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 float
MAX_ADJACENT_PHOSPHORUS_DISTANCE
protected static byte
P
private static byte[]
phosphorusOffsets
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Fields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, monomerIndex, offsets
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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 Modifier Constructor Description protected
PhosphorusMonomer()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description Object
getHelixData(int tokType, char qType, int mStep)
STR
getProteinStructureType()
javajs.util.Quat
getQuaternion(char qType)
(package private) javajs.util.P3
getQuaternionFrameCenter(char qType)
protected javajs.util.Quat
getQuaternionP()
Structure
getStructure()
protected boolean
isCA2(Monomer possiblyPreviousMonomer)
(package private) boolean
isConnectedAfter(Monomer possiblyPreviousMonomer)
boolean
isDna()
group ID-based definitionboolean
isNucleic()
group ID-based definitionboolean
isPurine()
group ID-based definitionboolean
isPyrimidine()
group ID-based definitionboolean
isRna()
group ID-based definition(package private) static Monomer
validateAndAllocateP(Chain chain, String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
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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, isNucleicMonomer, 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:Group
group ID-based definition
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validateAndAllocateP
static Monomer validateAndAllocateP(Chain chain, String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
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isDna
public boolean isDna()
Description copied from class:Group
group ID-based definition
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isRna
public boolean isRna()
Description copied from class:Group
group ID-based definition
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isPurine
public boolean isPurine()
Description copied from class:Group
group ID-based definition
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isPyrimidine
public boolean isPyrimidine()
Description copied from class:Group
group ID-based definition- Overrides:
isPyrimidine
in classGroup
- Returns:
- boolean
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getStructure
public Structure getStructure()
- Overrides:
getStructure
in classGroup
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getProteinStructureType
public STR getProteinStructureType()
- Overrides:
getProteinStructureType
in classMonomer
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isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Specified by:
isConnectedAfter
in classMonomer
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isCA2
protected boolean isCA2(Monomer possiblyPreviousMonomer)
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getQuaternion
public javajs.util.Quat getQuaternion(char qType)
- Overrides:
getQuaternion
in 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:
getQuaternionFrameCenter
in classMonomer
- Returns:
- center
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getHelixData
public Object getHelixData(int tokType, char qType, int mStep)
- Overrides:
getHelixData
in classGroup
- Returns:
- helix data of some sort
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