Package org.jmol.modelsetbio
Class CarbohydrateMonomer
- java.lang.Object
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- org.jmol.modelset.Group
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- org.jmol.modelsetbio.Monomer
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- org.jmol.modelsetbio.CarbohydrateMonomer
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Field Summary
Fields Modifier and Type Field Description private static byte[]alphaOffsets-
Fields inherited from class org.jmol.modelsetbio.Monomer
bioPolymer, monomerIndex, offsets
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Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
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Constructor Summary
Constructors Modifier Constructor Description privateCarbohydrateMonomer()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) voidfindNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)Selects LeadAtom when this Monomer is clicked iff it is closer to the user.STRgetProteinStructureType()booleanisCarbohydrate()(package private) booleanisConnectedAfter(Monomer possiblyPreviousMonomer)booleanisConnectedPrevious()(package private) static MonomervalidateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex)-
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getQuaternionFrameCenter, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, isCrossLinked, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, setStrucNo, updateOffsetsForAlternativeLocations
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Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getHelixData, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, getStructure, haveSequenceNumber, isAdded, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isProtein, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility, toString
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Method Detail
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validateAndAllocate
static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex)
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isCarbohydrate
public boolean isCarbohydrate()
- Overrides:
isCarbohydratein classGroup
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getProteinStructureType
public STR getProteinStructureType()
- Overrides:
getProteinStructureTypein classMonomer
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isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Specified by:
isConnectedAfterin classMonomer
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findNearestAtomIndex
void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)Description copied from class:MonomerSelects LeadAtom when this Monomer is clicked iff it is closer to the user.- Overrides:
findNearestAtomIndexin classMonomer
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isConnectedPrevious
public boolean isConnectedPrevious()
- Overrides:
isConnectedPreviousin classMonomer
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