Class DisplayAFP


  • public class DisplayAFP
    extends java.lang.Object
    A utility class for visualistion of structure alignments
    Author:
    Andreas Prlic
    • Constructor Detail

      • DisplayAFP

        public DisplayAFP()
    • Method Detail

      • getEQRAlignmentPos

        public static final java.util.List<java.lang.Integer> getEQRAlignmentPos​(AFPChain afpChain)
      • getPDBresnum

        public static final java.util.List<java.lang.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
      • showAlignmentImage

        public static void showAlignmentImage​(AFPChain afpChain,
                                              java.lang.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