gov.nih.ncats.molwitch.cdk

Class CdkChemicalImpl

java.lang.Object

gov.nih.ncats.molwitch.cdk.CdkChemicalImpl

All Implemented Interfaces:

gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

public class CdkChemicalImpl
extends Object
implements gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

Nested Class Summary

Nested classes/interfaces inherited from interface gov.nih.ncats.molwitch.spi.ChemicalImpl

gov.nih.ncats.molwitch.spi.ChemicalImpl.PreparationOptions

Constructor Summary

Constructors

Constructor and Description
CdkChemicalImpl(org.openscience.cdk.interfaces.IAtomContainer container, gov.nih.ncats.molwitch.ChemicalSource source)
CdkChemicalImpl(org.openscience.cdk.interfaces.IAtomContainer container, java.util.function.Supplier<? extends gov.nih.ncats.molwitch.ChemicalSource> source)

Method Summary

Modifier and Type	Method and Description
gov.nih.ncats.molwitch.Atom	addAtom(gov.nih.ncats.molwitch.Atom a)
gov.nih.ncats.molwitch.Atom	addAtom(gov.nih.ncats.molwitch.isotopes.Isotope isotope)
gov.nih.ncats.molwitch.Atom	addAtom(String symbol)
gov.nih.ncats.molwitch.Atom	addAtomByAtomicNum(int atomicNumber)
gov.nih.ncats.molwitch.Bond	addBond(gov.nih.ncats.molwitch.Atom atom1, gov.nih.ncats.molwitch.Atom atom2, gov.nih.ncats.molwitch.Bond.BondType type)
gov.nih.ncats.molwitch.Bond	addBond(gov.nih.ncats.molwitch.Bond b)
void	addChemical(gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl> other)
gov.nih.ncats.molwitch.SGroup	addSgroup(gov.nih.ncats.molwitch.SGroup.SGroupType type)
void	aromatize()
Iterator<CdkChemicalImpl>	connectedComponents()
CdkChemicalImpl	deepCopy()
void	expandSGroups()
void	flipChirality(gov.nih.ncats.molwitch.Stereocenter s)
void	generateCoordinates()
gov.nih.ncats.molwitch.Atom	getAtom(int i)
int	getAtomCount()
gov.nih.ncats.molwitch.Bond	getBond(int i)
int	getBondCount()
gov.nih.ncats.molwitch.BondTable	getBondTable()
org.openscience.cdk.interfaces.IAtomContainer	getContainer()
List<gov.nih.ncats.molwitch.DoubleBondStereochemistry>	getDoubleBondStereochemistry()
List<gov.nih.ncats.molwitch.ExtendedTetrahedralChirality>	getExtendedTetrahedrals()
String	getFormula()
String	getFormula(boolean includeImplicitHydrogen)
gov.nih.ncats.molwitch.GraphInvariant	getGraphInvariant()
double	getMass()
String	getName()
String	getProperty(String key)
int	getSGroupCount()
List<gov.nih.ncats.molwitch.SGroup>	getSGroups()
int	getSmallestRingSize()
gov.nih.ncats.molwitch.ChemicalSource	getSource()
List<gov.nih.ncats.molwitch.TetrahedralChirality>	getTetrahedrals()
Object	getWrappedObject() Get the IAtomContainer.
boolean	has2DCoordinates()
boolean	has3DCoordinates()
boolean	hasCoordinates()
boolean	hasImplicitHydrogens()
boolean	hasSGroups()
int	indexOf(gov.nih.ncats.molwitch.Atom a)
int	indexOf(gov.nih.ncats.molwitch.Bond b)
boolean	isAromatic()
void	kekulize()
void	makeHydrogensExplicit()
void	makeHydrogensImplicit()
void	prepareForBuild(gov.nih.ncats.molwitch.spi.ChemicalImpl.PreparationOptions options)
Iterator<Map.Entry<String,String>>	properties()
gov.nih.ncats.molwitch.Atom	removeAtom(gov.nih.ncats.molwitch.Atom a)
gov.nih.ncats.molwitch.Atom	removeAtom(int i)
gov.nih.ncats.molwitch.Bond	removeBond(gov.nih.ncats.molwitch.Atom a, gov.nih.ncats.molwitch.Atom b)
gov.nih.ncats.molwitch.Bond	removeBond(gov.nih.ncats.molwitch.Bond b)
gov.nih.ncats.molwitch.Bond	removeBond(int i)
void	removeProperty(String name)
void	removeSGroup(gov.nih.ncats.molwitch.SGroup sgroup)
protected void	setImplicitHydrogens()
protected int	setImplicitHydrogens(org.openscience.cdk.interfaces.IAtom atom)
void	setName(String name)
void	setProperty(String key, String value)
CdkChemicalImpl	shallowCopy()

Methods inherited from class java.lang.Object

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

Constructor Detail

CdkChemicalImpl

public CdkChemicalImpl(org.openscience.cdk.interfaces.IAtomContainer container,
                       java.util.function.Supplier<? extends gov.nih.ncats.molwitch.ChemicalSource> source)

CdkChemicalImpl

public CdkChemicalImpl(org.openscience.cdk.interfaces.IAtomContainer container,
                       gov.nih.ncats.molwitch.ChemicalSource source)

Method Detail

flipChirality

public void flipChirality(gov.nih.ncats.molwitch.Stereocenter s)

Specified by:

flipChirality in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getSource

public gov.nih.ncats.molwitch.ChemicalSource getSource()

Specified by:

getSource in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getSmallestRingSize

public int getSmallestRingSize()

Specified by:

getSmallestRingSize in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getWrappedObject

public Object getWrappedObject()

Get the IAtomContainer.

Specified by:

getWrappedObject in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

shallowCopy

public CdkChemicalImpl shallowCopy()

Specified by:

shallowCopy in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

deepCopy

public CdkChemicalImpl deepCopy()

Specified by:

deepCopy in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

addAtom

public gov.nih.ncats.molwitch.Atom addAtom(String symbol)

Specified by:

addAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

addChemical

public void addChemical(gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl> other)

Specified by:

addChemical in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

addAtom

public gov.nih.ncats.molwitch.Atom addAtom(gov.nih.ncats.molwitch.Atom a)

Specified by:

addAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

addAtom

public gov.nih.ncats.molwitch.Atom addAtom(gov.nih.ncats.molwitch.isotopes.Isotope isotope)

Specified by:

addAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

addAtomByAtomicNum

public gov.nih.ncats.molwitch.Atom addAtomByAtomicNum(int atomicNumber)

Specified by:

addAtomByAtomicNum in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getSGroupCount

public int getSGroupCount()

Specified by:

getSGroupCount in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

makeHydrogensExplicit

public void makeHydrogensExplicit()

Specified by:

makeHydrogensExplicit in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

hasImplicitHydrogens

public boolean hasImplicitHydrogens()

Specified by:

hasImplicitHydrogens in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

makeHydrogensImplicit

public void makeHydrogensImplicit()

Specified by:

makeHydrogensImplicit in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

isAromatic

public boolean isAromatic()

hasCoordinates

public boolean hasCoordinates()

Specified by:

hasCoordinates in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

has2DCoordinates

public boolean has2DCoordinates()

Specified by:

has2DCoordinates in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

has3DCoordinates

public boolean has3DCoordinates()

Specified by:

has3DCoordinates in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getName

public String getName()

Specified by:

getName in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

setName

public void setName(String name)

Specified by:

setName in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getMass

public double getMass()

Specified by:

getMass in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getAtomCount

public int getAtomCount()

Specified by:

getAtomCount in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getBondCount

public int getBondCount()

Specified by:

getBondCount in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getAtom

public gov.nih.ncats.molwitch.Atom getAtom(int i)

Specified by:

getAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

removeAtom

public gov.nih.ncats.molwitch.Atom removeAtom(int i)

Specified by:

removeAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

removeAtom

public gov.nih.ncats.molwitch.Atom removeAtom(gov.nih.ncats.molwitch.Atom a)

Specified by:

removeAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

removeBond

public gov.nih.ncats.molwitch.Bond removeBond(int i)

Specified by:

removeBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

removeBond

public gov.nih.ncats.molwitch.Bond removeBond(gov.nih.ncats.molwitch.Bond b)

Specified by:

removeBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

removeBond

public gov.nih.ncats.molwitch.Bond removeBond(gov.nih.ncats.molwitch.Atom a,
                                              gov.nih.ncats.molwitch.Atom b)

Specified by:

removeBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getContainer

public org.openscience.cdk.interfaces.IAtomContainer getContainer()

aromatize

public void aromatize()

Specified by:

aromatize in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

expandSGroups

public void expandSGroups()

Specified by:

expandSGroups in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

generateCoordinates

public void generateCoordinates()
                         throws gov.nih.ncats.molwitch.ChemkitException

Specified by:

generateCoordinates in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

Throws:

gov.nih.ncats.molwitch.ChemkitException

prepareForBuild

public void prepareForBuild(gov.nih.ncats.molwitch.spi.ChemicalImpl.PreparationOptions options)

Specified by:

prepareForBuild in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

kekulize

public void kekulize()

Specified by:

kekulize in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getFormula

public String getFormula()

Specified by:

getFormula in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getFormula

public String getFormula(boolean includeImplicitHydrogen)

Specified by:

getFormula in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getExtendedTetrahedrals

public List<gov.nih.ncats.molwitch.ExtendedTetrahedralChirality> getExtendedTetrahedrals()

Specified by:

getExtendedTetrahedrals in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getTetrahedrals

public List<gov.nih.ncats.molwitch.TetrahedralChirality> getTetrahedrals()

Specified by:

getTetrahedrals in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

addBond

public gov.nih.ncats.molwitch.Bond addBond(gov.nih.ncats.molwitch.Bond b)

Specified by:

addBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getSGroups

public List<gov.nih.ncats.molwitch.SGroup> getSGroups()

Specified by:

getSGroups in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

removeSGroup

public void removeSGroup(gov.nih.ncats.molwitch.SGroup sgroup)

Specified by:

removeSGroup in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

addSgroup

public gov.nih.ncats.molwitch.SGroup addSgroup(gov.nih.ncats.molwitch.SGroup.SGroupType type)

Specified by:

addSgroup in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

hasSGroups

public boolean hasSGroups()

Specified by:

hasSGroups in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

addBond

public gov.nih.ncats.molwitch.Bond addBond(gov.nih.ncats.molwitch.Atom atom1,
                                           gov.nih.ncats.molwitch.Atom atom2,
                                           gov.nih.ncats.molwitch.Bond.BondType type)

Specified by:

addBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

setImplicitHydrogens

protected void setImplicitHydrogens()

setImplicitHydrogens

protected int setImplicitHydrogens(org.openscience.cdk.interfaces.IAtom atom)

connectedComponents

public Iterator<CdkChemicalImpl> connectedComponents()

Specified by:

connectedComponents in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

indexOf

public int indexOf(gov.nih.ncats.molwitch.Atom a)

Specified by:

indexOf in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

indexOf

public int indexOf(gov.nih.ncats.molwitch.Bond b)

Specified by:

indexOf in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getGraphInvariant

public gov.nih.ncats.molwitch.GraphInvariant getGraphInvariant()

Specified by:

getGraphInvariant in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getBond

public gov.nih.ncats.molwitch.Bond getBond(int i)

Specified by:

getBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getBondTable

public gov.nih.ncats.molwitch.BondTable getBondTable()

Specified by:

getBondTable in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getDoubleBondStereochemistry

public List<gov.nih.ncats.molwitch.DoubleBondStereochemistry> getDoubleBondStereochemistry()

Specified by:

getDoubleBondStereochemistry in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

getProperty

public String getProperty(String key)

Specified by:

getProperty in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

removeProperty

public void removeProperty(String name)

Specified by:

removeProperty in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

setProperty

public void setProperty(String key,
                        String value)

Specified by:

setProperty in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>

properties

public Iterator<Map.Entry<String,String>> properties()

Specified by:

properties in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>