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 and Description
static boolean	debug

Constructor Summary

Constructors

Constructor and Description
AFPChainer()

Method Summary

Modifier and Type	Method and 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 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