public class StructureAlignmentJmol extends AbstractAlignmentJmol
colorPalette, COMMAND_LINE_HELP, DEFAULT_HEIGHT, DEFAULT_SCRIPT, DEFAULT_WIDTH, frame, jmolPanel, nrOpenWindows, status, structure, text
Constructor and Description |
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StructureAlignmentJmol() |
StructureAlignmentJmol(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
Modifier and Type | Method and Description |
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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 interface java.awt.event.ActionListener
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