public class CdkAtom extends Object implements gov.nih.ncats.molwitch.Atom
| Constructor and Description |
|---|
CdkAtom(org.openscience.cdk.interfaces.IAtom atom,
CdkChemicalImpl parent) |
| 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() |
public CdkAtom(org.openscience.cdk.interfaces.IAtom atom,
CdkChemicalImpl parent)
public static org.openscience.cdk.interfaces.IAtom getIAtomFor(gov.nih.ncats.molwitch.Atom a)
public boolean isValidAtomicSymbol()
isValidAtomicSymbol in interface gov.nih.ncats.molwitch.Atompublic int getSmallestRingSize()
getSmallestRingSize in interface gov.nih.ncats.molwitch.Atompublic boolean isQueryAtom()
isQueryAtom in interface gov.nih.ncats.molwitch.Atompublic OptionalInt getAtomToAtomMap()
getAtomToAtomMap in interface gov.nih.ncats.molwitch.Atompublic void setAtomToAtomMap(int value)
setAtomToAtomMap in interface gov.nih.ncats.molwitch.Atompublic boolean isInRing()
isInRing in interface gov.nih.ncats.molwitch.Atompublic String getSymbol()
getSymbol in interface gov.nih.ncats.molwitch.Atompublic boolean isIsotope()
isIsotope in interface gov.nih.ncats.molwitch.Atompublic List<? extends gov.nih.ncats.molwitch.Bond> getBonds()
getBonds in interface gov.nih.ncats.molwitch.Atompublic int getAtomicNumber()
getAtomicNumber in interface gov.nih.ncats.molwitch.Atompublic void setAtomicNumber(int atomicNumber)
setAtomicNumber in interface gov.nih.ncats.molwitch.Atompublic boolean hasAromaticBond()
hasAromaticBond in interface gov.nih.ncats.molwitch.Atompublic int getCharge()
getCharge in interface gov.nih.ncats.molwitch.Atompublic int getRadical()
getRadical in interface gov.nih.ncats.molwitch.Atompublic void setRadical(int radical)
setRadical in interface gov.nih.ncats.molwitch.Atompublic gov.nih.ncats.molwitch.AtomCoordinates getAtomCoordinates()
getAtomCoordinates in interface gov.nih.ncats.molwitch.Atompublic void setAtomCoordinates(gov.nih.ncats.molwitch.AtomCoordinates atomCoordinates)
setAtomCoordinates in interface gov.nih.ncats.molwitch.Atompublic gov.nih.ncats.molwitch.Chirality getChirality()
getChirality in interface gov.nih.ncats.molwitch.Atompublic void setChirality(gov.nih.ncats.molwitch.Chirality chirality)
setChirality in interface gov.nih.ncats.molwitch.Atompublic int getMassNumber()
getMassNumber in interface gov.nih.ncats.molwitch.Atompublic double getExactMass()
getExactMass in interface gov.nih.ncats.molwitch.Atompublic void setCharge(int charge)
setCharge in interface gov.nih.ncats.molwitch.Atompublic void setMassNumber(int mass)
setMassNumber in interface gov.nih.ncats.molwitch.Atompublic int getImplicitHCount()
getImplicitHCount in interface gov.nih.ncats.molwitch.Atompublic void setImplicitHCount(Integer implicitH)
setImplicitHCount in interface gov.nih.ncats.molwitch.Atompublic int getRadicalValue()
getRadicalValue in interface gov.nih.ncats.molwitch.Atompublic OptionalInt getValence()
getValence in interface gov.nih.ncats.molwitch.Atompublic boolean hasValenceError()
hasValenceError in interface gov.nih.ncats.molwitch.Atompublic boolean isRGroupAtom()
isRGroupAtom in interface gov.nih.ncats.molwitch.Atompublic OptionalInt getRGroupIndex()
getRGroupIndex in interface gov.nih.ncats.molwitch.Atompublic void setRGroup(Integer rGroup)
setRGroup in interface gov.nih.ncats.molwitch.Atompublic Optional<String> getAlias()
getAlias in interface gov.nih.ncats.molwitch.Atompublic void setAlias(String alias)
setAlias in interface gov.nih.ncats.molwitch.Atompublic int getAtomIndexInParent()
getAtomIndexInParent in interface gov.nih.ncats.molwitch.AtomCopyright © 2019 NIH/NCATS. All rights reserved.