public class Nucleotide {

  String name;
  color fillcolor;
  int opacity = 255;
  float fade;
  int numAtoms;
  PdbRecord[] AdenineRecords;
  String AdenineRecords_url = "dAMP_strip.pdb"; 

  PdbRecord[] CytosineRecords;
  String CytosineRecords_url = "dCMP_strip.pdb"; 

  PdbRecord[] GuanineRecords;
  String GuanineRecords_url = "dGMP_strip.pdb"; 

  PdbRecord[] ThymineRecords;
  String ThymineRecords_url = "TMP_strip.pdb"; 

  int recordcount;
  int NumCols=7;

  Atom a = new Atom("A");


  Nucleotide (String s){
    name = s;
  }  

  void loadAdenine() {
    //a.loadCoords();
    String[] lines = loadStrings(AdenineRecords_url);
    AdenineRecords = new PdbRecord[lines.length];
    recordcount = 0;

    // println("there are " + lines.length + "ATOMS");
    for (int i = 0; i < lines.length; i++) {
      String[] peices = splitTokens(lines[i]);
      if (peices.length == NumCols) {
        AdenineRecords[recordcount] = new PdbRecord(peices);
        recordcount++;
      }
    }

  }

  void loadCytosine() {
    //a.loadCoords();
    String[] lines = loadStrings(CytosineRecords_url);
    CytosineRecords = new PdbRecord[lines.length];
    recordcount = 0;

    // println("there are " + lines.length + "ATOMS");
    for (int i = 0; i < lines.length; i++) {
      String[] peices = splitTokens(lines[i]);
      if (peices.length == NumCols) {
        CytosineRecords[recordcount] = new PdbRecord(peices);
        recordcount++;
      }
    }
    // println(recordcount);
  }

  void loadGuanine() {
    //a.loadCoords();
    String[] lines = loadStrings(GuanineRecords_url);
    GuanineRecords = new PdbRecord[lines.length];
    recordcount = 0;

    // println("there are " + lines.length + "ATOMS");
    for (int i = 0; i < lines.length; i++) {
      String[] peices = splitTokens(lines[i]);
      if (peices.length == NumCols) {
        GuanineRecords[recordcount] = new PdbRecord(peices);
        recordcount++;
      }
    }
    //println(recordcount);
  }

  void loadThymine() {
    //a.loadCoords();
    String[] lines = loadStrings(ThymineRecords_url);
    ThymineRecords = new PdbRecord[lines.length];
    recordcount = 0;

    //println("there are " + lines.length + "ATOMS");
    for (int i = 0; i < lines.length; i++) {
      String[] peices = splitTokens(lines[i]);
      if (peices.length == NumCols) {
        ThymineRecords[recordcount] = new PdbRecord(peices);
        recordcount++;
      }
    }
    //println(recordcount);
  }

  void AdenineDisplay(int x, int y, int z, float br, float br2, float yr, int g) {
    for (int n = 0; n < recordcount; n++) {
      pushMatrix();
      translate(x, y, z);
      rotateX(br);
      rotateZ(br2);
      rotateY(yr);
      translate((AdenineRecords[n].x_coord*10+g), AdenineRecords[n].y_coord*10, AdenineRecords[n].z_coord*10);
      noStroke();
      assignOpacity((AdenineRecords[n].x_coord*10+g), AdenineRecords[n].y_coord*10, AdenineRecords[n].z_coord*10);
      AssignColor(AdenineRecords[n].Chem_Formula, opacity);
      a.renderAtom(fillcolor, 'A');
      a.spinAtom();
      //a.moveAtom();
      popMatrix();
    }
  }

  void CytosineDisplay(int x, int y, int z, float br, float br2, float yr, int g) {
    for (int n = 0; n < recordcount; n++) {
      pushMatrix();
      translate(x, y, z);
      rotateX(br);
      rotateZ(br2);
      rotateY(yr);
      translate((CytosineRecords[n].x_coord*10+g), CytosineRecords[n].y_coord*10, CytosineRecords[n].z_coord*10);
      noStroke();
      assignOpacity((CytosineRecords[n].x_coord*10+g), CytosineRecords[n].y_coord*10, CytosineRecords[n].z_coord*10);
      AssignColor(CytosineRecords[n].Chem_Formula, opacity);
      a.renderAtom(fillcolor, 'C');
      a.spinAtom();
      //a.moveAtom();
      popMatrix();
    }
  }

  void GuanineDisplay(int x, int y, int z, float br, float br2,  float yr, int g) {
    for (int n = 0; n < recordcount; n++) {
      pushMatrix();
      translate(x, y, z);
      rotateX(br);
      rotateZ(br2);
      rotateY(yr);
      translate((GuanineRecords[n].x_coord*10+g), GuanineRecords[n].y_coord*10, GuanineRecords[n].z_coord*10);
      noStroke();
      assignOpacity((GuanineRecords[n].x_coord*10+g), GuanineRecords[n].y_coord*10, GuanineRecords[n].z_coord*10);
      AssignColor(GuanineRecords[n].Chem_Formula, opacity);
      a.renderAtom(fillcolor, 'G');
      a.spinAtom();
      //a.moveAtom();
      popMatrix();
    }
  }

  void ThymineDisplay(int x, int y, int z, float br, float br2, int g) {
    for (int n = 0; n < recordcount; n++) {
      pushMatrix();
      translate(x, y, z);
      rotateX(br);
      rotateZ(br2);
      translate((ThymineRecords[n].x_coord*10+g), ThymineRecords[n].y_coord*10, ThymineRecords[n].z_coord*10);
      noStroke();
      assignOpacity((ThymineRecords[n].x_coord*10+g), ThymineRecords[n].y_coord*10, ThymineRecords[n].z_coord*10);
      opacity = int(fade);
      AssignColor(ThymineRecords[n].Chem_Formula, opacity);
      a.renderAtom(fillcolor, 'T');
      a.spinAtom();
      //a.moveAtom();
      popMatrix();
    }
  }
  
  void AssignColor(String x, int o){
          if(x.equals("H")){
        fillcolor = color(75, 75, 75, o);   //Hydrogen
      }
      else if (x.equals("O")){
        fillcolor = color(125,125,125, o);      //Oxygen
      }
      else if (x.equals("C")){
        fillcolor = color(155,155,155, o);      //Carbon
      }
      else if (x.equals("N")){
        fillcolor = color(100,100,100, o);      //Nitrogen
      }
      else if (x.equals("P")){
        fillcolor = color(200,200,200, o);      //Phosphorous
      }
  }
  
  void assignOpacity(float x, float y, float z){
      fade = screenZ(x, y, z);
      fade = 1-fade;
      fade = map(fade, 0.0, .1, 0, 255);
      opacity = int(fade);  
  }
  
}