public static void main(String[] args) {
   Point3d[] pts = SecondaryStructTools.obtain(NAME);
   if (smooth) pts = CS.getSmoothedPoints(pts);
   SecondaryStruct s = new SecondaryStruct(pts, smooth);
   File f = new File("data/smooth_" + NAME + ".pdb");
   Chain c = new ChainImpl();
   c.setChainID(NAME.split("\\.")[1]);
   try (PrintWriter pw = new PrintWriter(f)) {
     for (int i = 0; i < pts.length; i++) {
       Atom a = new AtomImpl();
       a = new AtomImpl();
       a.setName(CA_NAME);
       a.setAltLoc(' ');
       Group g = new AminoAcidImpl();
       g.setPDBName(GROUP_NAME);
       g.addAtom(a);
       g.setResidueNumber(chainID, i + 1, null);
       c.addGroup(g);
       a.setX(pts[i].x);
       a.setY(pts[i].y);
       a.setZ(pts[i].z);
       pw.print(a.toPDB());
     }
   } catch (FileNotFoundException e) {
     e.printStackTrace();
   }
   // SecondaryStructureSequenceFeature sf = s.getSequenceFeature();
   System.out.println("Start");
   System.out.println(NAME);
   System.out.println(s.getAlphaLength());
   try (Scanner scan = new Scanner(System.in)) {
     String in;
     while (!(in = scan.next()).equals("X")) {
       if (in.equals("g")) {
         int st = scan.nextInt();
         System.out.println(
             SecondaryStructTools.distsToString(s.getRange(st - 1, scan.nextInt()), st));
       } else if (in.equals("a")) s.printHelices();
       else if (in.equals("b")) s.printStrands();
       else if (in.equals("l")) System.out.println(s.length());
       else if (in.equals("c")) s.printPoints();
       // else if (in.equals("sf"))
       // for (int i = 0; i < s.length(); i++)
       // System.out.println((i + 1) + ":\t" + sf.toString(i));
       else if (in.equals("test")) s.printVectors(s.getAlpha().getFeatures());
       else if (in.equals("test1"))
         System.out.println("=(0,0,0)\t=" + s.normP + "*50\t=" + s.normX + "*50");
       else if (in.equals("test2"))
         SecondaryStruct.printProjection(s.getAlphaNormProjection((byte) 0b00000000));
     }
   }
   // sc.close();
 }
 /**
  * Makes dummy CA atoms at 1A intervals. Only the x coordinate increments by one at each
  * consecutive Atom.
  */
 private Atom[] makeDummyCA(int len) {
   Atom[] ca1;
   Chain chain1 = new ChainImpl();
   ca1 = new Atom[len];
   for (int i = 0; i < len; i++) {
     ca1[i] = new AtomImpl();
     ca1[i].setName("CA");
     ca1[i].setCoords(new double[] {i, 0, 0});
     Group aa = new AminoAcidImpl();
     aa.setPDBName("GLY");
     aa.setResidueNumber(ResidueNumber.fromString(i + ""));
     aa.addAtom(ca1[i]);
     chain1.addGroup(aa);
   }
   return ca1;
 }