public void align ( Structure s1 , String chainId1 , Structure s2 , String chainId2 , StrucAligParameters params ) throws StructureException { reset ( ) ; this . params = params ; Chain c1 = s1 . getPolyChainByPDB ( chainId1 ) ; Chain c2 = s2 . getPolyChainByPDB ( chainId2 ) ; Structure s3 = new StructureImpl ( ) ; s3 . addChain ( c1 ) ; Structure s4 = new StructureImpl ( ) ; s4 . addChain ( c2 ) ; Atom [ ] ca1 = getAlignmentAtoms ( s3 ) ; Atom [ ] ca2 = getAlignmentAtoms ( s4 ) ; notifyStartingAlignment ( s1 . getName ( ) , ca1 , s2 . getName ( ) , ca2 ) ; align ( ca1 , ca2 , params ) ; }
Aligns two chains from the structures using user provided parameters .