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

Class FragmentJoiner

java.lang.Object
org.biojava.nbio.structure.align.pairwise.FragmentJoiner
public class FragmentJoiner extends Object
Joins the initial Fragments together to larger Fragments
Since:
1.5
Version:
%I% %G%
Author:
Andreas Prlic, Peter Lackner

  • Field Details

    • logger

      public static Logger logger

  • Constructor Details

    • FragmentJoiner

      public FragmentJoiner()

  • Method Details

    • resizeArray

      public static Object resizeArray(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(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.

    • approach_ap3

      public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params) throws StructureException
      Throws:
      StructureException

    • 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

    • angleCheckOk

      public boolean angleCheckOk(FragmentPair a, FragmentPair b, float distcutoff)

    • 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[]

    • extendFragments

      public void extendFragments(Atom[] ca1, Atom[] ca2, JointFragments[] fragments, StrucAligParameters params) throws StructureException
      Throws:
      StructureException

    • extendFragments

      public void extendFragments(Atom[] ca1, Atom[] ca2, JointFragments fragments, StrucAligParameters params) throws StructureException
      Throws:
      StructureException