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
FieldsModifier and TypeFieldDescriptionprivate static float
protected static final byte
private static final byte[]
Fields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, monomerIndex, 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) javajs.util.Quat
getQuaternion
(char qType) (package private) javajs.util.P3
getQuaternionFrameCenter
(char qType) protected javajs.util.Quat
protected boolean
(package private) boolean
isConnectedAfter
(Monomer possiblyPreviousMonomer) boolean
isDna()
group ID-based definitionfinal boolean
group ID-based definitionboolean
isPurine()
group ID-based definitionboolean
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) 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, toString, updateOffsetsForAlternativeLocations
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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phosphorusOffsets
private static final byte[] phosphorusOffsets -
MAX_ADJACENT_PHOSPHORUS_DISTANCE
private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
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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 -
validateAndAllocateP
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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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isConnectedAfter
- Specified by:
isConnectedAfter
in classMonomer
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isCA2
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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() -
getQuaternionFrameCenter
javajs.util.P3 getQuaternionFrameCenter(char qType) - Overrides:
getQuaternionFrameCenter
in classMonomer
- Returns:
- center
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getHelixData
- Overrides:
getHelixData
in classGroup
- Returns:
- helix data of some sort
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