java.lang.Object
- org.jmol.modelset.Group
- - org.jmol.modelsetbio.Monomer
  - - org.jmol.modelsetbio.AlphaMonomer
    - - org.jmol.modelsetbio.AminoMonomer

All Implemented Interfaces:: Structure

public class AminoMonomer
extends AlphaMonomer

Field Summary

Fields
Modifier and Type	Field	Description
`private static float`	`beta`
`private static byte`	`C`
`private static byte`	`CA`
`(package private) static byte[]`	`interestingAminoAtomIDs`
`private static byte`	`N`
`(package private) boolean`	`nhChecked`
`private static byte`	`O`
`private static byte`	`OT`
`private javajs.util.P3`	`ptTemp`

Fields inherited from class org.jmol.modelsetbio.AlphaMonomer
alphaOffsets, nitrogenHydrogenPoint, proteinStructure

Fields inherited from class org.jmol.modelsetbio.Monomer
bioPolymer, monomerIndex, offsets

Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList

Constructor Summary

Constructors
Modifier Constructor Description

protected AminoMonomer()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`clear(BS bs, Atom a, boolean andH)`
`(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.
`BS`	`getBSSideChain()`
`Atom`	`getCarbonylCarbonAtom()`
`Atom`	`getCarbonylOxygenAtom()`
`Atom`	`getExplicitNH()`
`(package private) Atom`	`getInitiatorAtom()`
`boolean`	`getNHPoint(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)`
`Atom`	`getNitrogenAtom()`
`(package private) javajs.util.P3`	`getNitrogenHydrogenPoint()`
`java.lang.String`	`getProteinStructureTag()`
`javajs.util.Quat`	`getQuaternion(char qType)`
`(package private) javajs.util.P3`	`getQuaternionFrameCenter(char qType)`
`java.lang.String`	`getStructureId()`
`(package private) Atom`	`getTerminatorAtom()`
`(package private) boolean`	`hasOAtom()`
`(package private) boolean`	`isAminoMonomer()`
`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`	`resetHydrogenPoint()`
`(package private) static Monomer`	`validateAndAllocate(Chain chain, java.lang.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.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, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setResno, setShapeVisibility, toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

CA
```
private static final byte CA
```
See Also:

Constant Field Values

O
```
private static final byte O
```
See Also:

Constant Field Values

N
```
private static final byte N
```
See Also:

Constant Field Values

C
```
private static final byte C
```
See Also:

Constant Field Values

OT
```
private static final byte OT
```
See Also:

Constant Field Values

interestingAminoAtomIDs

static final byte[] interestingAminoAtomIDs

nhChecked
```
boolean nhChecked
```

beta
```
private static final float beta
```
See Also:

Constant Field Values

ptTemp
```
private javajs.util.P3 ptTemp
```

Constructor Detail
- AminoMonomer
```
protected AminoMonomer()
```

Method Detail

validateAndAllocate

static Monomer validateAndAllocate(Chain chain,
                                   java.lang.String group3,
                                   int seqcode,
                                   int firstAtomIndex,
                                   int lastAtomIndex,
                                   int[] specialAtomIndexes,
                                   Atom[] atoms)

isBondedCorrectlyRange

private static boolean isBondedCorrectlyRange(int offset1,
                                              int offset2,
                                              int firstAtomIndex,
                                              byte[] offsets,
                                              Atom[] atoms)

isBondedCorrectly

private static boolean isBondedCorrectly(int firstAtomIndex,
                                         byte[] offsets,
                                         Atom[] atoms)

isAminoMonomer
```
boolean isAminoMonomer()
```

getNitrogenAtom
```
public Atom getNitrogenAtom()
```
Overrides:

getNitrogenAtom in class Group

getCarbonylCarbonAtom
```
public Atom getCarbonylCarbonAtom()
```

getCarbonylOxygenAtom
```
public Atom getCarbonylOxygenAtom()
```
Overrides:

getCarbonylOxygenAtom in class Group

getInitiatorAtom
```
Atom getInitiatorAtom()
```
Overrides:

getInitiatorAtom in class Monomer

getTerminatorAtom
```
Atom getTerminatorAtom()
```
Overrides:

getTerminatorAtom in class Monomer

hasOAtom
```
boolean hasOAtom()
```

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)

Overrides:: isConnectedAfter in class AlphaMonomer

findNearestAtomIndex

void findNearestAtomIndex(int x,
                          int y,
                          Atom[] closest,
                          short madBegin,
                          short madEnd)

Description copied from class: Monomer

Selects LeadAtom when this Monomer is clicked iff it is closer to the user.

Overrides:: findNearestAtomIndex in class Monomer

resetHydrogenPoint
```
public void resetHydrogenPoint()
```

getNitrogenHydrogenPoint

javajs.util.P3 getNitrogenHydrogenPoint()

getExplicitNH
```
public Atom getExplicitNH()
```

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 class AlphaMonomer

Returns:

center

getQuaternion
```
public javajs.util.Quat getQuaternion(char qType)
```
Overrides:

getQuaternion in class AlphaMonomer

Returns:

quaternion

getStructureId
```
public java.lang.String getStructureId()
```
Overrides:

getStructureId in class Monomer

getProteinStructureTag
```
public java.lang.String getProteinStructureTag()
```
Overrides:

getProteinStructureTag in class Group

getBSSideChain
```
public BS getBSSideChain()
```
Overrides:

getBSSideChain in class Group

clear

private void clear(BS bs,
                   Atom a,
                   boolean andH)

Class AminoMonomer

Field Summary

Fields inherited from class org.jmol.modelsetbio.AlphaMonomer

Fields inherited from class org.jmol.modelsetbio.Monomer

Fields inherited from class org.jmol.modelset.Group

Constructor Summary

Method Summary

Methods inherited from class org.jmol.modelsetbio.AlphaMonomer

Methods inherited from class org.jmol.modelsetbio.Monomer

Methods inherited from class org.jmol.modelset.Group

Methods inherited from class java.lang.Object

Field Detail

CA

O

N

C

OT

interestingAminoAtomIDs

nhChecked

beta

ptTemp

Constructor Detail

AminoMonomer

Method Detail

validateAndAllocate

isBondedCorrectlyRange

isBondedCorrectly

isAminoMonomer

getNitrogenAtom

getCarbonylCarbonAtom

getCarbonylOxygenAtom

getInitiatorAtom

getTerminatorAtom

hasOAtom

isConnectedAfter

findNearestAtomIndex

resetHydrogenPoint

getNitrogenHydrogenPoint

getExplicitNH

getNHPoint

getQuaternionFrameCenter

getQuaternion

getStructureId

getProteinStructureTag

getBSSideChain

clear