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
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Fields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, monomerIndex, offsets
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Fields inherited from class org.jmol.modelset.Group
chain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
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Constructor Summary
Constructors Modifier Constructor Description private
CarbohydrateMonomer()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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.STR
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)
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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, isNucleicMonomer, 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, String group3, int seqcode, int firstIndex, int lastIndex)
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isCarbohydrate
public boolean isCarbohydrate()
- Overrides:
isCarbohydrate
in classGroup
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getProteinStructureType
public STR getProteinStructureType()
- Overrides:
getProteinStructureType
in classMonomer
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isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Specified by:
isConnectedAfter
in classMonomer
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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 classMonomer
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isConnectedPrevious
public boolean isConnectedPrevious()
- Overrides:
isConnectedPrevious
in classMonomer
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