org.jmol.modelsetbio

Class ProteinStructure

public abstract class ProteinStructure extends Object

Field Summary
AlphaPolymerapolymer
Point3faxisA
Point3faxisB
Vector3faxisUnitVector
static intglobalSerialID
intmonomerCount
intmonomerIndexFirst
intmonomerIndexLast
Point3f[]segments
bytetype
intuniqueID
Vector3fvectorProjection
Constructor Summary
ProteinStructure(AlphaPolymer apolymer, byte type, int monomerIndex, int monomerCount)
Method Summary
voidaddMonomer(int index)
Note that this method does not check to see that there are no overlapping protein structures.
voidcalcAxis()
voidcalcSegments()
Point3fgetAxisEndPoint()
Point3fgetAxisStartPoint()
intgetIndex(Monomer monomer)
voidgetInfo(Hashtable info)
intgetMonomerCount()
intgetMonomerIndex()
Point3f[]getSegments()
Point3fgetStructureMidPoint(int index)
booleanlowerNeighborIsHelixOrSheet()
intremoveMonomer(int monomerIndex)
should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.
voidresetAxes()
booleanupperNeighborIsHelixOrSheet()

Field Detail

apolymer

AlphaPolymer apolymer

axisA

Point3f axisA

axisB

Point3f axisB

axisUnitVector

Vector3f axisUnitVector

globalSerialID

static int globalSerialID

monomerCount

int monomerCount

monomerIndexFirst

int monomerIndexFirst

monomerIndexLast

int monomerIndexLast

segments

Point3f[] segments

type

byte type

uniqueID

int uniqueID

vectorProjection

final Vector3f vectorProjection

Constructor Detail

ProteinStructure

ProteinStructure(AlphaPolymer apolymer, byte type, int monomerIndex, int monomerCount)

Method Detail

addMonomer

void addMonomer(int index)
Note that this method does not check to see that there are no overlapping protein structures.

Parameters: index

calcAxis

public void calcAxis()

calcSegments

void calcSegments()

getAxisEndPoint

public Point3f getAxisEndPoint()

getAxisStartPoint

public Point3f getAxisStartPoint()

getIndex

public int getIndex(Monomer monomer)

getInfo

public void getInfo(Hashtable info)

getMonomerCount

public int getMonomerCount()

getMonomerIndex

public int getMonomerIndex()

getSegments

public Point3f[] getSegments()

getStructureMidPoint

Point3f getStructureMidPoint(int index)

lowerNeighborIsHelixOrSheet

boolean lowerNeighborIsHelixOrSheet()

removeMonomer

int removeMonomer(int monomerIndex)
should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.

Parameters: monomerIndex

Returns: the number of monomers AFTER this one that have been abandoned

resetAxes

void resetAxes()

upperNeighborIsHelixOrSheet

boolean upperNeighborIsHelixOrSheet()