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;
}