org.jmol.modelsetbio

Class AminoMonomer

java.lang.Object

org.jmol.modelset.Group

org.jmol.modelsetbio.Monomer

org.jmol.modelsetbio.AlphaMonomer

org.jmol.modelsetbio.AminoMonomer

public class AminoMonomer
extends AlphaMonomer

Field Summary

Fields

Modifier and Type	Field and 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 javax.vecmath.Point3f	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, groupID, groupIndex, isProtein, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags

Constructor Summary

Constructors

Modifier	Constructor and Description
private	AminoMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)

Method Summary

Methods

Modifier and Type	Method and Description
(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.
(package private) Atom	getCarbonylCarbonAtom()
Atom	getCarbonylOxygenAtom()
(package private) javax.vecmath.Point3f	getExplicitNH()
(package private) Atom	getInitiatorAtom()
boolean	getNHPoint(javax.vecmath.Point3f aminoHydrogenPoint, javax.vecmath.Vector3f vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)
Atom	getNitrogenAtom()
(package private) javax.vecmath.Point3f	getNitrogenHydrogenPoint()
java.lang.String	getProteinStructureTag()
Quaternion	getQuaternion(char qType)
(package private) javax.vecmath.Point3f	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	isBondedCorrectly(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)
(package private) boolean	isConnectedAfter(Monomer possiblyPreviousMonomer)
boolean	isWithinStructure(EnumStructure type)
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, getProteinStructure, getProteinStructureSubType, getProteinStructureType, getStrucNo, getStructure, isAlphaMonomer, isHelix, isProtein, isSheet, setProteinStructureId, setProteinStructureType, setStructure, validateAndAllocate

Methods inherited from class org.jmol.modelsetbio.Monomer

calcBioParameters, checkOptional, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLeadAtomIndexes, getHelixData2, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocations

Methods inherited from class org.jmol.modelset.Group

addAtoms, fixIndices, getChainID, getGroup1, getGroup3, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupInfo, getGroupParameter, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getMinZ, getModel, getModelIndex, getModelSet, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, haveSequenceNumber, isAdded, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, 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

ptTemp

private final javax.vecmath.Point3f ptTemp

beta

private static final float beta

See Also:

Constant Field Values

Constructor Detail

AminoMonomer

private AminoMonomer(Chain chain,
            java.lang.String group3,
            int seqcode,
            int firstAtomIndex,
            int lastAtomIndex,
            byte[] offsets)

Method Detail

validateAndAllocate

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

isBondedCorrectly

private static boolean isBondedCorrectly(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

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

javax.vecmath.Point3f getNitrogenHydrogenPoint()

getExplicitNH

javax.vecmath.Point3f getExplicitNH()

getNHPoint

public boolean getNHPoint(javax.vecmath.Point3f aminoHydrogenPoint,
                 javax.vecmath.Vector3f vNH,
                 boolean jmolHPoint,
                 boolean dsspIgnoreHydrogens)

getQuaternionFrameCenter

javax.vecmath.Point3f getQuaternionFrameCenter(char qType)

Overrides:

getQuaternionFrameCenter in class AlphaMonomer

Returns:

center

getQuaternion

public Quaternion getQuaternion(char qType)

Overrides:

getQuaternion in class AlphaMonomer

Returns:

quaternion

isWithinStructure

public boolean isWithinStructure(EnumStructure type)

Overrides:

isWithinStructure in class Group

Returns:

T/F

getStructureId

public java.lang.String getStructureId()

Overrides:

getStructureId in class Monomer

getProteinStructureTag

public java.lang.String getProteinStructureTag()

Overrides:

getProteinStructureTag in class Group