org.jmol.modelsetbio
Class ProteinStructure
java.lang.Object
org.jmol.modelsetbio.ProteinStructure
- Direct Known Subclasses:
- Helix, Sheet, Turn
public abstract class ProteinStructure
- extends java.lang.Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
globalSerialID
static int globalSerialID
apolymer
AlphaPolymer apolymer
type
byte type
subtype
byte subtype
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
structureID
java.lang.String structureID
serialID
int serialID
strandCount
int strandCount
ProteinStructure
ProteinStructure(AlphaPolymer apolymer,
byte type,
int monomerIndex,
int monomerCount,
int id)
- Parameters:
apolymer
- type
- monomerIndex
- monomerCount
- id
- UNUSED
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()
isWithin
public boolean isWithin(int monomerIndex)
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.Map info)
resetAxes
void resetAxes()