org.biojava.nbio.structure.align.gui

Class DisplayAFP

java.lang.Object

org.biojava.nbio.structure.align.gui.DisplayAFP

public class DisplayAFP
extends Object

A utility class for visualistion of structure alignments

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
DisplayAFP()

Method Summary

Modifier and Type	Method and Description
static Structure	createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
static StructureAlignmentJmol	display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms1, List<Group> hetatms2) Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
static Structure	getAlignedStructure(Atom[] ca1, Atom[] ca2) Get an artifical Structure containing both chains.
static Atom[]	getAtomArray(Atom[] ca, List<Group> hetatms) Returns the first atom for each group
static Atom	getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious) return the atom at alignment position aligPos. at the present only works with block 0
static int	getBlockNrForAlignPos(AFPChain afpChain, int aligPos) Deprecated. use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
static List<Integer>	getEQRAlignmentPos(AFPChain afpChain)
static List<String>	getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca) Return a list of pdb Strings corresponding to the aligned positions of the molecule.
static void	showAlignmentImage(AFPChain afpChain, String result)
static void	showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)

Methods inherited from class java.lang.Object

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

Constructor Detail

DisplayAFP

public DisplayAFP()

Method Detail

getEQRAlignmentPos

public static final List<Integer> getEQRAlignmentPos(AFPChain afpChain)

getPDBresnum

public static final List<String> getPDBresnum(int aligPos,
                                              AFPChain afpChain,
                                              Atom[] ca)

Return a list of pdb Strings corresponding to the aligned positions of the molecule. Only supports a pairwise alignment with the AFPChain DS.

Parameters:

aligPos -

afpChain -

ca -

getBlockNrForAlignPos

@Deprecated
public static int getBlockNrForAlignPos(AFPChain afpChain,
                                                    int aligPos)

Deprecated. use AFPAlignmentDisplay.getBlockNrForAlignPos instead...

get the block number for an aligned position

Parameters:

afpChain -

aligPos -

Returns:

getAtomForAligPos

public static final Atom getAtomForAligPos(AFPChain afpChain,
                                           int chainNr,
                                           int aligPos,
                                           Atom[] ca,
                                           boolean getPrevious)
                                    throws StructureException

return the atom at alignment position aligPos. at the present only works with block 0

Parameters:

chainNr - the number of the aligned pair. 0... first chain, 1... second chain.

afpChain - an afpChain object

aligPos - position on the alignment

getPrevious - gives the previous position if false, gives the next posible atom

Returns:

a CA atom that is at a particular position of the alignment

Throws:

StructureException

getAlignedStructure

public static final Structure getAlignedStructure(Atom[] ca1,
                                                  Atom[] ca2)
                                           throws StructureException

Get an artifical Structure containing both chains. Does NOT rotate anything

Parameters:

ca1 -

ca2 -

Returns:

a structure object containing two models, one for each set of Atoms.

Throws:

StructureException

getAtomArray

public static final Atom[] getAtomArray(Atom[] ca,
                                        List<Group> hetatms)
                                 throws StructureException

Returns the first atom for each group

Parameters:

ca -

hetatms -

Returns:

Throws:

StructureException

display

public static final StructureAlignmentJmol display(AFPChain afpChain,
                                                   Group[] twistedGroups,
                                                   Atom[] ca1,
                                                   Atom[] ca2,
                                                   List<Group> hetatms1,
                                                   List<Group> hetatms2)
                                            throws StructureException

Note: ca2, hetatoms2 and nucleotides2 should not be rotated. This will be done here...

Throws:

StructureException

showAlignmentPanel

public static void showAlignmentPanel(AFPChain afpChain,
                                      Atom[] ca1,
                                      Atom[] ca2,
                                      AbstractAlignmentJmol jmol)
                               throws StructureException

Throws:

StructureException

showAlignmentImage

public static void showAlignmentImage(AFPChain afpChain,
                                      String result)

createArtificalStructure

public static Structure createArtificalStructure(AFPChain afpChain,
                                                 Atom[] ca1,
                                                 Atom[] ca2)
                                          throws StructureException

Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.

Parameters:

afpChain - the container of the alignment

ca1 - atoms for protein 1

ca2 - atoms for protein 2

Returns:

a protein structure with 2 models.

Throws:

StructureException