org.biojava.bio.structure.align
Class AFPTwister

java.lang.Object
  extended by org.biojava.bio.structure.align.AFPTwister

public class AFPTwister
extends Object


Constructor Summary
AFPTwister()
           
 
Method Summary
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