gov.nih.ncats.molwitch.cdk

Class CdkChemical2FactoryImpl

java.lang.Object

gov.nih.ncats.molwitch.cdk.CdkChemical2FactoryImpl

All Implemented Interfaces:

gov.nih.ncats.molwitch.spi.ChemicalImplFactory

public class CdkChemical2FactoryImpl
extends Object
implements gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Constructor Summary

Constructors

Constructor and Description
CdkChemical2FactoryImpl()

Method Summary

Modifier and Type	Method and Description
protected void	addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer container) Copied from CDK CDKTestCase.java adds implicit hydrogens to given container.
gov.nih.ncats.molwitch.spi.ChemicalImplReader	create(byte[] molBytes, int start, int length)
gov.nih.ncats.molwitch.spi.ChemicalImplReader	create(File file)
gov.nih.ncats.molwitch.spi.ChemicalImplReader	create(InputStream in)
gov.nih.ncats.molwitch.spi.ChemicalImplReader	create(gov.nih.ncats.common.io.InputStreamSupplier in)
gov.nih.ncats.molwitch.spi.ChemicalImpl	create(String unknownFormattedInput)
gov.nih.ncats.molwitch.spi.ChemicalImplReader	create(String format, File file)
gov.nih.ncats.molwitch.spi.ChemicalImplReader	create(String format, InputStream in)
gov.nih.ncats.molwitch.spi.ChemicalImplReader	create(String format, gov.nih.ncats.common.io.InputStreamSupplier in)
gov.nih.ncats.molwitch.spi.ChemicalImpl	createFromSmarts(String smarts)
gov.nih.ncats.molwitch.spi.ChemicalImpl	createFromSmiles(String smiles)
gov.nih.ncats.molwitch.spi.ChemicalImpl	createNewEmptyChemical()
boolean	isDefault()
boolean	isFormatAgnostic()
boolean	supports(String format)

Methods inherited from class java.lang.Object

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

Constructor Detail

CdkChemical2FactoryImpl

public CdkChemical2FactoryImpl()

Method Detail

createNewEmptyChemical

public gov.nih.ncats.molwitch.spi.ChemicalImpl createNewEmptyChemical()

Specified by:

createNewEmptyChemical in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

addImplicitHydrogens

protected void addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer container)
                             throws Exception

Copied from CDK CDKTestCase.java adds implicit hydrogens to given container.

Parameters:

container - the IAtomContainer to add the hydrogens to.

Throws:

Exception - if any problems are encountered adding the hydrogens.

createFromSmiles

public gov.nih.ncats.molwitch.spi.ChemicalImpl createFromSmiles(String smiles)
                                                         throws IOException

Specified by:

createFromSmiles in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

create

public gov.nih.ncats.molwitch.spi.ChemicalImpl create(String unknownFormattedInput)
                                               throws IOException

Specified by:

create in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

isFormatAgnostic

public boolean isFormatAgnostic()

Specified by:

isFormatAgnostic in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

createFromSmarts

public gov.nih.ncats.molwitch.spi.ChemicalImpl createFromSmarts(String smarts)
                                                         throws IOException

Specified by:

createFromSmarts in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

create

public gov.nih.ncats.molwitch.spi.ChemicalImplReader create(byte[] molBytes,
                                                            int start,
                                                            int length)
                                                     throws IOException

Specified by:

create in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

create

public gov.nih.ncats.molwitch.spi.ChemicalImplReader create(String format,
                                                            gov.nih.ncats.common.io.InputStreamSupplier in)
                                                     throws IOException

Specified by:

create in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

create

public gov.nih.ncats.molwitch.spi.ChemicalImplReader create(gov.nih.ncats.common.io.InputStreamSupplier in)
                                                     throws IOException

Specified by:

create in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

create

public gov.nih.ncats.molwitch.spi.ChemicalImplReader create(String format,
                                                            InputStream in)
                                                     throws IOException

Specified by:

create in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

create

public gov.nih.ncats.molwitch.spi.ChemicalImplReader create(String format,
                                                            File file)
                                                     throws IOException

Specified by:

create in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

supports

public boolean supports(String format)

Specified by:

supports in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

create

public gov.nih.ncats.molwitch.spi.ChemicalImplReader create(File file)
                                                     throws IOException

Specified by:

create in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

create

public gov.nih.ncats.molwitch.spi.ChemicalImplReader create(InputStream in)
                                                     throws IOException

Specified by:

create in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory

Throws:

IOException

isDefault

public boolean isDefault()

Specified by:

isDefault in interface gov.nih.ncats.molwitch.spi.ChemicalImplFactory