Package 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	Description
DisplayAFP()

Method Summary

Modifier and Type	Method	Description
static org.biojava.nbio.structure.Structure	createArtificalStructure(org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.Atom[] ca1, org.biojava.nbio.structure.Atom[] ca2)	Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
static StructureAlignmentJmol	display(org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.Group[] twistedGroups, org.biojava.nbio.structure.Atom[] ca1, org.biojava.nbio.structure.Atom[] ca2, List<org.biojava.nbio.structure.Group> hetatms1, List<org.biojava.nbio.structure.Group> hetatms2)	Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
static org.biojava.nbio.structure.Atom[]	getAtomArray(org.biojava.nbio.structure.Atom[] ca, List<org.biojava.nbio.structure.Group> hetatms)	Returns the first atom for each group
static org.biojava.nbio.structure.Atom	getAtomForAligPos(org.biojava.nbio.structure.align.model.AFPChain afpChain, int chainNr, int aligPos, org.biojava.nbio.structure.Atom[] ca, boolean getPrevious)	Return the atom at alignment position aligPos.
static List<Integer>	getEQRAlignmentPos(org.biojava.nbio.structure.align.model.AFPChain afpChain)
static List<String>	getPDBresnum(int aligPos, org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.Atom[] ca)	Return a list of pdb Strings corresponding to the aligned positions of the molecule.
static void	showAlignmentImage(org.biojava.nbio.structure.align.model.AFPChain afpChain, String result)
static void	showAlignmentPanel(org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.Atom[] ca1, org.biojava.nbio.structure.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(org.biojava.nbio.structure.align.model.AFPChain afpChain)

getPDBresnum

public static final List<String> getPDBresnum(int aligPos,
                                              org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                              org.biojava.nbio.structure.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 -

getAtomForAligPos

public static final org.biojava.nbio.structure.Atom getAtomForAligPos(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                                                      int chainNr,
                                                                      int aligPos,
                                                                      org.biojava.nbio.structure.Atom[] ca,
                                                                      boolean getPrevious)
                                                               throws org.biojava.nbio.structure.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:

org.biojava.nbio.structure.StructureException

getAtomArray

public static final org.biojava.nbio.structure.Atom[] getAtomArray(org.biojava.nbio.structure.Atom[] ca,
                                                                   List<org.biojava.nbio.structure.Group> hetatms)
                                                            throws org.biojava.nbio.structure.StructureException

Returns the first atom for each group

Parameters:

ca -

hetatms -

Returns:

Throws:

org.biojava.nbio.structure.StructureException

display

public static final StructureAlignmentJmol display(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                                   org.biojava.nbio.structure.Group[] twistedGroups,
                                                   org.biojava.nbio.structure.Atom[] ca1,
                                                   org.biojava.nbio.structure.Atom[] ca2,
                                                   List<org.biojava.nbio.structure.Group> hetatms1,
                                                   List<org.biojava.nbio.structure.Group> hetatms2)
                                            throws org.biojava.nbio.structure.StructureException

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

Throws:

org.biojava.nbio.structure.StructureException

showAlignmentPanel

public static void showAlignmentPanel(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                      org.biojava.nbio.structure.Atom[] ca1,
                                      org.biojava.nbio.structure.Atom[] ca2,
                                      AbstractAlignmentJmol jmol)
                               throws org.biojava.nbio.structure.StructureException

Throws:

org.biojava.nbio.structure.StructureException

showAlignmentImage

public static void showAlignmentImage(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                      String result)

createArtificalStructure

public static org.biojava.nbio.structure.Structure createArtificalStructure(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                                                            org.biojava.nbio.structure.Atom[] ca1,
                                                                            org.biojava.nbio.structure.Atom[] ca2)
                                                                     throws org.biojava.nbio.structure.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:

org.biojava.nbio.structure.StructureException