Package org.jmol.modelsetbio
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 org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, offsetsFields inherited from class org.jmol.modelset.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()group ID-based definitionfinal booleangroup ID-based definitionbooleanisPurine()group ID-based definitionbooleangroup ID-based definitionbooleanisRna()group ID-based definitionMethods 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, getStructureId, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setGroupID, setLeadAtomIndex, setStrucNo, toString, updateOffsetsForAlternativeLocationsMethods inherited from class org.jmol.modelset.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
public final boolean isNucleic()Description copied from class:Groupgroup ID-based definition -
isDna
public boolean isDna()Description copied from class:Groupgroup ID-based definition -
isRna
public boolean isRna()Description copied from class:Groupgroup ID-based definition -
isPurine
public boolean isPurine()Description copied from class:Groupgroup ID-based definition -
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
- 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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