Package org.jmol.modelsetbio
Class AlphaMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.AlphaMonomer
- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
AminoMonomer
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Field Summary
FieldsModifier and TypeFieldDescription(package private) static final byte[]
protected javajs.util.P3
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 TypeMethodDescriptionfinal Atom
getAtom
(byte specialAtomID) final javajs.util.P3
getAtomPoint
(byte specialAtomID) getHelixData
(int tokType, char qType, int mStep) javajs.util.Quat
getQuaternion
(char qType) protected javajs.util.Quat
getQuaternionAlpha
(char qType) (package private) javajs.util.P3
getQuaternionFrameCenter
(char qType) protected javajs.util.P3
getQuaternionFrameCenterAlpha
(char qType) int
(package private) boolean
(package private) boolean
isConnectedAfter
(Monomer possiblyPreviousMonomer) boolean
isHelix()
boolean
group ID-based definitionboolean
isSheet()
boolean
isWithinStructure
(STR type) int
setProteinStructureType
(STR type, int monomerIndexCurrent) void
setStrucNo
(int n) (package private) void
(package private) static Monomer
validateAndAllocateA
(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, isLeadAtom, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, toString, updateOffsetsForAlternativeLocations
Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureTag, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isNucleicMonomer, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setResno, setShapeVisibility
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Field Details
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alphaOffsets
static final byte[] alphaOffsets -
proteinStructure
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nitrogenHydrogenPoint
protected javajs.util.P3 nitrogenHydrogenPoint
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Constructor Details
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AlphaMonomer
protected AlphaMonomer()
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Method Details
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isProtein
public boolean isProtein()Description copied from class:Group
group ID-based definition -
validateAndAllocateA
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isAlphaMonomer
boolean isAlphaMonomer() -
getStructure
- Overrides:
getStructure
in classGroup
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setStructure
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setStrucNo
public void setStrucNo(int n) - Overrides:
setStrucNo
in classMonomer
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getProteinStructureType
- Overrides:
getProteinStructureType
in classMonomer
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getProteinStructureSubType
- Overrides:
getProteinStructureSubType
in classGroup
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getStrucNo
public int getStrucNo()- Overrides:
getStrucNo
in classGroup
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isHelix
public boolean isHelix() -
isSheet
public boolean isSheet() -
setProteinStructureType
- Overrides:
setProteinStructureType
in classGroup
- Parameters:
type
-monomerIndexCurrent
- a pointer to the current ProteinStructure- Returns:
- a pointer to this ProteinStructure
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getAtom
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getAtomPoint
public final javajs.util.P3 getAtomPoint(byte specialAtomID) -
isConnectedAfter
- Specified by:
isConnectedAfter
in classMonomer
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getQuaternionFrameCenter
javajs.util.P3 getQuaternionFrameCenter(char qType) - Overrides:
getQuaternionFrameCenter
in classMonomer
- Returns:
- center
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isWithinStructure
- Overrides:
isWithinStructure
in classGroup
- Returns:
- T/F
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getQuaternionFrameCenterAlpha
protected javajs.util.P3 getQuaternionFrameCenterAlpha(char qType) -
getHelixData
- Overrides:
getHelixData
in classGroup
- Returns:
- helix data of some sort
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getQuaternion
public javajs.util.Quat getQuaternion(char qType) - Overrides:
getQuaternion
in classGroup
- Returns:
- quaternion
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getQuaternionAlpha
protected javajs.util.Quat getQuaternionAlpha(char qType)
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