Package org.biojava.nbio.structure.align.fatcat.calc

Class AFPChainer

java.lang.Object
org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
public class AFPChainer extends Object
a class to chain AFPs to an alignment
Author:
Andreas Prlic

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final boolean
    debug
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    AFPChainer()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static boolean
    afpPairConn(int afp1, int afp2, FatCatParameters params, AFPChain afpChain)
    //Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
    protected static double
    calAfpRmsd(int afpn, int[] afpPositions, int listStart, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
    //return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
    static void
    doChainAfp(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
    // Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

  • Constructor Details

    • AFPChainer

      public AFPChainer()

  • Method Details

    • doChainAfp

      public static void doChainAfp(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
      // Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg. AFP(k-1) -> AFP(k) ) requiring // AFP(k-1) < AFP(k)(refer AFP.h definition), // ie i(k-1) < i(k) and j(k-1) < j(k) // in the figure, only (2) AFP can extend to AFP(k) // Key features: a coordination transformation is allowed in the AFP extension // gap penalties are also considered // // protein1 // --------------------------- // | \ | // | \(1) | // | \ \ | // | \(2) \ | // p | \ | // r | \ | // o | \(3) \(i,j, k) | // t | \ \ | // e | \ | // i | | // n | | // 2 --------------------------- // schematic of AFP chaining

    • afpPairConn

      public static boolean afpPairConn(int afp1, int afp2, FatCatParameters params, AFPChain afpChain)
      //Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
      Parameters:
      afp1 -
      afp2 -
      Returns:
      flag if they are connected

    • calAfpRmsd

      protected static double calAfpRmsd(int afpn, int[] afpPositions, int listStart, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
      //return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
      Parameters:
      afpn -
      afpPositions - the positions of AFPs to work on.
      listStart - the starting position in the list of AFPs
      afpChain -
      ca1 -
      ca2 -
      Returns:
      rmsd