org.biojava.bio.structure.align.gui
Class DisplayAFP

java.lang.Object
  org.biojava.bio.structure.align.gui.DisplayAFP

public class DisplayAFP
extends Object

A utility class for visualistion of structure alignments

Author:

Andreas Prlic

Field Summary

static boolean

debug

Constructor Summary

DisplayAFP()

Method Summary

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> hetatms, List<Group> nucleotides, List<Group> hetatms2, List<Group> nucleotides2) 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, List<Group> nucleotides)
static Atom	getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious) return the atom at alignment position aligPos.
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)
static void	showAlignmentImage(AFPChain afpChain, Atom[] ca1, Atom[] ca2, StructureAlignmentJmol jmol)
static void	showAlignmentImage(AFPChain afpChain, String result)

Methods inherited from class java.lang.Object

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

Field Detail

debug

public static final boolean debug

See Also:

Constant Field Values

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)

getBlockNrForAlignPos

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,
                                        List<Group> nucleotides)
                                 throws StructureException

Throws:

StructureException

display

public static final StructureAlignmentJmol display(AFPChain afpChain,
                                                   Group[] twistedGroups,
                                                   Atom[] ca1,
                                                   Atom[] ca2,
                                                   List<Group> hetatms,
                                                   List<Group> nucleotides,
                                                   List<Group> hetatms2,
                                                   List<Group> nucleotides2)
                                            throws StructureException

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

Throws:

StructureException

showAlignmentImage

public static void showAlignmentImage(AFPChain afpChain,
                                      Atom[] ca1,
                                      Atom[] ca2,
                                      StructureAlignmentJmol jmol)

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