ambit2.tautomers.processor

Class StructureStandardizer

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

ambit2.tautomers.processor.StructureStandardizer

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

public class StructureStandardizer
extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	clearIsotopes
static String	ERROR_TAG
protected FragmentProcessor	fragments
protected boolean	generate2D
protected boolean	generateInChI
protected boolean	generateSMILES
protected boolean	generateSMILES_Aromatic
protected boolean	generateSMILES_Canonical
protected boolean	generateStereofrom2D
protected boolean	generateTautomers
protected org.openscience.cdk.tools.CDKHydrogenAdder	hadder
protected org.openscience.cdk.inchi.InChIGeneratorFactory	igf
protected boolean	implicitHydrogens
protected IsotopesProcessor	isotopesProcessor
protected boolean	neutralise
protected NeutraliseProcessor	neutraliser
protected List<net.sf.jniinchi.INCHI_OPTION>	options
protected org.openscience.cdk.layout.StructureDiagramGenerator	sdg
protected org.openscience.cdk.smiles.SmilesGenerator	smiles_generator
protected boolean	splitFragments
protected Map<Object,Property>	tags
protected TautomerProcessor	tautomers

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
StructureStandardizer()
StructureStandardizer(Logger logger)

Method Summary

Modifier and Type	Method and Description
net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>	getCallback()
protected org.openscience.cdk.smiles.SmilesGenerator	getSmilesGenerator()
protected String	InChI2SMILES(String inchi) This is last resort, when creating SMILES from structure fails for whatever reason
boolean	isClearIsotopes()
boolean	isGenerate2D()
boolean	isGenerateInChI()
boolean	isGenerateSMILES_Aromatic()
boolean	isGenerateSMILES_Canonical()
boolean	isGenerateSMILES()
boolean	isGenerateStereofrom2D()
boolean	isGenerateTautomers()
boolean	isImplicitHydrogens()
boolean	isNeutralise()
boolean	isSplitFragments()
org.openscience.cdk.interfaces.IAtomContainer	process(org.openscience.cdk.interfaces.IAtomContainer mol)
static void	renameTags(org.openscience.cdk.interfaces.IAtomContainer processed, Map<Object,Property> tags)
static void	renameTags(org.openscience.cdk.interfaces.IAtomContainer processed, Map<Object,Property> tags, boolean removeIfDisabled)
void	setCallback(net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> callback)
void	setClearIsotopes(boolean clearIsotopes)
void	setGenerate2D(boolean generate2d)
void	setGenerateInChI(boolean generateInChI)
void	setGenerateSMILES_Aromatic(boolean generateSMILES_Aromatic)
void	setGenerateSMILES_Canonical(boolean generateSMILES_Canonical)
void	setGenerateSMILES(boolean generateSMILES)
void	setGenerateStereofrom2D(boolean generateStereofrom2D)
void	setGenerateTautomers(boolean generateTautomers)
void	setImplicitHydrogens(boolean implicitHydrogens)
void	setInchiKeyTag(String tag)
void	setInchiTag(String tag)
void	setNeutralise(boolean neutralise)
void	setRankTag(String tag)
void	setSMILESTag(String tag)
void	setSplitFragments(boolean splitFragments)

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, close, getID, isEnabled, open, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

Methods inherited from class java.lang.Object

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

Field Detail

tags

protected Map<Object,Property> tags

generateInChI

protected boolean generateInChI

generateSMILES_Canonical

protected boolean generateSMILES_Canonical

generateSMILES_Aromatic

protected boolean generateSMILES_Aromatic

splitFragments

protected boolean splitFragments

generateTautomers

protected boolean generateTautomers

generateSMILES

protected boolean generateSMILES

neutralise

protected boolean neutralise

generate2D

protected boolean generate2D

implicitHydrogens

protected boolean implicitHydrogens

generateStereofrom2D

protected boolean generateStereofrom2D

clearIsotopes

protected boolean clearIsotopes

options

protected List<net.sf.jniinchi.INCHI_OPTION> options

tautomers

protected transient TautomerProcessor tautomers

fragments

protected transient FragmentProcessor fragments

neutraliser

protected transient NeutraliseProcessor neutraliser

isotopesProcessor

protected transient IsotopesProcessor isotopesProcessor

sdg

protected transient org.openscience.cdk.layout.StructureDiagramGenerator sdg

hadder

protected transient org.openscience.cdk.tools.CDKHydrogenAdder hadder

igf

protected transient org.openscience.cdk.inchi.InChIGeneratorFactory igf

smiles_generator

protected transient org.openscience.cdk.smiles.SmilesGenerator smiles_generator

ERROR_TAG

public static final String ERROR_TAG

See Also:

Constant Field Values

Constructor Detail

StructureStandardizer

public StructureStandardizer()

StructureStandardizer

public StructureStandardizer(Logger logger)

Method Detail

isGenerateSMILES_Aromatic

public boolean isGenerateSMILES_Aromatic()

setGenerateSMILES_Aromatic

public void setGenerateSMILES_Aromatic(boolean generateSMILES_Aromatic)

isGenerate2D

public boolean isGenerate2D()

setGenerate2D

public void setGenerate2D(boolean generate2d)

isNeutralise

public boolean isNeutralise()

setNeutralise

public void setNeutralise(boolean neutralise)

isGenerateStereofrom2D

public boolean isGenerateStereofrom2D()

setGenerateStereofrom2D

public void setGenerateStereofrom2D(boolean generateStereofrom2D)

isClearIsotopes

public boolean isClearIsotopes()

setClearIsotopes

public void setClearIsotopes(boolean clearIsotopes)

isGenerateSMILES_Canonical

public boolean isGenerateSMILES_Canonical()

setGenerateSMILES_Canonical

public void setGenerateSMILES_Canonical(boolean generateSMILES_Canonical)

getSmilesGenerator

protected org.openscience.cdk.smiles.SmilesGenerator getSmilesGenerator()

isGenerateSMILES

public boolean isGenerateSMILES()

setGenerateSMILES

public void setGenerateSMILES(boolean generateSMILES)

isGenerateInChI

public boolean isGenerateInChI()

setGenerateInChI

public void setGenerateInChI(boolean generateInChI)

isSplitFragments

public boolean isSplitFragments()

setSplitFragments

public void setSplitFragments(boolean splitFragments)

isGenerateTautomers

public boolean isGenerateTautomers()

setGenerateTautomers

public void setGenerateTautomers(boolean generateTautomers)

isImplicitHydrogens

public boolean isImplicitHydrogens()

setImplicitHydrogens

public void setImplicitHydrogens(boolean implicitHydrogens)

getCallback

public net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> getCallback()

setCallback

public void setCallback(net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> callback)

process

public org.openscience.cdk.interfaces.IAtomContainer process(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                      throws Exception

Throws:

Exception

renameTags

public static void renameTags(org.openscience.cdk.interfaces.IAtomContainer processed,
                              Map<Object,Property> tags)

renameTags

public static void renameTags(org.openscience.cdk.interfaces.IAtomContainer processed,
                              Map<Object,Property> tags,
                              boolean removeIfDisabled)

setInchiTag

public void setInchiTag(String tag)

setInchiKeyTag

public void setInchiKeyTag(String tag)

setSMILESTag

public void setSMILESTag(String tag)

setRankTag

public void setRankTag(String tag)

InChI2SMILES

protected String InChI2SMILES(String inchi)
                       throws Exception

This is last resort, when creating SMILES from structure fails for whatever reason

Parameters:

inchi -

Returns:

Throws:

Exception