org.jmol.util
Interface JmolNode

All Known Implementing Classes:
Atom, SmilesAtom

public interface JmolNode


Method Summary
 short getAtomicAndIsotopeNumber()
           
 java.lang.String getAtomName()
           
 int getAtomSite()
           
 java.lang.String getBioStructureTypeName()
           
 int getBondedAtomIndex(int j)
           
 char getChainID()
           
 int getCovalentBondCount()
           
 int getCovalentHydrogenCount()
           
 boolean getCrossLinkLeadAtomIndexes(java.util.List<java.lang.Integer> vReturn)
           
 JmolEdge[] getEdges()
           
 short getElementNumber()
           
 int getFormalCharge()
           
 java.lang.String getGroup1(char c0)
           
 java.lang.String getGroup3(boolean allowNull)
           
 void getGroupBits(java.util.BitSet bs)
           
 int getImplicitHydrogenCount()
           
 int getIndex()
           
 short getIsotopeNumber()
           
 int getModelIndex()
           
 int getOffsetResidueAtom(java.lang.String name, int offset)
           
 int getResno()
           
 int getValence()
           
 boolean isCrossLinked(JmolNode node)
           
 boolean isDeleted()
           
 boolean isDna()
           
 boolean isLeadAtom()
           
 boolean isNucleic()
           
 boolean isProtein()
           
 boolean isPurine()
           
 boolean isPyrimidine()
           
 boolean isRna()
           
 void set(float x, float y, float z)
           
 

Method Detail

set

void set(float x,
         float y,
         float z)

getAtomSite

int getAtomSite()

getBondedAtomIndex

int getBondedAtomIndex(int j)

getCovalentHydrogenCount

int getCovalentHydrogenCount()

getEdges

JmolEdge[] getEdges()

getElementNumber

short getElementNumber()

getFormalCharge

int getFormalCharge()

getIndex

int getIndex()

getIsotopeNumber

short getIsotopeNumber()

getModelIndex

int getModelIndex()

getValence

int getValence()

getCovalentBondCount

int getCovalentBondCount()

getImplicitHydrogenCount

int getImplicitHydrogenCount()

getAtomicAndIsotopeNumber

short getAtomicAndIsotopeNumber()

getAtomName

java.lang.String getAtomName()

getBioStructureTypeName

java.lang.String getBioStructureTypeName()

getGroup1

java.lang.String getGroup1(char c0)

getGroup3

java.lang.String getGroup3(boolean allowNull)

getResno

int getResno()

getChainID

char getChainID()

getOffsetResidueAtom

int getOffsetResidueAtom(java.lang.String name,
                         int offset)

getCrossLinkLeadAtomIndexes

boolean getCrossLinkLeadAtomIndexes(java.util.List<java.lang.Integer> vReturn)

getGroupBits

void getGroupBits(java.util.BitSet bs)

isLeadAtom

boolean isLeadAtom()

isCrossLinked

boolean isCrossLinked(JmolNode node)

isProtein

boolean isProtein()

isNucleic

boolean isNucleic()

isDna

boolean isDna()

isRna

boolean isRna()

isPurine

boolean isPurine()

isPyrimidine

boolean isPyrimidine()

isDeleted

boolean isDeleted()