Package org.jmol.modelsetbio
Class CarbohydrateMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.CarbohydrateMonomer
- All Implemented Interfaces:
Structure
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Field Summary
FieldsFields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, monomerIndex, offsets
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 -
Method Summary
Modifier and TypeMethodDescription(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.boolean
(package private) boolean
isConnectedAfter
(Monomer possiblyPreviousMonomer) boolean
(package private) static Monomer
validateAndAllocate
(Chain chain, 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, toString, updateOffsetsForAlternativeLocations
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
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Field Details
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alphaOffsets
private static final byte[] alphaOffsets
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Constructor Details
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CarbohydrateMonomer
private CarbohydrateMonomer()
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Method Details
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validateAndAllocate
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isCarbohydrate
public boolean isCarbohydrate()- Overrides:
isCarbohydrate
in classGroup
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getProteinStructureType
- Overrides:
getProteinStructureType
in classMonomer
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isConnectedAfter
- Specified by:
isConnectedAfter
in classMonomer
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findNearestAtomIndex
Description copied from class:Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.- Overrides:
findNearestAtomIndex
in classMonomer
- Parameters:
x
-y
-closest
-madBegin
-madEnd
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isConnectedPrevious
public boolean isConnectedPrevious()- Overrides:
isConnectedPrevious
in classMonomer
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