Class 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 boolean debug  
    • Constructor Summary

      Constructors 
      Constructor Description
      AFPChainer()  
    • Method Detail

      • 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