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, omega, phi, psi, shapeVisibilityFlags, straightness
 
Constructor Summary
private CarbohydrateMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
           
 
Method Summary
 boolean isCarbohydrate()
           
(package private)  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
(package private) static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes, Atom[] atoms)
           
 
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndex, getBioPolymerLength, getInitiatorAtom, getLeadAtom, getLeadAtomIndex, getLeadAtomPoint, getMonomerSequenceAtoms, getMyInfo, getPointAtomPoint, getProteinStructure, getProteinStructureType, getQuaternionFrameCenter, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureTypeName, getTerminatorAtom, getWingAtom, getWingAtomPoint, isDna, isHelix, isNucleic, isProtein, isRna, isSheet, resetHydrogenPoint, scanForOffsets, setBioPolymer, setStructure, updateOffsetsForAlternativeLocations
 
Methods inherited from class org.jmol.modelset.Group
getChainID, getFirstAtomIndex, getGroup1, getGroup3, getGroupID, getGroupID, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLastAtomIndex, getLeadAtom, getMinZ, getModel, getModelIndex, getOmega, getPhi, getProteinStructureID, getPsi, getQuaternion, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStraightness, getStructure, haveSequenceNumber, isAtomHidden, isCursorOnTopOf, isPurine, isPyrimidine, isSelected, lookupGroupID, scaleToScreen, selectAtoms, setMinZ, setModelSet, setOmega, setPhi, setProteinStructureType, setPsi, setShapeVisibility, setStraightness, 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,
                            java.lang.String group3,
                            int seqcode,
                            int firstAtomIndex,
                            int lastAtomIndex,
                            byte[] offsets)
Method Detail

validateAndAllocate

static Monomer validateAndAllocate(Chain chain,
                                   java.lang.String group3,
                                   int seqcode,
                                   int firstIndex,
                                   int lastIndex,
                                   int[] specialAtomIndexes,
                                   Atom[] atoms)

isCarbohydrate

public boolean isCarbohydrate()
Overrides:
isCarbohydrate in class Group

isConnectedAfter

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