org.jmol.modelsetbio
Class ProteinStructure

java.lang.Object
  extended by org.jmol.modelsetbio.ProteinStructure
Direct Known Subclasses:
Helix, Sheet, Turn

public abstract class ProteinStructure
extends java.lang.Object


Field Summary
(package private)  AlphaPolymer apolymer
           
(package private)  javax.vecmath.Point3f axisA
           
(package private)  javax.vecmath.Point3f axisB
           
(package private)  javax.vecmath.Vector3f axisUnitVector
           
(package private) static int globalSerialID
           
(package private)  int monomerCount
           
(package private)  int monomerIndexFirst
           
(package private)  int monomerIndexLast
           
(package private)  javax.vecmath.Point3f[] segments
           
(package private)  byte type
           
(package private)  int uniqueID
           
(package private)  javax.vecmath.Vector3f vectorProjection
           
 
Constructor Summary
ProteinStructure(AlphaPolymer apolymer, byte type, int monomerIndex, int monomerCount)
           
 
Method Summary
(package private)  void addMonomer(int index)
          Note that this method does not check to see that there are no overlapping protein structures.
 void calcAxis()
           
(package private)  void calcSegments()
           
 javax.vecmath.Point3f getAxisEndPoint()
           
 javax.vecmath.Point3f getAxisStartPoint()
           
 int getIndex(Monomer monomer)
           
 void getInfo(java.util.Hashtable info)
           
 int getMonomerCount()
           
 int getMonomerIndex()
           
 javax.vecmath.Point3f[] getSegments()
           
(package private)  javax.vecmath.Point3f getStructureMidPoint(int index)
           
(package private)  boolean lowerNeighborIsHelixOrSheet()
           
(package private)  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.
(package private)  void resetAxes()
           
(package private)  boolean upperNeighborIsHelixOrSheet()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

globalSerialID

static int globalSerialID

apolymer

AlphaPolymer apolymer

type

byte type

monomerIndexFirst

int monomerIndexFirst

monomerIndexLast

int monomerIndexLast

monomerCount

int monomerCount

axisA

javax.vecmath.Point3f axisA

axisB

javax.vecmath.Point3f axisB

axisUnitVector

javax.vecmath.Vector3f axisUnitVector

vectorProjection

final javax.vecmath.Vector3f vectorProjection

segments

javax.vecmath.Point3f[] segments

uniqueID

int uniqueID
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 -

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

calcAxis

public void calcAxis()

calcSegments

void calcSegments()

lowerNeighborIsHelixOrSheet

boolean lowerNeighborIsHelixOrSheet()

upperNeighborIsHelixOrSheet

boolean upperNeighborIsHelixOrSheet()

getMonomerCount

public int getMonomerCount()

getMonomerIndex

public int getMonomerIndex()

getIndex

public int getIndex(Monomer monomer)

getSegments

public javax.vecmath.Point3f[] getSegments()

getAxisStartPoint

public javax.vecmath.Point3f getAxisStartPoint()

getAxisEndPoint

public javax.vecmath.Point3f getAxisEndPoint()

getStructureMidPoint

javax.vecmath.Point3f getStructureMidPoint(int index)

getInfo

public void getInfo(java.util.Hashtable info)

resetAxes

void resetAxes()