Package org.jmol.modelsetbio
Class PhosphorusMonomer
- java.lang.Object
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- org.jmol.modelset.Group
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- org.jmol.modelsetbio.Monomer
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- org.jmol.modelsetbio.PhosphorusMonomer
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- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
NucleicMonomer
public class PhosphorusMonomer extends Monomer
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Field Summary
Fields Modifier and Type Field Description private static floatMAX_ADJACENT_PHOSPHORUS_DISTANCEprotected static bytePprivate static byte[]phosphorusOffsets-
Fields inherited from class org.jmol.modelsetbio.Monomer
bioPolymer, monomerIndex, offsets
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Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
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Constructor Summary
Constructors Modifier Constructor Description protectedPhosphorusMonomer()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.ObjectgetHelixData(int tokType, char qType, int mStep)STRgetProteinStructureType()javajs.util.QuatgetQuaternion(char qType)(package private) javajs.util.P3getQuaternionFrameCenter(char qType)protected javajs.util.QuatgetQuaternionP()StructuregetStructure()protected booleanisCA2(Monomer possiblyPreviousMonomer)(package private) booleanisConnectedAfter(Monomer possiblyPreviousMonomer)booleanisDna()group ID-based definitionbooleanisNucleic()group ID-based definitionbooleanisPurine()group ID-based definitionbooleanisPyrimidine()group ID-based definitionbooleanisRna()group ID-based definition(package private) static MonomervalidateAndAllocateP(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)-
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, setStrucNo, updateOffsetsForAlternativeLocations
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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, isProtein, isPurineByID, isPyrimidineByID, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility, toString
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Field Detail
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P
protected static final byte P
- See Also:
- Constant Field Values
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phosphorusOffsets
private static final byte[] phosphorusOffsets
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MAX_ADJACENT_PHOSPHORUS_DISTANCE
private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
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Method Detail
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isNucleic
public final boolean isNucleic()
Description copied from class:Groupgroup ID-based definition
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validateAndAllocateP
static Monomer validateAndAllocateP(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
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isDna
public boolean isDna()
Description copied from class:Groupgroup ID-based definition
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isRna
public boolean isRna()
Description copied from class:Groupgroup ID-based definition
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isPurine
public boolean isPurine()
Description copied from class:Groupgroup ID-based definition
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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
public Structure getStructure()
- Overrides:
getStructurein classGroup
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getProteinStructureType
public STR getProteinStructureType()
- Overrides:
getProteinStructureTypein classMonomer
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isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Specified by:
isConnectedAfterin classMonomer
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isCA2
protected boolean isCA2(Monomer possiblyPreviousMonomer)
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getQuaternion
public javajs.util.Quat getQuaternion(char qType)
- Overrides:
getQuaternionin classGroup- Returns:
- quaternion
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getQuaternionP
protected javajs.util.Quat getQuaternionP()
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getQuaternionFrameCenter
javajs.util.P3 getQuaternionFrameCenter(char qType)
- Overrides:
getQuaternionFrameCenterin classMonomer- Returns:
- center
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getHelixData
public java.lang.Object getHelixData(int tokType, char qType, int mStep)- Overrides:
getHelixDatain classGroup- Returns:
- helix data of some sort
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