Package org.jmol.modelsetbio
Class ProteinStructure
- java.lang.Object
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- org.jmol.modelsetbio.ProteinStructure
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Field Summary
Fields Modifier and Type Field Description AlphaPolymer
apolymer
protected javajs.util.P3
axisA
protected javajs.util.P3
axisB
protected javajs.util.V3
axisUnitVector
private static int
globalStrucNo
protected int
monomerIndexFirst
(package 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
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Constructor Summary
Constructors Constructor Description ProteinStructure()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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()
private void
calcSegments()
Monomer
findMonomer(javajs.util.BS bsAtoms, boolean isFirst)
javajs.util.P3
getAxisEndPoint()
javajs.util.P3
getAxisStartPoint()
int
getIndex(Monomer monomer)
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()
void
setAtomBits(javajs.util.BS bs)
void
setAtomBitsAndClear(javajs.util.BS bs, javajs.util.BS bsOut)
protected void
setupPS(AlphaPolymer apolymer, STR type, int monomerIndex, int monomerCount)
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Field Detail
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type
STR type
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subtype
STR subtype
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structureID
java.lang.String structureID
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strucNo
int strucNo
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serialID
int serialID
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strandCount
int strandCount
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nRes
public int nRes
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apolymer
public AlphaPolymer apolymer
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monomerIndexFirst
protected int monomerIndexFirst
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monomerIndexLast
int monomerIndexLast
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axisA
protected javajs.util.P3 axisA
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axisB
protected javajs.util.P3 axisB
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axisUnitVector
protected javajs.util.V3 axisUnitVector
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vectorProjection
protected javajs.util.V3 vectorProjection
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globalStrucNo
private static int globalStrucNo
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segments
private javajs.util.P3[] segments
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resMap
private java.util.Map<Monomer,java.lang.Integer> resMap
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Method Detail
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setupPS
protected void setupPS(AlphaPolymer apolymer, STR type, int monomerIndex, int monomerCount)
- Parameters:
apolymer
-type
-monomerIndex
-monomerCount
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addMonomer
void addMonomer(int index)
Note that this method does not check to see that there are no overlapping protein structures.- Parameters:
index
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removeMonomer
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.- Parameters:
index
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calcAxis
public void calcAxis()
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isWithin
public boolean isWithin(int monomerIndex)
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getIndex
public int getIndex(Monomer monomer)
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getSegments
public javajs.util.P3[] getSegments()
- Returns:
- points for rocket segment rendering
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getStructureMidPoint
javajs.util.P3 getStructureMidPoint(int index)
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calcSegments
private void calcSegments()
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getAxisStartPoint
public javajs.util.P3 getAxisStartPoint()
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getAxisEndPoint
public javajs.util.P3 getAxisEndPoint()
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resetAxes
void resetAxes()
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setAtomBits
public void setAtomBits(javajs.util.BS bs)
- Specified by:
setAtomBits
in interfaceStructure
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setAtomBitsAndClear
public void setAtomBitsAndClear(javajs.util.BS bs, javajs.util.BS bsOut)
- Specified by:
setAtomBitsAndClear
in interfaceStructure
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findMonomer
public Monomer findMonomer(javajs.util.BS bsAtoms, boolean isFirst)
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