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
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 TypeMethodDescriptionfinal Atom
getAtom
(byte specialAtomID) final P3
getAtomPoint
(byte specialAtomID) getHelixData
(int tokType, char qType, int mStep) getQuaternion
(char qType) protected Quat
getQuaternionAlpha
(char qType) protected P3
getQuaternionFrameCenterAlpha
(char qType) int
boolean
isHelix()
boolean
group ID-based definitionboolean
isSheet()
boolean
isWithinStructure
(STR type) int
setProteinStructureType
(STR type, int monomerIndexCurrent) void
setStrucNo
(int n) Methods 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, isLeadAtom, scanForOffsets, set2, setGroupID, setLeadAtomIndex, toString
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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proteinStructure
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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 -
getStructure
- Overrides:
getStructure
in classGroup
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setStrucNo
public void setStrucNo(int n) - Overrides:
setStrucNo
in classMonomer
- Parameters:
n
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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
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isWithinStructure
- Overrides:
isWithinStructure
in classGroup
- Parameters:
type
-- Returns:
- T/F
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getQuaternionFrameCenterAlpha
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getHelixData
- Overrides:
getHelixData
in classGroup
- Parameters:
tokType
-qType
-mStep
-- Returns:
- helix data of some sort
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getQuaternion
- Overrides:
getQuaternion
in classGroup
- Parameters:
qType
-- Returns:
- quaternion
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getQuaternionAlpha
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