org.biojava.nbio.structure.align

Class AFPTwister

java.lang.Object

org.biojava.nbio.structure.align.AFPTwister

public class AFPTwister
extends Object

Constructor Summary

Constructors

Constructor and Description
AFPTwister()

Method Summary

Methods

Modifier and Type	Method and Description
static int	afp2Res(AFPChain afpChain, int afpn, int[] afpPositions, int listStart) Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
static Group[]	twistOptimized(AFPChain afpChain, Atom[] ca1, Atom[] ca2) superimposing according to the optimized alignment
static Group[]	twistPDB(AFPChain afpChain, Atom[] ca1, Atom[] ca2) calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AFPTwister

public AFPTwister()

Method Detail

twistPDB

public static Group[] twistPDB(AFPChain afpChain,
               Atom[] ca1,
               Atom[] ca2)
                        throws StructureException

calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B

Returns:

twisted Groups

Throws:

StructureException

twistOptimized

public static Group[] twistOptimized(AFPChain afpChain,
                     Atom[] ca1,
                     Atom[] ca2)
                              throws StructureException

superimposing according to the optimized alignment

Parameters:

afpChain -

ca1 -

ca2 -

Returns:

Group array twisted.

Throws:

StructureException

afp2Res

public static int afp2Res(AFPChain afpChain,
          int afpn,
          int[] afpPositions,
          int listStart)

Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!

Parameters:

afpChain - the AFPChain to store resuts

afpn - nr of afp

afpPositions -

listStart -

Returns:

nr of eq residues