public abstract class ProteinStructure
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
protected AlphaPolymer |
apolymer |
protected javajs.util.P3 |
axisA |
protected javajs.util.P3 |
axisB |
protected javajs.util.V3 |
axisUnitVector |
private static int |
globalStrucNo |
protected int |
monomerIndexFirst |
private int |
monomerIndexLast |
int |
nRes |
private java.util.Map<Monomer,java.lang.Integer> |
resMap |
private javajs.util.P3[] |
segments |
(package private) int |
serialID |
(package private) int |
strandCount |
(package private) int |
strucNo |
(package private) java.lang.String |
structureID |
(package private) STR |
subtype |
(package private) STR |
type |
protected javajs.util.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() |
javajs.util.P3 |
getAxisEndPoint() |
javajs.util.P3 |
getAxisStartPoint() |
int |
getIndex(Monomer monomer) |
void |
getInfo(java.util.Map<java.lang.String,java.lang.Object> info) |
javajs.util.P3[] |
getSegments() |
(package private) javajs.util.P3 |
getStructureMidPoint(int index) |
boolean |
isWithin(int monomerIndex) |
(package private) void |
removeMonomer(int index)
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,
STR type,
int monomerIndex,
int monomerCount) |
STR type
STR subtype
java.lang.String structureID
int strucNo
int serialID
int strandCount
public int nRes
protected AlphaPolymer apolymer
protected int monomerIndexFirst
protected javajs.util.P3 axisA
protected javajs.util.P3 axisB
protected javajs.util.V3 axisUnitVector
protected javajs.util.V3 vectorProjection
private static int globalStrucNo
private int monomerIndexLast
private javajs.util.P3[] segments
private java.util.Map<Monomer,java.lang.Integer> resMap
protected void setupPS(AlphaPolymer apolymer, STR type, int monomerIndex, int monomerCount)
apolymer
- type
- monomerIndex
- monomerCount
- void addMonomer(int index)
index
- void removeMonomer(int index)
index
- public void calcAxis()
void calcSegments()
public boolean isWithin(int monomerIndex)
public int getIndex(Monomer monomer)
public javajs.util.P3[] getSegments()
public javajs.util.P3 getAxisStartPoint()
public javajs.util.P3 getAxisEndPoint()
javajs.util.P3 getStructureMidPoint(int index)
public void getInfo(java.util.Map<java.lang.String,java.lang.Object> info)
void resetAxes()