Modifier and Type | Field and Description |
---|---|
(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) int |
serialID |
(package private) int |
strandCount |
(package private) java.lang.String |
structureID |
(package private) EnumStructure |
subtype |
(package private) EnumStructure |
type |
(package private) int |
uniqueID |
(package private) javax.vecmath.Vector3f |
vectorProjection |
Constructor and Description |
---|
ProteinStructure(AlphaPolymer apolymer,
EnumStructure type,
int monomerIndex,
int monomerCount,
int id) |
Modifier and Type | Method and Description |
---|---|
(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.Map<java.lang.String,java.lang.Object> info) |
int |
getMonomerCount() |
int |
getMonomerIndex() |
javax.vecmath.Point3f[] |
getSegments() |
(package private) javax.vecmath.Point3f |
getStructureMidPoint(int index) |
boolean |
isWithin(int monomerIndex) |
(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() |
static int globalSerialID
AlphaPolymer apolymer
EnumStructure type
EnumStructure subtype
int monomerIndexFirst
int monomerIndexLast
int monomerCount
javax.vecmath.Point3f axisA
javax.vecmath.Point3f axisB
javax.vecmath.Vector3f axisUnitVector
final javax.vecmath.Vector3f vectorProjection
javax.vecmath.Point3f[] segments
int uniqueID
java.lang.String structureID
int serialID
int strandCount
ProteinStructure(AlphaPolymer apolymer, EnumStructure type, int monomerIndex, int monomerCount, int id)
apolymer
- type
- monomerIndex
- monomerCount
- id
- UNUSEDvoid addMonomer(int index)
index
- int removeMonomer(int monomerIndex)
monomerIndex
- public void calcAxis()
void calcSegments()
boolean lowerNeighborIsHelixOrSheet()
boolean upperNeighborIsHelixOrSheet()
public int getMonomerCount()
public boolean isWithin(int monomerIndex)
public int getMonomerIndex()
public int getIndex(Monomer monomer)
public javax.vecmath.Point3f[] getSegments()
public javax.vecmath.Point3f getAxisStartPoint()
public javax.vecmath.Point3f getAxisEndPoint()
javax.vecmath.Point3f getStructureMidPoint(int index)
public void getInfo(java.util.Map<java.lang.String,java.lang.Object> info)
void resetAxes()