UnityMol  0.9.6-875
UnityMol viewer / In developement
AtomCubeStyle.cs
Go to the documentation of this file.
1 
66 
67 namespace Molecule.View.DisplayAtom {
68  using System;
69  using UnityEngine;
70  using System.Collections;
71  using System.Collections.Generic;
72  using Molecule.Model;
73  using UI;
74  using Molecule.Control;
75  using System.Globalization;
76 
77  public class AtomCubeStyle : IAtomStyle {
78 
79  private float[] scale=new float[7];
80  public static ArrayList atomOrderList;
81  public static ArrayList atomOrderListArray;
82  private Camera mainCamera = null;
83 
84  public static GameObject AtomCubeParent = new GameObject("AtomCubeParent");
85 
86  private UIData.AtomType atomtype;
87  //private GameObject[] hyperballs;
88 
89  public AtomCubeStyle() {
90 
91 
92  scale[0]=(MoleculeModel.carbonScale)/100;
93  scale[1]=(MoleculeModel.nitrogenScale)/100;
94  scale[2]=(MoleculeModel.oxygenScale)/100;
95  scale[3]=(MoleculeModel.sulphurScale)/100;
96  scale[4]=(MoleculeModel.phosphorusScale)/100;
97  scale[5]=(MoleculeModel.hydrogenScale)/100;
98  scale[6]=(MoleculeModel.unknownScale)/100;
99  }
100 
101  //Create atoms according to type. Particles are created only once except if display is forced
102  public void DisplayAtoms (UIData.AtomType type_atom, bool force_display = false) {
103  if(mainCamera == null)
104  mainCamera = Camera.main;
105  UIData.shadow = false;
106 
107  if(type_atom != UIData.AtomType.particleball || !UIData.isParticlesInitialized ||force_display) {
108  //if(!UIData.isCubeLoaded){
109 
110  if(AtomCubeParent == null)
111  AtomCubeParent = new GameObject("AtomCubeParent");
112 
113  AtomCubeParent.tag = "HBCubes";
114 
115  if(MoleculeModel.atoms != null) {
116  MoleculeModel.atoms.Clear();
117  MoleculeModel.atoms=null;
118  }
119 
120  MoleculeModel.atoms=new ArrayList();
121  atomtype = type_atom;
122  DisplayAtomMethodByCube();
123  if(UIData.atomtype == UIData.AtomType.cube){
124  UIData.shadow = true;
125  UIData.isCubeLoaded = true;
126  }
127  else if(UIData.atomtype == UIData.AtomType.hyperball)
128  UIData.isHBallLoaded = true;
129  //}
130  }
131  }
132 
133 
134  private void DisplayAtomMethodByCube() {
135 
136 // ArrayList atomListByType;
137 
138  if(atomtype != UIData.AtomType.particleball && atomtype != UIData.AtomType.particleballalphablend) {
139  if(UIData.secondarystruct)
140  DisplayAtomCube(MoleculeModel.CaSplineList, MoleculeModel.CaSplineTypeList);
141  else
142  DisplayAtomCube(MoleculeModel.atomsLocationlist, MoleculeModel.atomsTypelist);
143  }
144 
145  if(UIData.secondarystruct)
146  MoleculeModel.atomsnumber=MoleculeModel.CaSplineList.Count;
147  else
148  MoleculeModel.atomsnumber=MoleculeModel.atomsLocationlist.Count;
149 
150  if(atomtype==UIData.AtomType.combinemeshball) {
151  GameObject SpriteManager=GameObject.Find("SpriteManager");
152  Meshcombine combineComp = SpriteManager.GetComponent<Meshcombine>();
153  combineComp.GoOn();
154  }
155 
156  //Aurélien : the reaction is now ready to start :)
157  Reaction.isReady = true;//The arraylist MoleculeModel.atoms contains a GameObject for each atom and can now be used in Molecule3D's Update() method.
158  }
159 
160  public static Color HexToColor(string hexColor) {
161  //Remove # if present
162  if (hexColor.IndexOf('#') != -1)
163  hexColor = hexColor.Replace("#", "");
164 
165  int red = 0;
166  int green = 0;
167  int blue = 0;
168 
169  if (hexColor.Length == 6) {
170  //#RRGGBB
171  red = int.Parse(hexColor.Substring(0, 2), NumberStyles.AllowHexSpecifier);
172  green = int.Parse(hexColor.Substring(2, 2), NumberStyles.AllowHexSpecifier);
173  blue = int.Parse(hexColor.Substring(4, 2), NumberStyles.AllowHexSpecifier);
174  } else if (hexColor.Length == 3) {
175  //#RGB
176  red = int.Parse(hexColor[0].ToString() + hexColor[0].ToString(), NumberStyles.AllowHexSpecifier);
177  green = int.Parse(hexColor[1].ToString() + hexColor[1].ToString(), NumberStyles.AllowHexSpecifier);
178  blue = int.Parse(hexColor[2].ToString() + hexColor[2].ToString(), NumberStyles.AllowHexSpecifier);
179  }
180 
181  Color hexcolor= new Color(red/255f,green/255f,blue/255f);
182  return hexcolor;
183  }
184 
185 // private ArrayList AtomListByAxisOrder(ArrayList alist)
186  public ArrayList AtomListByAxisOrder(IList alist) {
187  Debug.Log("Entering :: AtomListByAxisOrder");
188  ArrayList atomListByOrder=new ArrayList();
189 
190  for(int i=0;i<alist.Count;i++) {
191  float typenumber=0f;
192  string type;
193  if(UIData.secondarystruct)
194  type = (MoleculeModel.CaSplineTypeList[i] as AtomModel).type;
195  else
196  type = (MoleculeModel.atomsTypelist[i] as AtomModel).type;
197 
198  switch(type) {
199  case "C":
200  typenumber=0f;
201  break;
202  case "N":
203  typenumber=1f;
204  break;
205  case "O":
206  typenumber=2f;
207  break;
208  case "S":
209  typenumber=3f;
210  break;
211  case "P":
212  typenumber=4f;
213  break;
214  case "H":
215  typenumber=5f;
216  break;
217  default:
218  typenumber=6f;
219  break;
220  }
221  float[] atom=new float[5];
222  atom[0]=(alist[i] as float[])[0];
223  atom[1]=(alist[i] as float[])[1];
224  atom[2]=(alist[i] as float[])[2];
225  atom[3]=typenumber;
226  atom[4]=i;
227  atomListByOrder.Add(atom);
228  }
229 // atomListByOrder=alist;//if we write like this directly, it will change the order of alist.
230  atomListByOrder.Sort(new StructComparer());
231 
232  return atomListByOrder;
233  }
234 
235 
236 
237 
238 
239  private void DisplayAtomCube(IList coordinates, IList atomModels) {
240  List<GameObject> goList = new List<GameObject>();
241  for(int i=0; i < coordinates.Count; i++){
242  goList.Add(CreateAtomHB(i, coordinates, atomModels));
243  }
244  CubeManager.cubeGameObjects = goList.ToArray();
245 
246  if(UIData.atomtype == UIData.AtomType.hyperball) {
247  GameObject hbManagerObj = GameObject.FindGameObjectWithTag("HBallManager");
248  HBallManager hbManager = hbManagerObj.GetComponent<HBallManager>();
249  hbManager.Init();
250  }
251  else if(UIData.atomtype == UIData.AtomType.optihb){
252  GameObject hbmeshManagerObj = GameObject.FindGameObjectWithTag("HBallMeshManager");
253  HBallMeshManager hbmeshManager = hbmeshManagerObj.GetComponent<HBallMeshManager>();
254  hbmeshManager.Init();
255  }
256  else {
257  GameObject cubeManagerObj = GameObject.FindGameObjectWithTag("CubeManager");
258  CubeManager cubeManager = cubeManagerObj.GetComponent<CubeManager>();
259  cubeManager.Init();
260  }
261 
262  }
263 
264  //iType : Atom category
265  private void DisplayAtomCube(ArrayList atomsLocation,int iType) {
266  Color c = new Color();
267  Vector3 v = new Vector3();
268 
269 // int atom1number = 0;
270 // int atom2number = 0;
271  bool isxgmml = UI.GUIDisplay.file_extension=="xgmml";
272  if(isxgmml) {
273 // atom1number=AtomCubeStyle.atomOrderList.IndexOf(oratom1number);
274 // atom2number=AtomCubeStyle.atomOrderList.IndexOf(oratom2number);
275  }
276  else {
277  switch(iType) {
278  case 0:c= (MoleculeModel.carbonColor.color);v=new Vector3(1.7f*scale[0],1.7f*scale[0],1.7f*scale[0]);break;//c
279  case 1:c= (MoleculeModel.nitrogenColor.color);v=new Vector3(1.55f*scale[1],1.55f*scale[1],1.55f*scale[1]);break;//n
280  case 2:c= (MoleculeModel.oxygenColor.color);v=new Vector3(1.52f*scale[2],1.52f*scale[2],1.52f*scale[2]);break;//o
281  case 3:c= (MoleculeModel.sulphurColor.color);v=new Vector3(2.27f*scale[3],2.27f*scale[3],2.27f*scale[3]);break;//s
282  case 4:c= (MoleculeModel.phosphorusColor.color);v=new Vector3(1.18f*scale[4],1.18f*scale[4],1.18f*scale[4]);break;//p
283  case 5:c= (MoleculeModel.hydrogenColor.color);v=new Vector3(1.2f*scale[5],1.2f*scale[5],1.2f*scale[5]);break;//h
284  default:c= (MoleculeModel.unknownColor.color);v=new Vector3(1.0f*scale[6],1.0f*scale[6],1.0f*scale[6]);break;//unknown
285  }
286  }
287 
288  int Number=atomsLocation.Count;
289 // CreateAtomArray(Number);
290  for(int k=0;k<Number;k++) {
291  int order=(int)((atomOrderListArray[iType] as ArrayList)[k]);
292  if(isxgmml) {
293  float pointradius=((MoleculeModel.CSRadiusList[order]) as float[])[0];
294  c=HexToColor((MoleculeModel.CSColorList[order] as string[])[0]);
295  v=new Vector3(pointradius,pointradius,pointradius);
296  }
297 // Debug.Log(order);
298 
299  if(atomtype==UIData.AtomType.hyperball||atomtype==UIData.AtomType.cube) {
300  CreateAtomHB(iType,k,atomsLocation,c,v,order);
301 // EfficientCreateAtomHB(iType, k, atomsLocation, c, v, order);
302  }
303 
304  else if(atomtype==UIData.AtomType.raycasting)
305  CreateAtomRC(iType,k,(k+1),atomsLocation,c,v,order);
306  else if(atomtype==UIData.AtomType.rcbillboard)
307  CreateAtomRCBB(iType,k,(k+1),atomsLocation,c,v,order);
308  else if(atomtype==UIData.AtomType.hbbillboard)
309  CreateAtomHBBB(iType,k,(k+1),atomsLocation,c,v,order);
310  else if(atomtype==UIData.AtomType.rcsprite)
311  CreateAtomRCSprite(iType,k,(k+1),atomsLocation,c,v,order);
312  else if(atomtype==UIData.AtomType.multihyperball)
313  CreateAtomMtHyperBall(iType,k,(k+1),atomsLocation,c,v,order);
314  else if(atomtype==UIData.AtomType.combinemeshball)
315  CreateCombineMeshHyperBall(iType,k,(k+1),atomsLocation,c,v,order);
316  else if(atomtype==UIData.AtomType.particleball)
317  CreateAtomHB(iType,k,atomsLocation,c,v,order);
318 
319  }
320 
321  }
322 
323 /*
324  private void CreateAtomArray(int size) {
325  Debug.Log("AtomArray");
326  Debug.Log(size);
327  hyperballs = new GameObject[size];
328  GameObject first = GameObject.CreatePrimitive(PrimitiveType.Cube);
329  first.transform.parent = AtomCubeParent.transform;
330  hyperballs[0] = first;
331  for(int i=1; i<size; i++)
332  hyperballs[i] = (GameObject) GameObject.Instantiate(first);
333  }
334 */
335 
336  //iAtom : Atom index in atomLocationalist
337  private GameObject CreateAtomHB(int iAtom, IList coordinates, IList atomModels) {
338  GameObject Atom;
339 
340  if(atomtype==UIData.AtomType.hyperball)
341  Atom = (GameObject)GameObject.Instantiate(Resources.Load("CubeHBPrefab"));
342  else
343  Atom = (GameObject)GameObject.Instantiate(Resources.Load("CubeCubePrefab"));
344 
345  Atom.SetActive(true);
346  // Atom = GameObject.CreatePrimitive(PrimitiveType.Cube);
347  float[] fLocation = coordinates[iAtom] as float[];
348  Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
349 
350  AtomModel atomModel = atomModels[iAtom] as AtomModel;
351 
352  Atom.transform.Translate(location);
353  Atom.transform.parent = AtomCubeParent.transform;
354 
355  MoleculeModel.atoms.Add(Atom);
356 
357  if(atomtype==UIData.AtomType.hyperball) {
358  //Test platform to choose the good shader
359  /*RuntimePlatform platform = Application.platform;
360  switch(platform) {
361  case RuntimePlatform.WindowsPlayer:
362  case RuntimePlatform.WindowsWebPlayer:
363  case RuntimePlatform.WindowsEditor:
364  Atom.GetComponent<Renderer>().material.shader=Shader.Find("FvNano/Ball HyperBalls OpenGL 2");
365  break;
366  default :
367  Atom.GetComponent<Renderer>().material.shader=Shader.Find("FvNano/Ball HyperBalls OpenGL 2");
368 // Atom.renderer.material.shader=Shader.Find("Custom/BallImprovedZ");
369  break;
370  }*/
371 
372  // Atom.AddComponent<BallUpdateHB>();
373  if(UI.GUIDisplay.file_extension=="xgmml")
374  Atom.GetComponent<BallUpdateHB>().z=(float)(fLocation[2]);
375  }
376  else {
377  // Atom.AddComponent<BallUpdateCube>();
378  BallUpdateCube comp1 = Atom.GetComponent<BallUpdateCube>();
379  comp1.SetRayonFactor(atomModel.scale/100);
380  }
381 
382 
383  BallUpdate comp = Atom.GetComponent<BallUpdate>();
384 
385 // Debug.Log ("%%%%%%%%%%%%%%%%%%%%% Creating Atom");
386 // Debug.Log (iAtom);
387  comp.rayon = atomModel.radius;
388  comp.atomcolor = atomModel.baseColor;
389  comp.number = iAtom;
390 // Debug.Log (comp.number);
391  comp.oldrayonFactor = atomModel.scale/100; // Why division by 100 ???
392 
393  if(UI.GUIDisplay.file_extension=="xgmml") {
394  comp.rayon = ((MoleculeModel.CSRadiusList[iAtom]) as float[])[0];
395  comp.atomcolor = HexToColor((MoleculeModel.CSColorList[iAtom] as string[])[0]);
396  }
397 
398  Atom.GetComponent<Renderer>().material.SetColor("_Color", comp.atomcolor);
399 
400  comp.enabled = true;
401  comp.isSplineNode = UIData.secondarystruct;
402 
403  Atom.tag = atomModel.type;
404 
405  if(atomtype==UIData.AtomType.particleball)
406  Atom.GetComponent<Renderer>().enabled = false;
407 
408  BoxCollider collider = Atom.GetComponent<Collider>() as BoxCollider;
409  float newSize = atomModel.radius * 60 / 100;
410  collider.size = new Vector3(newSize,newSize,newSize);
411 
412  //Aurélien : Adding the atom's index to the GameObject
413  // Atom.AddComponent<AtomIndex>();
414  AtomIndex link = Atom.GetComponent<AtomIndex>();
415  link.index = (int)fLocation[3];
416 
417  return Atom;
418  }
419 
420  //iType : Atom type index (element)
421  //iAtom : Atom index in atomLocationalist
422  private void CreateAtomHB(int iType, int iAtom, ArrayList atomLocationalist, Color c, Vector3 v, int order) {
423  GameObject Atom;
424 
425  if(atomtype==UIData.AtomType.hyperball)
426  Atom = (GameObject)GameObject.Instantiate(Resources.Load("CubeHBPrefab"));
427  else
428  Atom = (GameObject)GameObject.Instantiate(Resources.Load("CubeCubePrefab"));
429 
430  Atom.SetActive(true);
431 
432 /*
433  UnityEngine.Object.Destroy(Atom.collider);
434  Object.DestroyImmediate(Atom.collider);
435  GameObject.DestroyImmediate(Atom.collider); // "good" one
436  Atom.AddComponent<Rigidbody>();
437  Atom.rigidbody.isKinematic = true;
438  Debug.Log("Atom collider?");
439  Debug.Log(Atom.collider.ToString());
440  GameObject.DestroyObject(Atom.collider);
441 */
442  float[] fLocation=atomLocationalist[iAtom] as float[];
443  Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
444 
445  Atom.transform.Translate(location);
446  Atom.GetComponent<Renderer>().material.SetColor("_Color",c);
447  Atom.transform.parent = AtomCubeParent.transform;
448 // Debug.Log(Atom.collider.ToString());
449 
450  MoleculeModel.atoms.Add(Atom);
451 
452  BallUpdate script;
453  if(atomtype==UIData.AtomType.hyperball) {
454  BallUpdateHB comp = Atom.GetComponent<BallUpdateHB>();
455  script = comp;
456  comp.rayon=(float)(v[0]);
457  comp.atomcolor=c;
458  comp.number=order;
459  comp.z=(float)(fLocation[2]);
460 // if(UI.GUIDisplay.file_extension=="xgmml")comp.xgmml=true;
461  comp.enabled = true;
462  switch(iType) {
463  case 0:
464  comp.oldrayonFactor=(MoleculeModel.carbonScale)/100;break;
465  case 1:
466  comp.oldrayonFactor=(MoleculeModel.nitrogenScale)/100;break;
467  case 2:
468  comp.oldrayonFactor=(MoleculeModel.oxygenScale)/100;break;
469  case 3:
470  comp.oldrayonFactor=(MoleculeModel.sulphurScale)/100;break;
471  case 4:
472  comp.oldrayonFactor=(MoleculeModel.phosphorusScale)/100;break;
473  case 5:
474  comp.oldrayonFactor=(MoleculeModel.hydrogenScale)/100;break;
475  default:
476  comp.oldrayonFactor=2.0f;break;
477  }
478  }
479  else {
480  // Atom.AddComponent<BallUpdateCube>();
481  BallUpdateCube comp1 = Atom.GetComponent<BallUpdateCube>();
482  script = comp1;
483 // comp1.rayon = Atom.transform.localScale.x*2;
484  comp1.rayon = (float)(v[0])*2;
485  float rayonfactor;
486  switch(iType) {
487  case 0:
488  rayonfactor=(MoleculeModel.carbonScale)/100;break;
489  case 1:
490  rayonfactor=(MoleculeModel.nitrogenScale)/100;break;
491  case 2:
492  rayonfactor=(MoleculeModel.oxygenScale)/100;break;
493  case 3:
494  rayonfactor=(MoleculeModel.sulphurScale)/100;break;
495  case 4:
496  rayonfactor=(MoleculeModel.phosphorusScale)/100;break;
497  case 5:
498  rayonfactor=(MoleculeModel.hydrogenScale)/100;break;
499  default:
500  rayonfactor=1.0f;break;
501  }
502  comp1.SetRayonFactor(rayonfactor);
503  comp1.number=order;
504  comp1.enabled = true;
505  }
506 
507  switch(iType) {
508  case 0:Atom.tag="C";break;
509  case 1:Atom.tag="N";break;
510  case 2:Atom.tag="O";break;
511  case 3:Atom.tag="S";break;
512  case 4:Atom.tag="P";break;
513  case 5:Atom.tag="H";break;
514  default:Atom.tag="X";break;
515  }
516  if(atomtype==UIData.AtomType.particleball)
517  Atom.GetComponent<Renderer>().enabled = false;
518 
519  BoxCollider collider = Atom.GetComponent<Collider>() as BoxCollider;
520  float newSize = script.rayon * 60 / 100;
521  collider.size = new Vector3(newSize,newSize,newSize);
522 
523  //Aurélien : Adding the atom's index to the GameObject
524  // Atom.AddComponent<AtomIndex>();
525  AtomIndex link = Atom.GetComponent<AtomIndex>();
526  link.index = (int)fLocation[3];
527  }
528 
529  private void CreateAtomRC(int type, int start, int end, ArrayList atomLocationalist, Color c, Vector3 v, int order) {
530  GameObject Atom;
531  Atom=GameObject.CreatePrimitive(PrimitiveType.Cube);
532  Atom.transform.parent = AtomCubeParent.transform;
533  float[] fLocation=atomLocationalist[start] as float[];
534  Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
535  Atom.transform.Translate(location);
536  Atom.GetComponent<Renderer>().material.SetColor("_Color",c);
537  MoleculeModel.atoms.Add(Atom);
538  Atom.GetComponent<Renderer>().material.shader=Shader.Find("FvNano/HyperBalls GL_D3D");
539  Atom.AddComponent<BallUpdateRC>();
540  BallUpdateRC comp = Atom.GetComponent<BallUpdateRC>();
541  comp.rayon=(float)(v[0]);
542  comp.atomcolor=c;
543  comp.number=order;
544  comp.enabled = true;
545  switch(type) {
546  case 0:Atom.tag="C";break;
547  case 1:Atom.tag="N";break;
548  case 2:Atom.tag="O";break;
549  case 3:Atom.tag="S";break;
550  case 4:Atom.tag="P";break;
551  case 5:Atom.tag="H";break;
552  default:Atom.tag="X";break;
553  }
554 
555  //Aurélien : Adding the atom's index to the GameObject
556  Atom.AddComponent<AtomIndex>();
557  AtomIndex link = Atom.GetComponent<AtomIndex>();
558  link.index = (int)fLocation[3];
559  }
560 
561  private void CreateAtomRCBB(int type,int start ,int end,ArrayList atomLocationalist,Color c,Vector3 v,int order) {
562  GameObject Atom;
563  if(UIData.toggleClip)
564  Atom=Clip4RayCasting.CreateClip();
565  else
566  Atom=GameObject.CreatePrimitive(PrimitiveType.Plane);
567 
568  float[] fLocation=atomLocationalist[start] as float[];
569  Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
570 
571  Atom.transform.Translate(location);
572  Atom.GetComponent<Renderer>().material.SetColor("_Color",c);
573  MoleculeModel.atoms.Add(Atom);
574  Atom.AddComponent<CameraFacingBillboard>();
575  Atom.GetComponent<CameraFacingBillboard>().cameraToLookAt = mainCamera;
576  Atom.transform.GetComponent<Renderer>().material.shader=Shader.Find("FvNano/HyperBalls GL_D3D");
577  Atom.AddComponent<BallUpdateRC>();
578  BallUpdateRC comp = Atom.GetComponent<BallUpdateRC>();
579  comp.rayon=(float)(v[0]);
580  comp.atomcolor=c;
581  comp.number=order;
582  comp.enabled = true;
583  switch(type) {
584  case 0:Atom.tag="C";break;
585  case 1:Atom.tag="N";break;
586  case 2:Atom.tag="O";break;
587  case 3:Atom.tag="S";break;
588  case 4:Atom.tag="P";break;
589  case 5:Atom.tag="H";break;
590  default:Atom.tag="X";break;
591  }
592 
593  //Aurélien : Adding the atom's index to the GameObject
594  Atom.AddComponent<AtomIndex>();
595  AtomIndex link = Atom.GetComponent<AtomIndex>();
596  link.index = (int)fLocation[3];
597  }
598 
599  private void CreateAtomHBBB(int type,int start ,int end,ArrayList atomLocationalist,Color c,Vector3 v,int order) {
600  GameObject Atom;
601  if(UIData.toggleClip)
602  Atom=Clip4RayCasting.CreateClip();
603  else
604  Atom=GameObject.CreatePrimitive(PrimitiveType.Plane);
605 
606  float[] fLocation=atomLocationalist[start] as float[];
607  Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
608 
609  Atom.transform.Translate(location);
610  Atom.GetComponent<Renderer>().material.SetColor("_Color",c);
611  MoleculeModel.atoms.Add(Atom);
612  Atom.AddComponent<CameraFacingBillboard>();
613  Atom.GetComponent<CameraFacingBillboard>().cameraToLookAt = mainCamera;
614  Atom.transform.GetComponent<Renderer>().material.shader=Shader.Find("FvNano/HyperBalls GL_D3D");
615  Atom.AddComponent<BallUpdateHB>();
616  BallUpdateHB comp = Atom.GetComponent<BallUpdateHB>();
617  comp.rayon=(float)(v[0]);
618  comp.atomcolor=c;
619 // Debug.Log(start+"/"+c);
620  comp.number=order;
621  comp.enabled = true;
622 
623  switch(type) {
624  case 0:Atom.tag="C";break;
625  case 1:Atom.tag="N";break;
626  case 2:Atom.tag="O";break;
627  case 3:Atom.tag="S";break;
628  case 4:Atom.tag="P";break;
629  case 5:Atom.tag="H";break;
630  default:Atom.tag="X";break;
631  }
632 
633  //Aurélien : Adding the atom's index to the GameObject
634  Atom.AddComponent<AtomIndex>();
635  AtomIndex link = Atom.GetComponent<AtomIndex>();
636  link.index = (int)fLocation[3];
637  }
638 
639  private void CreateAtomRCSprite(int type,int start ,int end,ArrayList atomLocationalist,Color c,Vector3 v,int order) {
640  LinkedSpriteManager linkedSpriteManager=null;
641  GameObject SpriteManager;
642  if(!GameObject.Find("SpriteManager")) {
643  SpriteManager=new GameObject();
644  SpriteManager.name="SpriteManager";
645  }
646  else
647  SpriteManager=GameObject.Find("SpriteManager");
648 
649  SpriteManager.GetComponent <MeshRenderer>().enabled=true;
650 
651  if(SpriteManager.GetComponent <LinkedSpriteManager>()==null) {
652  SpriteManager.AddComponent<LinkedSpriteManager>();
653  linkedSpriteManager= (LinkedSpriteManager)Component.FindObjectOfType(typeof(LinkedSpriteManager));
654  Material mat = Resources.Load("Materials/hyperballshader", typeof(Material)) as Material;
655  linkedSpriteManager.material=mat;
656  linkedSpriteManager.allocBlockSize=atomLocationalist.Count;
657  }
658  else {
659  linkedSpriteManager= (LinkedSpriteManager)Component.FindObjectOfType(typeof(LinkedSpriteManager));
660  linkedSpriteManager.allocBlockSize=atomLocationalist.Count;
661  linkedSpriteManager.enabled=true;
662  }
663  GameObject Atom;
664  float[] fLocation=atomLocationalist[start] as float[];
665  Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
666  UnityEngine.Object o;
667  o=MonoBehaviour.Instantiate(Resources.Load("HBspriteplane"),location,new Quaternion(0f,0f,0f,0f));
668  Atom=(GameObject)o;
669  MoleculeModel.atoms.Add(Atom);
670  Atom.GetComponent<Renderer>().material.SetColor("_Color",c);
671  BallUpdateHB comp = Atom.GetComponent<BallUpdateHB>();
672  comp.rayon=(float)(v[0]);
673  comp.atomcolor=c;
674  comp.number=order;
675  comp.enabled = true;
676  linkedSpriteManager.AddSprite(Atom, 1f, 1f, 0, 0, 256, 256, true);
677  switch(type) {
678  case 0:Atom.tag="C";break;
679  case 1:Atom.tag="N";break;
680  case 2:Atom.tag="O";break;
681  case 3:Atom.tag="S";break;
682  case 4:Atom.tag="P";break;
683  case 5:Atom.tag="H";break;
684  default:Atom.tag="X";break;
685  }
686 
687  //Aurélien : Adding the atom's index to the GameObject
688  Atom.AddComponent<AtomIndex>();
689  AtomIndex link = Atom.GetComponent<AtomIndex>();
690  link.index = (int)fLocation[3];
691  }
692 
693  private void CreateAtomMtHyperBall(int type,int start ,int end,ArrayList atomLocationalist,Color c,Vector3 v,int order) {
694  GameObject Atom;
695  if(!GameObject.Find("MultiHBCube")) {
696  Atom=GameObject.CreatePrimitive(PrimitiveType.Cube);
697  Atom.name="MultiHBCube";
698  Atom.transform.parent = AtomCubeParent.transform;
699  }
700  else
701  Atom=GameObject.Find("MultiHBCube");
702  float[] fLocation=atomLocationalist[start] as float[];
703  Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
704  Material newMat = new Material(Shader.Find("FvNano/HyperBalls GL_D3D"));
705  newMat.SetVector("_TexPos",location);
706  newMat.SetFloat("_Rayon",(float)(v[0])*0.1f);
707  newMat.SetColor("_Color",c);
708 
709  ArrayList materialArray= new ArrayList(Atom.transform.GetComponent<Renderer>().materials);
710  materialArray.Add(newMat);
711  Material[] array = new Material[materialArray.Count];
712  materialArray.CopyTo( array );
713  Atom.transform.GetComponent<Renderer>().materials = array;
714  switch(type) {
715  case 0:Atom.tag="C";break;
716  case 1:Atom.tag="N";break;
717  case 2:Atom.tag="O";break;
718  case 3:Atom.tag="S";break;
719  case 4:Atom.tag="P";break;
720  case 5:Atom.tag="H";break;
721  default:Atom.tag="X";break;
722  }
723  //Aurélien : Adding the atom's index to the GameObject
724  Atom.AddComponent<AtomIndex>();
725  AtomIndex link = Atom.GetComponent<AtomIndex>();
726  link.index = (int)fLocation[3];
727  }
728 
729  private void CreateCombineMeshHyperBall(int type,int start ,int end,ArrayList atomLocationalist,Color c,Vector3 v,int order) {
730  GameObject SpriteManager;
731  if(!GameObject.Find("SpriteManager")) {
732  SpriteManager=GameObject.CreatePrimitive(PrimitiveType.Cube);
733  SpriteManager.name="SpriteManager";
734  }
735  else
736  SpriteManager=GameObject.Find("SpriteManager");
737 
738  GameObject Atom;
739  if(UIData.toggleClip)
740  Atom=Clip4RayCasting.CreateClip();
741  else
742  Atom=GameObject.CreatePrimitive(PrimitiveType.Plane);
743 
744  Atom.transform.parent=SpriteManager.transform;
745  float[] fLocation=atomLocationalist[start] as float[];
746  Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
747  Atom.transform.Translate(location);
748  Atom.GetComponent<Renderer>().material.SetColor("_Color",c);
749  MoleculeModel.atoms.Add(Atom);
750  Atom.AddComponent<CameraFacingBillboard>();
751  Atom.GetComponent<CameraFacingBillboard>().cameraToLookAt = mainCamera;
752  Atom.transform.GetComponent<Renderer>().material.shader=Shader.Find("FvNano/HyperBalls GL_D3D");
753  Atom.AddComponent<BallUpdateHB>();
754  BallUpdateHB comp = Atom.GetComponent<BallUpdateHB>();
755  comp.rayon=(float)(v[0]);
756  comp.atomcolor=c;
757  comp.number=order;
758  comp.enabled = true;
759  switch(type) {
760  case 0:Atom.tag="C";break;
761  case 1:Atom.tag="N";break;
762  case 2:Atom.tag="O";break;
763  case 3:Atom.tag="S";break;
764  case 4:Atom.tag="P";break;
765  case 5:Atom.tag="H";break;
766  default:Atom.tag="X";break;
767  }
768  //Aurélien : Adding the atom's index to the GameObject
769  Atom.AddComponent<AtomIndex>();
770  AtomIndex link = Atom.GetComponent<AtomIndex>();
771  link.index = (int)fLocation[3];
772  }
773 
774 
775  }
776 }
Molecule.Model.MoleculeModel.CSColorList
static List< string[]> CSColorList
Definition: MoleculeModel.cs:218
BallUpdate.SetRayonFactor
virtual void SetRayonFactor(float rf)
Definition: BallUpdate.cs:97
HBallMeshManager.Init
override void Init()
Initalizes this instance.
Definition: HBallMeshManager.cs:33
Meshcombine.GoOn
void GoOn()
Definition: Meshcombine.cs:76
Molecule.Model.MoleculeModel.phosphorusColor
static ColorObject phosphorusColor
Definition: MoleculeModel.cs:351
UI.UIData.secondarystruct
static bool secondarystruct
Switch between all atoms and C-alpha trace or BFactor secondary structure representation.
Definition: UIData.cs:176
Molecule.Model.MoleculeModel.carbonColor
static ColorObject carbonColor
Definition: MoleculeModel.cs:347
SpriteManager.AddSprite
Sprite AddSprite(GameObject client, float width, float height, int leftPixelX, int bottomPixelY, int pixelWidth, int pixelHeight, bool billboarded)
Definition: SpriteManager.cs:492
Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube
void DisplayAtomCube(ArrayList atomsLocation, int iType)
Definition: AtomCubeStyle.cs:265
Molecule.View.DisplayAtom.AtomCubeStyle.AtomListByAxisOrder
ArrayList AtomListByAxisOrder(IList alist)
Definition: AtomCubeStyle.cs:186
UI.UIData.toggleClip
static bool toggleClip
Definition: UIData.cs:122
CubeManager.Init
override void Init()
Initializes this instance of the manager.
Definition: CubeManager.cs:13
AtomIndex.index
int index
Definition: AtomIndex.cs:7
Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtoms
void DisplayAtoms(UIData.AtomType type_atom, bool force_display=false)
Definition: AtomCubeStyle.cs:102
Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHBBB
void CreateAtomHBBB(int type, int start, int end, ArrayList atomLocationalist, Color c, Vector3 v, int order)
Definition: AtomCubeStyle.cs:599
Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomRCSprite
void CreateAtomRCSprite(int type, int start, int end, ArrayList atomLocationalist, Color c, Vector3 v, int order)
Definition: AtomCubeStyle.cs:639
Molecule.Model.MoleculeModel.atomsTypelist
static List< AtomModel > atomsTypelist
The type of each atom.
Definition: MoleculeModel.cs:104
ColorObject.color
Color color
Definition: ColorObject.cs:72
Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomMtHyperBall
void CreateAtomMtHyperBall(int type, int start, int end, ArrayList atomLocationalist, Color c, Vector3 v, int order)
Definition: AtomCubeStyle.cs:693
BallUpdate.atomcolor
Color atomcolor
Definition: BallUpdate.cs:86
Molecule.View.DisplayAtom.AtomCubeStyle.HexToColor
static Color HexToColor(string hexColor)
Definition: AtomCubeStyle.cs:160
Molecule.Model.MoleculeModel.CSRadiusList
static List< float[]> CSRadiusList
Definition: MoleculeModel.cs:217
Molecule.Model.MoleculeModel.nitrogenColor
static ColorObject nitrogenColor
Definition: MoleculeModel.cs:348
BallUpdate.number
long number
Definition: BallUpdate.cs:84
BallUpdate.rayon
float rayon
Definition: BallUpdate.cs:78
Molecule.Model.MoleculeModel.hydrogenColor
static ColorObject hydrogenColor
Definition: MoleculeModel.cs:349
Molecule.Model.MoleculeModel.oxygenColor
static ColorObject oxygenColor
Definition: MoleculeModel.cs:346
Molecule.View.DisplayAtom.AtomCubeStyle.CreateCombineMeshHyperBall
void CreateCombineMeshHyperBall(int type, int start, int end, ArrayList atomLocationalist, Color c, Vector3 v, int order)
Definition: AtomCubeStyle.cs:729
Molecule.Model.Reaction.isReady
static bool isReady
Definition: Reaction.cs:15
Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB
GameObject CreateAtomHB(int iAtom, IList coordinates, IList atomModels)
Definition: AtomCubeStyle.cs:337
Molecule.Model.MoleculeModel.CaSplineList
static List< float[]> CaSplineList
The coordinates of each Carbon alpha in the CA-Spline.
Definition: MoleculeModel.cs:99
UI.UIData
!WiP Includes FLAGS of GUI.
Definition: UIData.cs:78
UI.UIData.isParticlesInitialized
static bool isParticlesInitialized
Definition: UIData.cs:101
BallUpdate.isSplineNode
bool isSplineNode
Definition: BallUpdate.cs:90
SpriteManager.material
Material material
Definition: SpriteManager.cs:240
UI.GUIDisplay
!WiP manage GUI, and provide static strings for the GUI.
Definition: GUIDisplay.cs:94
UI.GUIDisplay.file_extension
static string file_extension
Definition: GUIDisplay.cs:121
Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomRCBB
void CreateAtomRCBB(int type, int start, int end, ArrayList atomLocationalist, Color c, Vector3 v, int order)
Definition: AtomCubeStyle.cs:561
UI.UIData.isCubeLoaded
static bool isCubeLoaded
Definition: UIData.cs:103
Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomRC
void CreateAtomRC(int type, int start, int end, ArrayList atomLocationalist, Color c, Vector3 v, int order)
Definition: AtomCubeStyle.cs:529
Molecule.Model.MoleculeModel.unknownColor
static ColorObject unknownColor
Definition: MoleculeModel.cs:352
Clip4RayCasting.CreateClip
static GameObject CreateClip()
Definition: Clip4RayCasting.cs:71
BallUpdate.oldrayonFactor
float oldrayonFactor
Definition: BallUpdate.cs:80
Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube
void DisplayAtomCube(IList coordinates, IList atomModels)
Definition: AtomCubeStyle.cs:239
UI.UIData.atomtype
static AtomType atomtype
Definition: UIData.cs:139
HBallManager.Init
override void Init()
Initalizes this instance.
Definition: HBallManager.cs:99
Molecule.Model.MoleculeModel.sulphurColor
static ColorObject sulphurColor
Definition: MoleculeModel.cs:350
UI.UIData.isHBallLoaded
static bool isHBallLoaded
Definition: UIData.cs:105
UI.UIData.shadow
static bool shadow
Definition: UIData.cs:198
CubeManager.cubeGameObjects
static GameObject[] cubeGameObjects
Definition: CubeManager.cs:11
Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB
void CreateAtomHB(int iType, int iAtom, ArrayList atomLocationalist, Color c, Vector3 v, int order)
Definition: AtomCubeStyle.cs:422
Molecule.Model.MoleculeModel.CaSplineTypeList
static List< AtomModel > CaSplineTypeList
Type of each carbon alpha in the CA-Spline.
Definition: MoleculeModel.cs:236
UI
Definition: GUIDisplay.cs:66
Molecule.Model.MoleculeModel.atomsLocationlist
static List< float[]> atomsLocationlist
The coordinates of each atom.
Definition: MoleculeModel.cs:79