:

master

Belongs to CDK module:

inchi

Constructor Summary

Constructors

Constructor and Description
InChINumbersTools()

Method Summary

Methods

Modifier and Type	Method and Description
static long[]	getNumbers(IAtomContainer atomContainer) Makes an array containing the InChI atom numbers of the non-hydrogen atoms in the atomContainer.
static long[]	getUSmilesNumbers(IAtomContainer container) Obtain the InChI numbers for the input container to be used to order atoms in Universal SMILES [O’Boyle, Noel, Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI, Journal of Cheminformatics, 2012, 4:?-?, doi:10.1186/1758-2946-4-22].
static void	parseAuxInfo(String aux, long[] numbers) Parse the atom numbering from the auxinfo.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

InChINumbersTools

public InChINumbersTools()

Method Detail

getNumbers

public static long[] getNumbers(IAtomContainer atomContainer)
                         throws CDKException

Makes an array containing the InChI atom numbers of the non-hydrogen atoms in the atomContainer. It returns zero for all hydrogens.

Parameters:

atomContainer - The IAtomContainer to analyze.

Returns:

The number from 1 to the number of heavy atoms.

Throws:

CDKException - When the InChI could not be generated

parseAuxInfo

public static void parseAuxInfo(String aux,
                long[] numbers)

Parse the atom numbering from the auxinfo.

Parameters:

aux - InChI AuxInfo

numbers - the atom numbers

getUSmilesNumbers

public static long[] getUSmilesNumbers(IAtomContainer container)
                                throws CDKException

Obtain the InChI numbers for the input container to be used to order atoms in Universal SMILES [O’Boyle, Noel, Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI, Journal of Cheminformatics, 2012, 4:?-?, doi:10.1186/1758-2946-4-22]. The numbers are obtained using the fixedH and RecMet options of the InChI. All non-bridged hydrogens are labelled as 0.

Parameters:

container - the structure to obtain the numbers of

Returns:

the atom numbers

Throws:

CDKException