Class PhosphorusMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.PhosphorusMonomer
- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
NucleicMonomer
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Field Summary
FieldsFields inherited from class Monomer
backboneBlockVis, bioPolymer, offsetsFields inherited from class Group
chain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList, strutPoint -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetHelixData(int tokType, char qType, int mStep) /////////////////////////////////////////////////////////////getQuaternion(char qType) protected Quatprotected booleanbooleanisDna()/////////////////////////////////////////////////////////////final booleangroup ID-based definitionbooleanisPurine()group ID-based definitionbooleangroup ID-based definitionbooleanisRna()group ID-based definitionMethods inherited from class Monomer
checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getLeadAtom, getMonomerIndex, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setGroupID, setLeadAtomIndex, setStrucNo, toString, updateOffsetsForAlternativeLocationsMethods inherited from class Group
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDnaByID, isNucleicMonomer, isProtein, isPurineByID, isPyrimidineByID, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility, unsetStrutPoint
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Field Details
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P
protected static final byte P- See Also:
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Constructor Details
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PhosphorusMonomer
protected PhosphorusMonomer()
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Method Details
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isNucleic
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isDna
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isRna
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isPurine
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isPyrimidine
public boolean isPyrimidine()Description copied from class:Groupgroup ID-based definition- Overrides:
isPyrimidinein classGroup- Returns:
- boolean
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getStructure
- Overrides:
getStructurein classGroup
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getProteinStructureType
Description copied from class:Monomer/////////////////////////////////////////////////////////////- Overrides:
getProteinStructureTypein classMonomer
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isCA2
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getQuaternion
- Overrides:
getQuaternionin classGroup- Parameters:
qType-- Returns:
- quaternion
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getQuaternionP
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getHelixData
- Overrides:
getHelixDatain classGroup- Parameters:
tokType-qType-mStep-- Returns:
- helix data of some sort
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