Class FragmentJoiner


  • public class FragmentJoiner
    extends java.lang.Object
    Joins the initial Fragments together to larger Fragments
    Since:
    1.5
    Version:
    %I% %G%
    Author:
    Andreas Prlic, Peter Lackner
    • Field Detail

      • logger

        public static java.util.logging.Logger logger
    • Constructor Detail

      • FragmentJoiner

        public FragmentJoiner()
    • Method Detail

      • resizeArray

        public static java.lang.Object resizeArray​(java.lang.Object oldArray,
                                                   int newSize)
        Reallocates an array with a new size, and copies the contents of the old array to the new array.
        Parameters:
        oldArray - the old array, to be reallocated.
        newSize - the new array size.
        Returns:
        A new array with the same contents.
      • reduceFragments

        public static boolean reduceFragments​(java.util.List<FragmentPair> fragments,
                                              FragmentPair f,
                                              Matrix rmsmat)
        In helices often many similar fragments can be found. To reduce these to a few representative ones this check can be used. It does a distance check between all known Fragments and a new one. If this one is on a similar diagonal and it has a lower rms, this one is a better representation. Note: shifts of one are not allowed.
        Parameters:
        fragments -
        f -
        rmsmat -
        Returns:
        true - if this is a better representant for a group of locala fragments.
      • getRMS

        public static double getRMS​(Atom[] ca1,
                                    Atom[] ca2,
                                    JointFragments frag)
                             throws StructureException
        get the RMS of the JointFragments pair frag
        Parameters:
        ca1 - the array of all atoms of structure1
        ca2 - the array of all atoms of structure1
        frag - the JointFragments object that contains the list of identical positions
        Returns:
        the rms
        Throws:
        StructureException
      • frag_pairwise_compat

        public JointFragments[] frag_pairwise_compat​(FragmentPair[] fraglst,
                                                     int angleDiff,
                                                     float fragCompatDist,
                                                     int maxRefine)
        Calculate the pairwise compatibility of fpairs. Iterates through a list of fpairs and joins them if they have compatible rotation and translation parameters.
        Parameters:
        fraglst - FragmentPair[] array
        angleDiff - angle cutoff
        fragCompatDist - distance cutoff
        maxRefine - max number of solutions to keep
        Returns:
        JointFragments[]