Modifier and Type | Field and Description |
---|---|
protected AlphaPolymer |
apolymer |
protected P3 |
axisA |
protected P3 |
axisB |
protected V3 |
axisUnitVector |
private static int |
globalStrucNo |
protected int |
monomerCount |
protected int |
monomerIndexFirst |
private int |
monomerIndexLast |
private P3[] |
segments |
(package private) int |
serialID |
(package private) int |
strandCount |
(package private) int |
strucNo |
(package private) java.lang.String |
structureID |
(package private) EnumStructure |
subtype |
(package private) EnumStructure |
type |
protected V3 |
vectorProjection |
Constructor and Description |
---|
ProteinStructure() |
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() |
P3 |
getAxisEndPoint() |
P3 |
getAxisStartPoint() |
int |
getIndex(Monomer monomer) |
void |
getInfo(java.util.Map<java.lang.String,java.lang.Object> info) |
int |
getMonomerCount() |
int |
getMonomerIndex() |
P3[] |
getSegments() |
(package private) P3 |
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() |
protected void |
setupPS(AlphaPolymer apolymer,
EnumStructure type,
int monomerIndex,
int monomerCount) |
(package private) boolean |
upperNeighborIsHelixOrSheet() |
EnumStructure type
EnumStructure subtype
java.lang.String structureID
int strucNo
int serialID
int strandCount
protected AlphaPolymer apolymer
protected int monomerIndexFirst
protected int monomerCount
protected P3 axisA
protected P3 axisB
protected V3 axisUnitVector
protected final V3 vectorProjection
private static int globalStrucNo
private int monomerIndexLast
private P3[] segments
protected void setupPS(AlphaPolymer apolymer, EnumStructure type, int monomerIndex, int monomerCount)
apolymer
- type
- monomerIndex
- monomerCount
- void 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 P3[] getSegments()
public P3 getAxisStartPoint()
public P3 getAxisEndPoint()
P3 getStructureMidPoint(int index)
public void getInfo(java.util.Map<java.lang.String,java.lang.Object> info)
void resetAxes()