Package org.biojava.nbio.structure.align.pairwise

Class AlternativeAlignment

  • All Implemented Interfaces:
    Serializable
    public class AlternativeAlignment
extends Object
implements Serializable
    Implements a class which handles one possible (alternative) solution. Alternative alignments arise from different seed alignments or seed FPairs. The AltAlg class contains methods for refinement (Dynamic Programming based) and filtering (i.e. removing probably wrongly matched APairs). In the refinement phase, different seed alignments can converge to the same solution.
    Since:
    3:04:26 PM
    Version:
    %I% %G%
    Author:
    Andreas Prlic,, Peter Lackner (original Python and C code)
    See Also:
    Serialized Form

    • Field Detail

      • logger

        public static final org.slf4j.Logger logger

    • Method Detail

      • toString

        public String toString()
        print the idx positions of this alignment
        Overrides:
        toString in class Object
        Returns:
        a String representation

      • getCluster

        public int getCluster()
        get the number of the cluster this alignment belongs to
        Returns:
        an int giving the number of the cluster

      • setCluster

        public void setCluster​(int cluster)
        set the number of the cluster this alignment belongs to. All alignments in a cluster are quite similar.
        Parameters:
        cluster - the number of the cluster

      • getRmsd

        public double getRmsd()

      • setRms

        public void setRms​(double rms)
        the rms in the structurally equivalent regions
        Parameters:
        rms -

      • getScore

        public float getScore()
        the alignment score
        Returns:
        the score of this alignment

      • setScore

        public void setScore​(float score)

      • getGaps

        public int getGaps()
        return the number of gaps in this alignment
        Returns:
        the number of Gaps

      • getEqr

        public int getEqr()
        returns the number of euqivalent residues in this alignment
        Returns:
        the number of equivalent residues

      • getIdx1

        public int[] getIdx1()
        the positions of the structure equivalent positions in atom set 1
        Returns:
        the array of the positions

      • getIdx2

        public int[] getIdx2()
        the positions of the structure equivalent atoms in atom set 2
        Returns:
        the array of the positions

      • setPercId

        public void setPercId​(int percId)

      • apairs_from_seed

        public void apairs_from_seed​(int l,
                             int i,
                             int j)
        Set apairs according to a seed position.
        Parameters:
        l -
        i -
        j -

      • getAltAligNumber

        public int getAltAligNumber()
        returns the sequential number of this alternative alignment
        Returns:
        the sequential number of this alternative alignment

      • refine

        public void refine​(StrucAligParameters params,
                   Atom[] ca1,
                   Atom[] ca2)
            throws StructureException
        Refinement procedure based on superposition and dynamic programming. Performs an iterative refinement. Several methods apply such a procedure, e.g. CE or ProSup. Here we additionally test for circular permutation, which are in the same frame of superposition as the optimal alignment. This feature may be switched off by setting permsize to -1.
        Parameters:
        params - the parameters
        ca1 - atoms of structure 1
        ca2 - atoms of structure 2
        Throws:
        StructureException

      • getRotationMatrix

        public Matrix getRotationMatrix()
        returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
        Returns:
        the rotation Matrix

      • getShift

        public Atom getShift()
        returns the shift vector that has to be applied on structure to to shift on structure one
        Returns:
        the shift vector

      • calcScores

        public void calcScores​(Atom[] ca1,
                       Atom[] ca2)
        calculates scores for this alignment ( %id )
        Parameters:
        ca1 - set of Atoms for molecule 1
        ca2 - set of Atoms for molecule 2

      • getAlignedStructure

        public Structure getAlignedStructure​(Structure s1,
                                     Structure s2)
        create an artifical Structure object that contains the two structures superimposed onto each other. Each structure is in a separate model. Model 1 is structure 1 and Model 2 is structure 2.
        Parameters:
        s1 - the first structure. its coordinates will not be changed
        s2 - the second structure, it will be cloned and the cloned coordinates will be rotated according to the alignment results.
        Returns:
        composite structure containing the 2 aligned structures as a models 1 and 2

      • toPDB

        public String toPDB​(Structure s1,
                    Structure s2)
        converts the alignment to a PDB file each of the structures will be represented as a model.
        Parameters:
        s1 -
        s2 -
        Returns:
        a PDB file as a String

      • getDistanceMatrix

        public Matrix getDistanceMatrix()
        The distance matrix this alignment is based on
        Returns:
        a Matrix object.

      • setDistanceMatrix

        public void setDistanceMatrix​(Matrix distanceMatrix)
        The distance matrix this alignment is based on
        Parameters:
        distanceMatrix -