public class StructureAlignmentJmol extends AbstractAlignmentJmol
colorPalette, COMMAND_LINE_HELP, DEFAULT_HEIGHT, DEFAULT_SCRIPT, DEFAULT_WIDTH, frame, jmolPanel, nrOpenWindows, status, structure, text
Constructor | Description |
---|---|
StructureAlignmentJmol() |
|
StructureAlignmentJmol(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
Modifier and Type | Method | Description |
---|---|---|
void |
actionPerformed(java.awt.event.ActionEvent e) |
|
void |
destroy() |
Set all the member variables to null.
|
java.util.List<Matrix> |
getDistanceMatrices() |
Returns a List of internal Distance Matrices,
one for each structure in the alignment.
|
static java.lang.String |
getJmolScript4Block(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
int blockNr) |
|
static java.lang.String |
getJmolString(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
|
protected void |
initCoords() |
Display the structures after the variable initialization in the
constructor.
|
static void |
main(java.lang.String[] args) |
|
void |
resetDisplay() |
Return to the initial state of the alignment visualization.
|
evalString, getColorPalette, getJmolPanel, getStructure, getTitle, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, setAtoms, setJmolPanel, setStructure, setTitle, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened
public static void main(java.lang.String[] args)
protected void initCoords()
AbstractAlignmentJmol
initCoords
in class AbstractAlignmentJmol
public void destroy()
AbstractAlignmentJmol
destroy
in class AbstractAlignmentJmol
public void actionPerformed(java.awt.event.ActionEvent e)
actionPerformed
in class AbstractAlignmentJmol
public static java.lang.String getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
public static java.lang.String getJmolScript4Block(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNr)
public void resetDisplay()
AbstractAlignmentJmol
resetDisplay
in class AbstractAlignmentJmol
public java.util.List<Matrix> getDistanceMatrices()
AbstractAlignmentJmol
getDistanceMatrices
in class AbstractAlignmentJmol