org.biojava.bio.structure.align.fatcat.calc
Class AFPChainer

java.lang.Object
  extended by org.biojava.bio.structure.align.fatcat.calc.AFPChainer

public class AFPChainer
extends Object

a class to chain AFPs to an alignment

Author:
Andreas Prlic

Field Summary
static boolean debug
           
 
Constructor Summary
AFPChainer()
           
 
Method Summary
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 Detail

debug

public static final boolean debug
See Also:
Constant Field Values
Constructor Detail

AFPChainer

public 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