public static void main ( String [ ] args ) { PDBFileReader pdbr = new PDBFileReader ( ) ; pdbr . setPath ( "/tmp/" ) ; //String pdb1 = "1crl"; //String pdb2 = "1ede"; String pdb1 = "1buz" ; String pdb2 = "1ali" ; //String pdb1 = "5pti"; //String pdb2 = "5pti"; // NO NEED TO DO CHANGE ANYTHING BELOW HERE... StructurePairAligner sc = new StructurePairAligner ( ) ; StrucAligParameters params = new StrucAligParameters ( ) ; params . setMaxIter ( 1 ) ; sc . setParams ( params ) ; // step1 : read molecules try { Structure s1 = pdbr . getStructureById ( pdb1 ) ; Structure s2 = pdbr . getStructureById ( pdb2 ) ; System . out . println ( "aligning " + pdb1 + " vs. " + pdb2 ) ; System . out . println ( s1 ) ; System . out . println ( ) ; System . out . println ( s2 ) ; // step 2 : do the calculations sc . align ( s1 , s2 ) ; ScaleableMatrixPanel smp = new ScaleableMatrixPanel ( ) ; JFrame frame = new JFrame ( ) ; frame . addWindowListener ( new WindowAdapter ( ) { @ Override public void windowClosing ( WindowEvent e ) { JFrame f = ( JFrame ) e . getSource ( ) ; f . setVisible ( false ) ; f . dispose ( ) ; } } ) ; smp . setMatrix ( sc . getDistMat ( ) ) ; smp . setFragmentPairs ( sc . getFragmentPairs ( ) ) ; smp . setAlternativeAligs ( sc . getAlignments ( ) ) ; for ( int i = 0 ; i < sc . getAlignments ( ) . length ; i ++ ) { AlternativeAlignment aa = sc . getAlignments ( ) [ i ] ; System . out . println ( aa ) ; } frame . getContentPane ( ) . add ( smp ) ; frame . pack ( ) ; frame . setVisible ( true ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; } }
Number of minor ticks per unit scaled