gov.nih.ncats.molwitch.cdk

Class CdkAtom

java.lang.Object

gov.nih.ncats.molwitch.cdk.CdkAtom

All Implemented Interfaces:

gov.nih.ncats.molwitch.Atom

public class CdkAtom
extends Object
implements gov.nih.ncats.molwitch.Atom

Constructor Summary

Constructors

Constructor and Description
CdkAtom(org.openscience.cdk.interfaces.IAtom atom, CdkChemicalImpl parent)

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
Optional<String>	getAlias()
gov.nih.ncats.molwitch.AtomCoordinates	getAtomCoordinates()
int	getAtomicNumber()
int	getAtomIndexInParent()
OptionalInt	getAtomToAtomMap()
List<? extends gov.nih.ncats.molwitch.Bond>	getBonds()
int	getCharge()
gov.nih.ncats.molwitch.Chirality	getChirality()
double	getExactMass()
static org.openscience.cdk.interfaces.IAtom	getIAtomFor(gov.nih.ncats.molwitch.Atom a)
int	getImplicitHCount()
int	getMassNumber()
int	getRadical()
int	getRadicalValue()
OptionalInt	getRGroupIndex()
int	getSmallestRingSize()
String	getSymbol()
OptionalInt	getValence()
boolean	hasAromaticBond()
int	hashCode()
boolean	hasValenceError()
boolean	isInRing()
boolean	isIsotope()
boolean	isQueryAtom()
boolean	isRGroupAtom()
boolean	isValidAtomicSymbol()
void	setAlias(String alias)
void	setAtomCoordinates(gov.nih.ncats.molwitch.AtomCoordinates atomCoordinates)
void	setAtomicNumber(int atomicNumber)
void	setAtomToAtomMap(int value)
void	setCharge(int charge)
void	setChirality(gov.nih.ncats.molwitch.Chirality chirality)
void	setImplicitHCount(Integer implicitH)
void	setMassNumber(int mass)
void	setRadical(int radical)
void	setRGroup(Integer rGroup)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface gov.nih.ncats.molwitch.Atom

bondTo, clearAtomToAtomMap, getBondCount, getBondCount, getNeighbors, hasAtomToAtomMap

Constructor Detail

CdkAtom

public CdkAtom(org.openscience.cdk.interfaces.IAtom atom,
               CdkChemicalImpl parent)

Method Detail

getIAtomFor

public static org.openscience.cdk.interfaces.IAtom getIAtomFor(gov.nih.ncats.molwitch.Atom a)

isValidAtomicSymbol

public boolean isValidAtomicSymbol()

Specified by:

isValidAtomicSymbol in interface gov.nih.ncats.molwitch.Atom

getSmallestRingSize

public int getSmallestRingSize()

Specified by:

getSmallestRingSize in interface gov.nih.ncats.molwitch.Atom

isQueryAtom

public boolean isQueryAtom()

Specified by:

isQueryAtom in interface gov.nih.ncats.molwitch.Atom

getAtomToAtomMap

public OptionalInt getAtomToAtomMap()

Specified by:

getAtomToAtomMap in interface gov.nih.ncats.molwitch.Atom

setAtomToAtomMap

public void setAtomToAtomMap(int value)

Specified by:

setAtomToAtomMap in interface gov.nih.ncats.molwitch.Atom

isInRing

public boolean isInRing()

Specified by:

isInRing in interface gov.nih.ncats.molwitch.Atom

getSymbol

public String getSymbol()

Specified by:

getSymbol in interface gov.nih.ncats.molwitch.Atom

isIsotope

public boolean isIsotope()

Specified by:

isIsotope in interface gov.nih.ncats.molwitch.Atom

getBonds

public List<? extends gov.nih.ncats.molwitch.Bond> getBonds()

Specified by:

getBonds in interface gov.nih.ncats.molwitch.Atom

getAtomicNumber

public int getAtomicNumber()

Specified by:

getAtomicNumber in interface gov.nih.ncats.molwitch.Atom

setAtomicNumber

public void setAtomicNumber(int atomicNumber)

Specified by:

setAtomicNumber in interface gov.nih.ncats.molwitch.Atom

hasAromaticBond

public boolean hasAromaticBond()

Specified by:

hasAromaticBond in interface gov.nih.ncats.molwitch.Atom

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getCharge

public int getCharge()

Specified by:

getCharge in interface gov.nih.ncats.molwitch.Atom

getRadical

public int getRadical()

Specified by:

getRadical in interface gov.nih.ncats.molwitch.Atom

setRadical

public void setRadical(int radical)

Specified by:

setRadical in interface gov.nih.ncats.molwitch.Atom

getAtomCoordinates

public gov.nih.ncats.molwitch.AtomCoordinates getAtomCoordinates()

Specified by:

getAtomCoordinates in interface gov.nih.ncats.molwitch.Atom

setAtomCoordinates

public void setAtomCoordinates(gov.nih.ncats.molwitch.AtomCoordinates atomCoordinates)

Specified by:

setAtomCoordinates in interface gov.nih.ncats.molwitch.Atom

getChirality

public gov.nih.ncats.molwitch.Chirality getChirality()

Specified by:

getChirality in interface gov.nih.ncats.molwitch.Atom

setChirality

public void setChirality(gov.nih.ncats.molwitch.Chirality chirality)

Specified by:

setChirality in interface gov.nih.ncats.molwitch.Atom

getMassNumber

public int getMassNumber()

Specified by:

getMassNumber in interface gov.nih.ncats.molwitch.Atom

getExactMass

public double getExactMass()

Specified by:

getExactMass in interface gov.nih.ncats.molwitch.Atom

setCharge

public void setCharge(int charge)

Specified by:

setCharge in interface gov.nih.ncats.molwitch.Atom

setMassNumber

public void setMassNumber(int mass)

Specified by:

setMassNumber in interface gov.nih.ncats.molwitch.Atom

getImplicitHCount

public int getImplicitHCount()

Specified by:

getImplicitHCount in interface gov.nih.ncats.molwitch.Atom

setImplicitHCount

public void setImplicitHCount(Integer implicitH)

Specified by:

setImplicitHCount in interface gov.nih.ncats.molwitch.Atom

getRadicalValue

public int getRadicalValue()

Specified by:

getRadicalValue in interface gov.nih.ncats.molwitch.Atom

getValence

public OptionalInt getValence()

Specified by:

getValence in interface gov.nih.ncats.molwitch.Atom

hasValenceError

public boolean hasValenceError()

Specified by:

hasValenceError in interface gov.nih.ncats.molwitch.Atom

isRGroupAtom

public boolean isRGroupAtom()

Specified by:

isRGroupAtom in interface gov.nih.ncats.molwitch.Atom

getRGroupIndex

public OptionalInt getRGroupIndex()

Specified by:

getRGroupIndex in interface gov.nih.ncats.molwitch.Atom

setRGroup

public void setRGroup(Integer rGroup)

Specified by:

setRGroup in interface gov.nih.ncats.molwitch.Atom

getAlias

public Optional<String> getAlias()

Specified by:

getAlias in interface gov.nih.ncats.molwitch.Atom

setAlias

public void setAlias(String alias)

Specified by:

setAlias in interface gov.nih.ncats.molwitch.Atom

toString

public String toString()

Overrides:

toString in class Object

getAtomIndexInParent

public int getAtomIndexInParent()

Specified by:

getAtomIndexInParent in interface gov.nih.ncats.molwitch.Atom