AFPTwister

java.lang.Object

org.biojava.nbio.structure.align.AFPTwister

public class AFPTwister extends Object

Constructor Summary

Constructors

Constructor

Description

AFPTwister()
Method Summary

Modifier and Type

Method

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 Details
- AFPTwister
  
  public AFPTwister()
Method Details
- 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