Class AFPTwister


  • public class AFPTwister
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      AFPTwister()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      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 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
      • 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