org.jmol.modelsetbio
Class CarbohydrateMonomer

java.lang.Object
  extended by org.jmol.modelset.Group
      extended by org.jmol.modelsetbio.Monomer
          extended by org.jmol.modelsetbio.CarbohydrateMonomer

public class CarbohydrateMonomer
extends Monomer


Field Summary
(package private) static byte[] alphaOffsets
           
 
Fields inherited from class org.jmol.modelsetbio.Monomer
bioPolymer, monomerIndex, offsets
 
Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, groupID, isAmino, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags
 
Constructor Summary
private CarbohydrateMonomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
           
 
Method Summary
(package private)  void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
          Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
 byte getProteinStructureType()
           
 boolean isCarbohydrate()
           
(package private)  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
 boolean isConnectedPrevious()
           
(package private) static Monomer validateAndAllocate(Chain chain, String group3, int seqcode, int firstIndex, int lastIndex)
           
 
Methods inherited from class org.jmol.modelsetbio.Monomer
calcBioParameters, checkOptional, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLeadAtomIndexes, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getProteinStructure, getQuaternionFrameCenter, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, haveParameters, isCrossLinked, isHelix, isLeadAtom, isProtein, isSheet, scanForOffsets, setBioPolymer, setProteinStructureId, setStructure, updateOffsetsForAlternativeLocations
 
Methods inherited from class org.jmol.modelset.Group
getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupParameter, getHelixData, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStrucNo, getStructure, haveSequenceNumber, isAtomHidden, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, setProteinStructureType, setShapeVisibility, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

alphaOffsets

static final byte[] alphaOffsets
Constructor Detail

CarbohydrateMonomer

private CarbohydrateMonomer(Chain chain,
                            String group3,
                            int seqcode,
                            int firstAtomIndex,
                            int lastAtomIndex,
                            byte[] offsets)
Method Detail

validateAndAllocate

static Monomer validateAndAllocate(Chain chain,
                                   String group3,
                                   int seqcode,
                                   int firstIndex,
                                   int lastIndex)

isCarbohydrate

public boolean isCarbohydrate()
Overrides:
isCarbohydrate in class Group

getProteinStructureType

public byte getProteinStructureType()
Overrides:
getProteinStructureType in class Monomer

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
Specified by:
isConnectedAfter in class Monomer

findNearestAtomIndex

void findNearestAtomIndex(int x,
                          int y,
                          Atom[] closest,
                          short madBegin,
                          short madEnd)
Description copied from class: Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.

Overrides:
findNearestAtomIndex in class Monomer

isConnectedPrevious

public boolean isConnectedPrevious()
Overrides:
isConnectedPrevious in class Monomer