Class AFPChainer
- java.lang.Object
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- org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
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public class AFPChainer extends Object
a class to chain AFPs to an alignment- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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Constructor Summary
Constructors Constructor Description AFPChainer()
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Method Summary
All Methods Static Methods Concrete Methods 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 optimizedprotected 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 AFPsstatic 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.
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Field Detail
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debug
public static final boolean debug
- See Also:
- Constant Field Values
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Constructor Detail
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AFPChainer
public AFPChainer()
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Method Detail
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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
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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
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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 AFPsafpChain
-ca1
-ca2
-- Returns:
- rmsd
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