Package org.jmol.modelsetbio
Class ProteinStructure
java.lang.Object
org.jmol.modelsetbio.ProteinStructure
- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
Annotation
,Helix
,Sheet
,Turn
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected javajs.util.P3
protected javajs.util.P3
protected javajs.util.V3
private static int
(package private) int
private static int
protected int
(package private) int
int
private javajs.util.P3[]
(package private) int
(package private) int
(package private) int
(package private) String
(package private) STR
(package private) STR
protected javajs.util.V3
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescription(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
findMonomer
(javajs.util.BS bsAtoms, boolean isFirst) javajs.util.P3
javajs.util.P3
int
javajs.util.P3[]
(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
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) toString()
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Field Details
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ids
private static int ids -
type
STR type -
subtype
STR subtype -
structureID
String structureID -
strucNo
int strucNo -
serialID
int serialID -
strandCount
int strandCount -
id
int id -
nRes
public int nRes -
apolymer
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monomerIndexFirst
protected int monomerIndexFirst -
monomerIndexLast
int monomerIndexLast -
axisA
protected javajs.util.P3 axisA -
axisB
protected javajs.util.P3 axisB -
axisUnitVector
protected javajs.util.V3 axisUnitVector -
vectorProjection
protected javajs.util.V3 vectorProjection -
globalStrucNo
private static int globalStrucNo -
segments
private javajs.util.P3[] segments -
resMap
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Constructor Details
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ProteinStructure
protected ProteinStructure()
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Method Details
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setupPS
- 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() -
isWithin
public boolean isWithin(int monomerIndex) -
getIndex
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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) -
calcSegments
private void calcSegments() -
getAxisStartPoint
public javajs.util.P3 getAxisStartPoint() -
getAxisEndPoint
public javajs.util.P3 getAxisEndPoint() -
resetAxes
void resetAxes() -
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
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toString
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