Package org.jmol.modelsetbio
Class AminoMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.AlphaMonomer
org.jmol.modelsetbio.AminoMonomer
- All Implemented Interfaces:
Structure
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Field Summary
Fields inherited from class org.jmol.modelsetbio.AlphaMonomer
nitrogenHydrogenPoint, proteinStructure
Fields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, 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 TypeMethodDescriptionboolean
getNHPoint
(P3 aminoHydrogenPoint, V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens) getQuaternion
(char qType) void
Methods inherited from class org.jmol.modelsetbio.AlphaMonomer
getAtom, getAtomPoint, getHelixData, getProteinStructureSubType, getProteinStructureType, getQuaternionAlpha, getQuaternionFrameCenterAlpha, getStrucNo, getStructure, isHelix, isProtein, isSheet, isWithinStructure, setProteinStructureType, setStrucNo
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getLeadAtom, getMonomerIndex, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setGroupID, setLeadAtomIndex, toString
Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isNucleicMonomer, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setResno, setShapeVisibility
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Constructor Details
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AminoMonomer
protected AminoMonomer()
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Method Details
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getNitrogenAtom
- Overrides:
getNitrogenAtom
in classGroup
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getCarbonylCarbonAtom
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getCarbonylOxygenAtom
- Overrides:
getCarbonylOxygenAtom
in classGroup
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resetHydrogenPoint
public void resetHydrogenPoint() -
getExplicitNH
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getNHPoint
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getQuaternion
- Overrides:
getQuaternion
in classAlphaMonomer
- Parameters:
qType
-- Returns:
- quaternion
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getStructureId
- Overrides:
getStructureId
in classMonomer
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getProteinStructureTag
- Overrides:
getProteinStructureTag
in classGroup
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getBSSideChain
- Overrides:
getBSSideChain
in classGroup
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