org.biojava.bio.structure.align.gui

Class StructureAlignmentDisplay

java.lang.Object

org.biojava.bio.structure.align.gui.StructureAlignmentDisplay

public class StructureAlignmentDisplay
extends Object

Constructor Summary

Constructors

Constructor and Description
StructureAlignmentDisplay()

Method Summary

Methods

Modifier and Type	Method and Description
static StructureAlignmentJmol	display(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Display the alignment
static Group[]	prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Rotate the Atoms/Groups so they are aligned for the 3D visualisation
static void	shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift, Group[] twistedGroups) only shift CA positions.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

StructureAlignmentDisplay

public StructureAlignmentDisplay()

Method Detail

display

public static StructureAlignmentJmol display(AFPChain afpChain,
                             Atom[] ca1,
                             Atom[] ca2)
                                      throws StructureException

Display the alignment

Parameters:

afpChain -

ca1 -

ca2 -

Returns:

a StructureAlignmentJmol instance

Throws:

StructureException

prepareGroupsForDisplay

public static Group[] prepareGroupsForDisplay(AFPChain afpChain,
                              Atom[] ca1,
                              Atom[] ca2)
                                       throws StructureException

Rotate the Atoms/Groups so they are aligned for the 3D visualisation

Parameters:

afpChain -

ca1 -

ca2 -

Returns:

an array of Groups that are transformed for 3D display

Throws:

StructureException

shiftCA2

public static void shiftCA2(AFPChain afpChain,
            Atom[] ca2,
            Matrix m,
            Atom shift,
            Group[] twistedGroups)

only shift CA positions.