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, 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 TypeMethodDescriptiongetHelixData
(int tokType, char qType, int mStep) getQuaternion
(char qType) protected Quat
protected boolean
boolean
isDna()
group ID-based definitionfinal boolean
group ID-based definitionboolean
isPurine()
group ID-based definitionboolean
group ID-based definitionboolean
isRna()
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
Methods 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
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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:Group
group ID-based definition -
isDna
public boolean isDna()Description copied from class:Group
group ID-based definition -
isRna
public boolean isRna()Description copied from class:Group
group ID-based definition -
isPurine
public boolean isPurine()Description copied from class:Group
group ID-based definition -
isPyrimidine
public boolean isPyrimidine()Description copied from class:Group
group ID-based definition- Overrides:
isPyrimidine
in classGroup
- Returns:
- boolean
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getStructure
- Overrides:
getStructure
in classGroup
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getProteinStructureType
- Overrides:
getProteinStructureType
in classMonomer
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isCA2
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getQuaternion
- Overrides:
getQuaternion
in classGroup
- Returns:
- quaternion
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getQuaternionP
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getHelixData
- Overrides:
getHelixData
in classGroup
- Returns:
- helix data of some sort
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