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 Details

    • DisplayAFP

      public DisplayAFP()

  • Method Details

    • 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