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| Packages that use Chain | |
| edu.sdsc.mbt | |
| edu.sdsc.mbt.viewables | This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties. |
| edu.sdsc.mbt.viewers.GLViewerImpl | |
| edu.sdsc.sirius.dialogs | |
| edu.sdsc.sirius.util | |
| edu.sdsc.sirius.viewers | |
| Uses of Chain in edu.sdsc.mbt |
| Methods in edu.sdsc.mbt that return Chain | |
Chain |
StructureMap.getChain(Atom atom)
Get the Chain object to which this Atom belongs. |
Chain |
StructureMap.getChain(java.lang.String chainId)
Get the Chain object given its ID. |
Chain |
StructureMap.getChain(int chainIndex)
Return the Chain at the given chain index. |
Chain |
Fragment.getChain()
Get the chain to which this Fragment belongs. |
| Methods in edu.sdsc.mbt with parameters of type Chain | |
int |
StructureMap.getChainIndex(Chain chain)
Get the index of the specified Chain. |
| Uses of Chain in edu.sdsc.mbt.viewables |
| Methods in edu.sdsc.mbt.viewables with parameters of type Chain | |
void |
StructureStyles.updateChain(Chain chain,
boolean fire)
This method determines whether the chain has any ribbon and whether its residues are selected. |
void |
StructureStyles.setRibbonVisible(Chain chain,
boolean visible,
boolean fire,
boolean batch)
|
boolean |
StructureStyles.isRibbonVisible(Chain chain)
|
int |
StructureStyles.getRibbonType(Chain chain)
|
void |
StructureStyles.setRibbonType(Chain chain,
int type)
|
void |
StructureStyles.removeRibbonType(Chain chain)
|
float |
StructureStyles.getRibbonDiameter(Chain chain)
|
void |
StructureStyles.setRibbonDiameter(Chain chain,
float diameter)
|
void |
StructureStyles.removeRibbonDiameter(Chain chain)
|
void |
StructureStyles.clearRibbon(Chain chain)
|
float |
StructureStyles.getRibbonQuality(Chain chain)
|
void |
StructureStyles.setRibbonQuality(Chain chain,
float q)
|
void |
StructureStyles.removeRibbonQuality(Chain chain)
|
void |
ChainColorById.getChainColor(Chain chain,
float[] color)
Produce a color based upon the chain id. |
void |
ChainColor.getChainColor(Chain chain,
float[] color)
|
| Uses of Chain in edu.sdsc.mbt.viewers.GLViewerImpl |
| Methods in edu.sdsc.mbt.viewers.GLViewerImpl with parameters of type Chain | |
static void |
SsGeometry.drawSs(Chain c,
javax.media.opengl.GL gl,
javax.media.opengl.glu.GLU glu,
com.sun.opengl.util.GLUT glut,
StructureMap structureMap,
StructureStyles styles,
boolean ribbon)
Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is
explicitely available in the data source file or from the Kabsch-Sander
algorithm. |
static void |
SsGeometry.drawSs(Chain c,
javax.media.opengl.GL gl,
javax.media.opengl.glu.GLU glu,
com.sun.opengl.util.GLUT glut,
StructureMap structureMap,
StructureStyles styles,
boolean ribbon,
int helixSmoothingSteps,
int strandSmoothingSteps,
int turnSmoothingSteps,
int coilSmoothingSteps)
Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is
explicitely available in the data source file or from the Kabsch-Sander
algorithm. |
static void |
SsGeometry.drawSs(Chain c,
javax.media.opengl.GL gl,
javax.media.opengl.glu.GLU glu,
com.sun.opengl.util.GLUT glut,
StructureMap structureMap,
StructureStyles styles,
boolean ribbon,
int helixSmoothingSteps,
int strandSmoothingSteps,
int turnSmoothingSteps,
int coilSmoothingSteps,
int helixSsShape)
Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is
explicitely available in the data source file or from the Kabsch-Sander
algorithm. |
static void |
SsGeometry.drawSs(Chain c,
javax.media.opengl.GL gl,
javax.media.opengl.glu.GLU glu,
com.sun.opengl.util.GLUT glut,
StructureMap structureMap,
StructureStyles styles,
boolean ribbon,
float helixQuality,
float strandQuality,
float turnQuality,
float coilQuality,
int helixSmoothingSteps,
int strandSmoothingSteps,
int turnSmoothingSteps,
int coilSmoothingSteps,
int helixCsType,
int strandCsType,
int turnCsType,
int coilCsType,
int helixSsShape)
Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is
explicitely available in the data source file or from the Kabsch-Sander
algorithm. |
void |
ChainGeometry.draw(Chain chain,
StructureStyles styles,
javax.media.opengl.GL gl,
javax.media.opengl.glu.GLU glu,
com.sun.opengl.util.GLUT glut)
Please complete the missing tags for main |
| Uses of Chain in edu.sdsc.sirius.dialogs |
| Constructors in edu.sdsc.sirius.dialogs with parameters of type Chain | |
ComponentRibbonDialog(javax.swing.JFrame f,
Manager p,
StructureViewer s,
java.lang.String title,
Chain c,
boolean add)
|
|
| Uses of Chain in edu.sdsc.sirius.util |
| Methods in edu.sdsc.sirius.util with parameters of type Chain | |
static java.util.Vector |
DataService.parseResidueList(Structure structure,
Chain chain,
java.lang.String input)
|
| Uses of Chain in edu.sdsc.sirius.viewers |
| Methods in edu.sdsc.sirius.viewers with parameters of type Chain | |
void |
StructureViewer.createRibbon(Chain chain,
int type,
float quality,
float diameter,
boolean updateView)
|
int |
StructureViewer.hasRibbon(Chain chain)
Checks whether there is a ribbon associated with this chain. |
void |
StructureViewer.addRibbon(Chain chain,
int ribbonType,
float ribbonQuality,
float ribbonDiameter,
boolean update)
|
void |
StructureViewer.removeRibbon(Chain chain,
boolean update)
|
void |
StructureViewer.colorRibbon(Chain chain,
int colorType,
java.awt.Color rColor)
|
void |
StructureViewer.setSelectedChain(Chain chain)
|
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