org.jmol.modelsetbio

Class CarbohydrateMonomer

java.lang.Object

org.jmol.modelset.Group

org.jmol.modelsetbio.Monomer

org.jmol.modelsetbio.CarbohydrateMonomer

public class CarbohydrateMonomer
extends Monomer

Field Summary

Fields

Modifier and Type	Field and Description
(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, groupIndex, isProtein, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags

Constructor Summary

Constructors

Modifier	Constructor and Description
private	CarbohydrateMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)

Method Summary

Methods

Modifier and Type	Method and Description
(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.
EnumStructure	getProteinStructureType()
boolean	isCarbohydrate()
(package private) boolean	isConnectedAfter(Monomer possiblyPreviousMonomer)
boolean	isConnectedPrevious()
(package private) static Monomer	validateAndAllocate(Chain chain, java.lang.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, isSheet, scanForOffsets, setBioPolymer, setProteinStructureId, setStructure, updateOffsetsForAlternativeLocations

Methods inherited from class org.jmol.modelset.Group

addAtoms, fixIndices, getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupInfo, getGroupParameter, getHelixData, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getMinZ, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStrucNo, getStructure, haveSequenceNumber, isAdded, isAtomHidden, isCursorOnTopOf, isDna, isNucleic, isProtein, 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,
                   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)

isCarbohydrate

public boolean isCarbohydrate()

Overrides:

isCarbohydrate in class Group

getProteinStructureType

public EnumStructure 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