Package org.jmol.modelsetbio
Class AminoMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.AlphaMonomer
org.jmol.modelsetbio.AminoMonomer
- All Implemented Interfaces:
Structure
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate static final float
private static final byte
private static final byte
(package private) static final byte[]
private static final byte
(package private) boolean
private static final byte
private static final byte
private javajs.util.P3
Fields inherited from class org.jmol.modelsetbio.AlphaMonomer
alphaOffsets, nitrogenHydrogenPoint, proteinStructure
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 TypeMethodDescriptionprivate void
(package private) void
findNearestAtomIndex
(int x, int y, Atom[] closest, short madBegin, short madEnd) Selects LeadAtom when this Monomer is clicked iff it is closer to the user.javajs.util.BS
(package private) Atom
boolean
getNHPoint
(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens) (package private) javajs.util.P3
javajs.util.Quat
getQuaternion
(char qType) (package private) javajs.util.P3
getQuaternionFrameCenter
(char qType) (package private) Atom
(package private) boolean
hasOAtom()
(package private) boolean
private static boolean
isBondedCorrectly
(int firstAtomIndex, byte[] offsets, Atom[] atoms) private static boolean
isBondedCorrectlyRange
(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms) (package private) boolean
isConnectedAfter
(Monomer possiblyPreviousMonomer) void
(package private) static Monomer
validateAndAllocate
(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms) Methods inherited from class org.jmol.modelsetbio.AlphaMonomer
getAtom, getAtomPoint, getHelixData, getProteinStructureSubType, getProteinStructureType, getQuaternionAlpha, getQuaternionFrameCenterAlpha, getStrucNo, getStructure, isAlphaMonomer, isHelix, isProtein, isSheet, isWithinStructure, setProteinStructureType, setStrucNo, setStructure, validateAndAllocateA
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, toString, updateOffsetsForAlternativeLocations
Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, 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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CA
private static final byte CA- See Also:
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O
private static final byte O- See Also:
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N
private static final byte N- See Also:
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C
private static final byte C- See Also:
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OT
private static final byte OT- See Also:
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interestingAminoAtomIDs
static final byte[] interestingAminoAtomIDs -
nhChecked
boolean nhChecked -
beta
private static final float beta- See Also:
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ptTemp
private javajs.util.P3 ptTemp
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Constructor Details
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AminoMonomer
protected AminoMonomer()
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Method Details
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validateAndAllocate
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isBondedCorrectlyRange
private static boolean isBondedCorrectlyRange(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms) -
isBondedCorrectly
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isAminoMonomer
boolean isAminoMonomer() -
getNitrogenAtom
- Overrides:
getNitrogenAtom
in classGroup
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getCarbonylCarbonAtom
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getCarbonylOxygenAtom
- Overrides:
getCarbonylOxygenAtom
in classGroup
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getInitiatorAtom
Atom getInitiatorAtom()- Overrides:
getInitiatorAtom
in classMonomer
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getTerminatorAtom
Atom getTerminatorAtom()- Overrides:
getTerminatorAtom
in classMonomer
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hasOAtom
boolean hasOAtom() -
isConnectedAfter
- Overrides:
isConnectedAfter
in classAlphaMonomer
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findNearestAtomIndex
Description copied from class:Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.- Overrides:
findNearestAtomIndex
in classMonomer
- Parameters:
x
-y
-closest
-madBegin
-madEnd
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resetHydrogenPoint
public void resetHydrogenPoint() -
getNitrogenHydrogenPoint
javajs.util.P3 getNitrogenHydrogenPoint() -
getExplicitNH
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getNHPoint
public boolean getNHPoint(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens) -
getQuaternionFrameCenter
javajs.util.P3 getQuaternionFrameCenter(char qType) - Overrides:
getQuaternionFrameCenter
in classAlphaMonomer
- Parameters:
qType
-- Returns:
- center
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getQuaternion
public javajs.util.Quat getQuaternion(char qType) - Overrides:
getQuaternion
in classAlphaMonomer
- Parameters:
qType
-- Returns:
- quaternion
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getStructureId
- Overrides:
getStructureId
in classMonomer
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getProteinStructureTag
- Overrides:
getProteinStructureTag
in classGroup
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getBSSideChain
public javajs.util.BS getBSSideChain()- Overrides:
getBSSideChain
in classGroup
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clear
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