org.biojava.bio.structure.align.fatcat.calc
Class AFPChainer
java.lang.Object
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
|
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 |
debug
public static final boolean debug
- See Also:
- Constant Field Values
AFPChainer
public AFPChainer()
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 AFPsafpChain
- ca1
- ca2
-
- Returns:
- rmsd