UnityMol  0.9.6-875
UnityMol viewer / In developement
GuidedNavigationManager.cs
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1 using UnityEngine;
2 using System.Collections;
3 using System.Collections.Generic;
4 using UI;
5 using GuidedNav;
6 using Molecule.Model;
7 using System;
8 using UnityEngine.EventSystems;
9 
10 public class GuidedNavigationManager {
11 
13  private GameObject originPoint;
14  private GameObject symmetryAxis;
15 
16  void OnEnable(){
17  Init();
18 
19  }
20  public void Init(){
21  GNParameters.mainCamera = Camera.main.gameObject;
22  }
23 
25  public void CreateAxeAndOrigin(){
26  originPoint = GameObject.CreatePrimitive (PrimitiveType.Sphere);
27  originPoint.transform.position = new Vector3 (0, 1, 0);
28  originPoint.transform.localScale = new Vector3 (4, 4, 4);
29 
30  symmetryAxis = GameObject.CreatePrimitive (PrimitiveType.Cylinder);
31  symmetryAxis.transform.position = new Vector3 (0, 1, 0);
32  symmetryAxis.transform.localScale = new Vector3 (1, (MoleculeModel.MaxValue.y - MoleculeModel.MinValue.y), 1);
33  symmetryAxis.GetComponent<Renderer>().material.color = Color.red;
34  }
35 
37  public void DestroyAxeAndOrigin(){
38  GameObject.Destroy(originPoint);
39  GameObject.Destroy(symmetryAxis);
40  }
41 
42  public void Clear(){
43  DestroyAxeAndOrigin();
44  UIData.guided = false;
45  GuidedNavigationOldGUI.showGuidedMenu = false;
46  GNParameters.ghost_target_instantiate = false;
47  GameObject.Destroy(GNParameters.ghost_target);
48  GameObject.Destroy(GNParameters.ghost_camera);
49  }
50 
51  public void UpdateManager(){
52  if(GNParameters.mainCamera == null)
53  Init();
54  if (UIData.guided) {
55 
56 
57  Debug.DrawRay (GNParameters.mainCamera.transform.position, GNParameters.mainCamera.transform.up * 5, Color.red);
58 
59  //Automatic constrained navigation up
60  if (Input.GetKeyUp (KeyCode.U)) {
61  GNParameters.navigationDown = false;
62  GNParameters.navigationUp = !GNParameters.navigationUp;
63 
64  }
65 
66  //Automatic constrained navigation down
67  if (Input.GetKeyUp (KeyCode.J)) {
68  GNParameters.navigationUp = false;
69  GNParameters.navigationDown = !GNParameters.navigationDown;
70  }
71 
72  //Enter panoramic mode
73  if (Input.GetKeyUp (KeyCode.I)) {
74  GNParameters.panoramic = !GNParameters.panoramic;
75  Debug.Log ("panoramic " + GNParameters.panoramic);
76 
77  if (!GNParameters.panoramic) {
78  GNParameters.reset_panoramic = true;
79  maxCamera.weight_cam = 0.0f;
80  }
81  }
82 
83  //Enter jump mode
84  if (Input.GetKeyUp (KeyCode.M)) {
85  GNParameters.monomer_jump = !GNParameters.monomer_jump;
86  Debug.Log ("monomer jump: " + GNParameters.monomer_jump);
87  }
88 
89  if (Input.GetKeyUp (KeyCode.L))
90  GNParameters.near_spread = !GNParameters.near_spread;
91 
92  if (GNParameters.near_spread)
93  NearSpreading ();
94 
95  // If the camera has not been reoriented after the molecule reorientation
96  // Is the molecule even reoriented anytime?
97  if (!GNParameters.reoriented) {
98  GNParameters.mainCamera.transform.eulerAngles = new Vector3 (0, GNParameters.mainCamera.transform.eulerAngles.y, 0);
99  GNParameters.reoriented = true;
100  }
101  LateUpdateManager();
102  }
103 
104  }
105  void LateUpdateManager(){
106 
107  if(!UIData.guided)
108  return;
109 
110  if (!maxCamera.cameraStop) {
111  keyboard ();
112 
113 
114  if (!GNParameters.mainCamera.GetComponent<Camera>().orthographic) { // only if the camera is in perspective mode
115  if (UIData.newUIActivated && !EventSystem.current.IsPointerOverGameObject ()) {
116  maxCamera.desiredDistance -= Input.GetAxis ("Mouse ScrollWheel") * Time.deltaTime * maxCamera.zoomRate;// * Mathf.Abs(desiredDistance);
117  }
118  if (maxCamera.desiredDistance != maxCamera.currentDistance) {
119  //currentDistance = Vector3.Distance (transform.position, target.position);
120  GNParameters.guidedzoom = true;
121  }
122  }
123  }
124 
125 
126  if (GNParameters.navigationUp) {
127  if(Vector3.Distance(GNParameters.mainCamera.transform.position, new Vector3(0, GNParameters.mainCamera.transform.position.y, 0)) > 4.0)
128  goUpConstrained();
129  }
130 
131 
132  if(GNParameters.navigationDown){
133  if(Vector3.Distance(GNParameters.mainCamera.transform.position, new Vector3(0, GNParameters.mainCamera.transform.position.y, 0)) > 4.0)
134  goDownConstrained();
135  }
136 
137  if(GNParameters.panoramic){
138  Vector3 v = GNParameters.mainCamera.transform.position;
139  maxCamera.weight_cam += Time.deltaTime ;
140  GNParameters.mainCamera.transform.position = Vector3.Lerp (v, new Vector3(0, v.y, 0), maxCamera.weight_cam);
141  }
142  else if(GNParameters.reset_panoramic){
143  Debug.Log ("Go back from panoramic view to normal view");
144  Vector3 v = GNParameters.mainCamera.transform.position;
145  maxCamera.weight_cam += Time.deltaTime ;
146  GNParameters.mainCamera.transform.position = Vector3.Lerp (v, new Vector3(-GNParameters.mainCamera.transform.forward.x * 100, v.y, -GNParameters.mainCamera.transform.forward.z * 100), maxCamera.weight_cam);
147  if(GNParameters.mainCamera.transform.position.Equals(new Vector3(-GNParameters.mainCamera.transform.forward.x * 100, v.y, -GNParameters.mainCamera.transform.forward.z * 100))){
148  GNParameters.reset_panoramic = false;
149  maxCamera.weight_cam = 0.0f;
150  }
151  }
152 
153  if(UIData.optim_view)
154  {
155  if(!GNParameters.ghost_target_instantiate){
156  GNParameters.ghost_target = GameObject.CreatePrimitive (PrimitiveType.Sphere);
157  GNParameters.ghost_target.name = "Target";
158  GNParameters.ghost_target.GetComponent<Renderer>().material.color = Color.magenta;
159  GNParameters.ghost_target.transform.localScale = new Vector3(4.0f, 4.0f, 4.0f);
160  GNParameters.ghost_target.transform.position = GNParameters.optim_target;
161  GNParameters.ghost_target.SetActive(true);
162  GNParameters.ghost_camera = GameObject.CreatePrimitive (PrimitiveType.Sphere);
163  GNParameters.ghost_camera.name = "CameraPOV";
164  GNParameters.ghost_camera.GetComponent<Renderer>().material.color = Color.cyan;
165  GNParameters.ghost_camera.transform.localScale = new Vector3(3.0f, 3.0f, 3.0f);
166  GNParameters.ghost_camera.transform.position = GNParameters.optim_user_cam_pos;
167  GNParameters.ghost_camera.SetActive(true);
168  GNParameters.ghost_target_instantiate = true;
169  }
170  if(GNParameters.mainCamera.transform.position != GNParameters.optim_user_cam_pos)
171  {
172  GNParameters.mainCamera.transform.position = Vector3.SmoothDamp(GNParameters.mainCamera.transform.position, GNParameters.optim_user_cam_pos, ref GNParameters.velocity, 3.0f);
173  GNParameters.mainCamera.transform.LookAt(GNParameters.optim_target);
174  }
175  else{
176  Debug.Log ("LookAt phase");
177  Quaternion lookat = Quaternion.LookRotation(GNParameters.optim_target - GNParameters.mainCamera.transform.position);
178  GNParameters.mainCamera.transform.rotation = Quaternion.Slerp(GNParameters.mainCamera.transform.rotation, lookat, Time.deltaTime);
179  }
180  }
181  if (GNParameters.next_right && GNParameters.rotation_done < 360/MoleculeModel.existingChain.Count){
182  GNParameters.mainCamera.transform.RotateAround(Vector3.zero, Vector3.up, - (360/MoleculeModel.existingChain.Count) * Time.deltaTime);
183  GNParameters.rotation_done += (360/MoleculeModel.existingChain.Count) * Time.deltaTime;
184  }
185  else if (GNParameters.next_left && GNParameters.rotation_done < 360/MoleculeModel.existingChain.Count){
186  GNParameters.mainCamera.transform.RotateAround(Vector3.zero, Vector3.up, (360/MoleculeModel.existingChain.Count) * Time.deltaTime);
187  GNParameters.rotation_done += (360/MoleculeModel.existingChain.Count) * Time.deltaTime;;
188  }
189  else if (GNParameters.rotation_done > 360/MoleculeModel.existingChain.Count){
190  GNParameters.next_right = false;
191  GNParameters.next_left = false;
192  GNParameters.rotation_done = 0.0f;
193  }
194 
195  // Temporary
196  if(GNParameters.guidedzoom){
197  //Dive into the channel if zoom above or under the structure
198  if((Vector3.Distance(GNParameters.mainCamera.transform.position , maxCamera.target.position) < 100) && GNParameters.isabove){
199  GNParameters.near_spread = false;
200  if(GNParameters.mainCamera.transform.position.y <= maxCamera.target.position.y+20)
201  maxCamera.target.position = new Vector3(0, maxCamera.target.position.y-1, 0);
202  GNParameters.mainCamera.transform.LookAt(maxCamera.target.position);
203  GNParameters.mainCamera.transform.Translate(new Vector3(0, 0, Input.GetAxis ("Mouse ScrollWheel") * Time.deltaTime * maxCamera.zoomRate));
204  }
205  else if (Vector3.Distance (GNParameters.mainCamera.transform.position, maxCamera.target.position) < 100 && GNParameters.isunder){
206  GNParameters.near_spread = false;
207  if(GNParameters.mainCamera.transform.position.y >= maxCamera.target.position.y-20)
208  maxCamera.target.position = new Vector3(0, maxCamera.target.position.y+1, 0);
209  GNParameters.mainCamera.transform.LookAt (maxCamera.target.position);
210  GNParameters.mainCamera.transform.Translate (new Vector3(0, 0, Input.GetAxis ("Mouse ScrollWheel") * Time.deltaTime * maxCamera.zoomRate));
211  }
212  else
213  GNParameters.mainCamera.transform.Translate(new Vector3(0, 0, Input.GetAxis ("Mouse ScrollWheel") * Time.deltaTime * maxCamera.zoomRate));
214  GNParameters.guidedzoom = false;
215  }
216 
217  }
218 
219  void keyboard(){
220  /*
221  * X Rotation
222  */
223 
224  if (Input.GetButton ("Guided Navigation Rotate X Right")){
225  GNParameters.nav_speed = (float) Math.Sqrt(Math.Abs (MoleculeModel.MinValue.y) + Math.Abs (MoleculeModel.MaxValue.y)) * (float) Math.Sqrt(Vector3.Distance(GNParameters.mainCamera.transform.position, maxCamera.target.position));
226  GNParameters.nav_speed *= 0.02f;
227  if (GNParameters.monomer_jump) {
228  GNParameters.next_right = true;
229  }
230 
231  GNParameters.mainCamera.transform.RotateAround( new Vector3(0, GNParameters.mainCamera.transform.position.y, 0), new Vector3(0, -1, 0), 3.0f* GNParameters.nav_speed);
232  Debug.Log(GNParameters.mainCamera.transform.up);
233 
234  }
235 
236  if (Input.GetButton ("Guided Navigation Rotate X Left")) {
237 
238  if (GNParameters.monomer_jump) {
239  GNParameters.next_left = true;
240  } else {
241  GNParameters.mainCamera.transform.RotateAround( new Vector3(0, GNParameters.mainCamera.transform.position.y, 0), new Vector3(0, 1, 0), 3.0f* GNParameters.nav_speed);
242  Debug.Log(GNParameters.mainCamera.transform.up);
243  }
244 
245  }
246 
247 
248 
249  if (Input.GetButton ("Guided Navigation Rotate Y Down")){
250 
251  if(GNParameters.panoramic){
252  Vector3 v = GNParameters.mainCamera.transform.position;
253  GNParameters.mainCamera.transform.eulerAngles = new Vector3 (0, GNParameters.mainCamera.transform.eulerAngles.y, 0);
254  v.y -= 1.0f;
255  GNParameters.mainCamera.transform.position = v;
256  }
257  else{
258  if(Vector3.Distance(GNParameters.mainCamera.transform.position, new Vector3(0, GNParameters.mainCamera.transform.position.y, 0)) > 4.0)
259  goDownConstrained();
260  }
261  }
262 
263  if (Input.GetButton ("Guided Navigation Rotate Y Up")){
264 
265  if(GNParameters.panoramic){
266  Vector3 v = GNParameters.mainCamera.transform.position;
267  GNParameters.mainCamera.transform.eulerAngles = new Vector3 (0, GNParameters.mainCamera.transform.eulerAngles.y, 0);
268  v.y += 1.0f;
269  GNParameters.mainCamera.transform.position = v;
270  }
271  else{
272  if(Vector3.Distance(GNParameters.mainCamera.transform.position, new Vector3(0, GNParameters.mainCamera.transform.position.y, 0)) > 4.0)
273  goUpConstrained();
274  }
275 
276  }
277 
279 
280  if (Input.GetKey (KeyCode.KeypadPlus) || Input.GetKey (KeyCode.B))
281  {
282  Debug.Log ("Spreading");
283  Spreading();
284  }
285 
286  if (Input.GetKey (KeyCode.KeypadMinus) || Input.GetKey(KeyCode.V))
287  Narrowing();
288 
289  if (Input.GetKey (KeyCode.KeypadMultiply) || Input.GetKey(KeyCode.T))
290  ResetChainsPos();
291 
292 
294  if(UIData.optim_view){
295  if(Input.GetKey (KeyCode.Keypad1))
296  GNParameters.optim_user_cam_pos = GNParameters.optim_cam_position[0];
297 
298  if(Input.GetKey (KeyCode.Keypad2))
299  GNParameters.optim_user_cam_pos = GNParameters.optim_cam_position[1];
300 
301  if(Input.GetKey (KeyCode.Keypad3))
302  GNParameters.optim_user_cam_pos = GNParameters.optim_cam_position[2];
303 
304  if(Input.GetKey (KeyCode.Keypad4))
305  GNParameters.optim_user_cam_pos = GNParameters.optim_cam_position[3];
306  if(Input.GetKey (KeyCode.O))
307  UIData.optim_view = false;
308  ReorientCamera();
309  }
310 
311  }
312 
316  private void NearSpreading(){
317  UIData.spread_tree = true;
318  if(GNParameters.rep == ""){
319  GNParameters.atomtree = AtomTree.Build();
320  }
321  GNParameters.rep = GNParameters.atomtree.GetClosestAtomType(GNParameters.mainCamera.transform.position);
322  GNParameters.closeatom = MoleculeModel.atomsLocationlist[int.Parse(GNParameters.rep)];
323  GNParameters.poscloseatom = new Vector3(GNParameters.closeatom[0], GNParameters.closeatom[1], GNParameters.closeatom[2]);
324  GNParameters.distclose = Vector3.Distance (GNParameters.mainCamera.transform.position, GNParameters.poscloseatom); // Distance Camera / Closest atom;
325  if((GNParameters.distclose < 15) && GNParameters.comp_spread < 0.3)
326  Spreading ();
327  else if ((GNParameters.distclose > 15) && GNParameters.comp_spread != 0)
328  ResetChainsPos ();
329  UIData.spread_tree = false;
330  }
331 
333  private void SpreadCAlpha(){
334  GNParameters.hballs = GameObject.FindObjectsOfType(typeof(BallUpdateHB)) as BallUpdateHB[];
335  Molecule.View.DisplayMolecule.DestroyBonds();
336 
337  int hballNumber;
338  string atomChain;
339  BallUpdateHB ball;
340 
341  for (int i=0; i<GNParameters.hballs.Length; i++) {
342  hballNumber = (int)GNParameters.hballs[i].number;
343  atomChain = MoleculeModel.CaSplineChainList[hballNumber];
344  ball = GNParameters.hballs[i];
345 
346  if(atomChain == "A")
347  ball.transform.Translate(GNParameters.spreadA);
348  if(atomChain == "B")
349  ball.transform.Translate(GNParameters.spreadB);
350  if(atomChain == "C")
351  ball.transform.Translate(GNParameters.spreadC);
352  if(atomChain == "D")
353  ball.transform.Translate(GNParameters.spreadD);
354  if(atomChain == "E")
355  ball.transform.Translate(GNParameters.spreadE);
356  }
357 
358  Molecule.View.DisplayMolecule.ChangeRepresentation(UIData.atomtype,UIData.bondtype);
359 
360  }
361 
363  private void SpreadHyperballs(){
364  GNParameters.hballs = GameObject.FindObjectsOfType(typeof(BallUpdateHB)) as BallUpdateHB[];
365  Molecule.View.DisplayMolecule.DestroyBonds();
366 
367  int hballNumber;
368  string atomChain;
369  BallUpdateHB ball;
370 
371  for (int i=0; i<GNParameters.hballs.Length; i++) {
372  hballNumber = (int)GNParameters.hballs[i].number;
373  atomChain = MoleculeModel.atomsChainList[hballNumber];
374  ball = GNParameters.hballs[i];
375 
376  if(atomChain == "A")
377  ball.transform.Translate(GNParameters.spreadA);
378  if(atomChain == "B")
379  ball.transform.Translate(GNParameters.spreadB);
380  if(atomChain == "C")
381  ball.transform.Translate(GNParameters.spreadC);
382  if(atomChain == "D")
383  ball.transform.Translate(GNParameters.spreadD);
384  if(atomChain == "E")
385  ball.transform.Translate(GNParameters.spreadE);
386  }
387 
388  Molecule.View.DisplayMolecule.ChangeRepresentation(UIData.atomtype,UIData.bondtype);
389 
390  }
391 
393  private void SpreadSpheres(){
394  GNParameters.sballs = GameObject.FindObjectsOfType(typeof(BallUpdateSphere)) as BallUpdateSphere[];
395  Molecule.View.DisplayMolecule.DestroyBonds();
396 
397  int sballNumber;
398  string atomChain;
399  BallUpdateSphere ball;
400 
401  if(GNParameters.comp_spread<2){
402  for (int i=0; i<GNParameters.sballs.Length; i++) {
403  sballNumber = (int)GNParameters.sballs[i].number;
404  atomChain = MoleculeModel.atomsChainList[sballNumber];
405  ball = GNParameters.sballs[i];
406 
407  if(atomChain == "A")
408  ball.transform.Translate(GNParameters.spreadA);
409  if(atomChain == "B")
410  ball.transform.Translate(GNParameters.spreadB);
411  if(atomChain == "C")
412  ball.transform.Translate(GNParameters.spreadC);
413  if(atomChain == "D")
414  ball.transform.Translate(GNParameters.spreadD);
415  if(atomChain == "E")
416  ball.transform.Translate(GNParameters.spreadE);
417  }
418  }else{
419  // Spread the upper subunit up.
420  for (int i=0; i<GNParameters.sballs.Length; i++) {
421  sballNumber = (int)GNParameters.sballs[i].number;
422  atomChain = MoleculeModel.atomsChainList[sballNumber];
423  ball = GNParameters.sballs[i];
424  int residueId = MoleculeModel.residueIds[sballNumber];
425 
426  if(residueId < GNParameters.reslim)
427  {
428  if(atomChain == "A"){
429  ball.transform.Translate(GNParameters.spreadA1);
430  }
431  if(atomChain == "B"){
432  ball.transform.Translate(GNParameters.spreadB1);
433  }
434  if(atomChain == "C"){
435  ball.transform.Translate(GNParameters.spreadC1);
436  }
437  if(atomChain == "D"){
438  ball.transform.Translate(GNParameters.spreadD1);
439  }
440  if(atomChain == "E"){
441  ball.transform.Translate(GNParameters.spreadE1);
442  }
443  }
444  else
445  {
446  if(atomChain == "A"){
447  ball.transform.Translate(GNParameters.spreadA2);
448  }
449  if(atomChain == "B"){
450  ball.transform.Translate(GNParameters.spreadB2);
451  }
452  if(atomChain == "C"){
453  ball.transform.Translate(GNParameters.spreadC2);
454  }
455  if(atomChain == "D"){
456  ball.transform.Translate(GNParameters.spreadD2);
457  }
458  if(atomChain == "E"){
459  ball.transform.Translate(GNParameters.spreadE2);
460  }
461  }
462  }
463  }
464  }
465 
467  private void SpreadSecondaryStructure(){
468  GameObject[] ribA = GameObject.FindGameObjectsWithTag("RibbonObjA");
469  GameObject[] ribB = GameObject.FindGameObjectsWithTag("RibbonObjB");
470  GameObject[] ribC = GameObject.FindGameObjectsWithTag("RibbonObjC");
471  GameObject[] ribD = GameObject.FindGameObjectsWithTag("RibbonObjD");
472  GameObject[] ribE = GameObject.FindGameObjectsWithTag("RibbonObjE");
473 
474  if(GNParameters.comp_spread > 2 && UIData.isGLIC){
475  if(UIData.guided){
476  ribA[0].transform.Translate(GNParameters.spreadE1);
477  ribA[1].transform.Translate (GNParameters.spreadE2);
478  ribB[0].transform.Translate(GNParameters.spreadD1);
479  ribB[1].transform.Translate (GNParameters.spreadD2);
480  ribC[0].transform.Translate(GNParameters.spreadC1);
481  ribC[1].transform.Translate (GNParameters.spreadC2);
482  ribD[0].transform.Translate(GNParameters.spreadB1);
483  ribD[1].transform.Translate (GNParameters.spreadB2);
484  ribE[0].transform.Translate(GNParameters.spreadA1);
485  ribE[1].transform.Translate (GNParameters.spreadA2);
486  }else{
487  ribA[0].transform.Translate(GNParameters.spreadA1);
488  ribA[1].transform.Translate (GNParameters.spreadA2);
489  ribB[0].transform.Translate(GNParameters.spreadB1);
490  ribB[1].transform.Translate (GNParameters.spreadB2);
491  ribC[0].transform.Translate(GNParameters.spreadC1);
492  ribC[1].transform.Translate (GNParameters.spreadC2);
493  ribD[0].transform.Translate(GNParameters.spreadD1);
494  ribD[1].transform.Translate (GNParameters.spreadD2);
495  ribE[0].transform.Translate(GNParameters.spreadE1);
496  ribE[1].transform.Translate (GNParameters.spreadE2);
497  }
498  }else{
499 
500  foreach( GameObject rib in ribC)
501  rib.transform.Translate(GNParameters.spreadC);
502 
503  if(UIData.guided)
504  {
505  foreach( GameObject rib in ribA)
506  {
507  rib.transform.Translate(GNParameters.spreadE);
508  }
509  foreach( GameObject rib in ribB)
510  {
511  rib.transform.Translate(GNParameters.spreadD);
512  }
513  foreach( GameObject rib in ribD)
514  {
515  rib.transform.Translate(GNParameters.spreadB);
516  }
517  foreach( GameObject rib in ribE)
518  {
519  rib.transform.Translate(GNParameters.spreadA);
520  }
521  }
522  else
523  {
524  foreach( GameObject rib in ribA)
525  {
526  rib.transform.Translate(GNParameters.spreadA);
527  }
528  foreach( GameObject rib in ribB)
529  {
530  rib.transform.Translate(GNParameters.spreadB);
531  }
532  foreach( GameObject rib in ribD)
533  {
534  rib.transform.Translate(GNParameters.spreadD);
535  }
536  foreach( GameObject rib in ribE)
537  {
538  rib.transform.Translate(GNParameters.spreadE);
539  }
540  }
541  }
542  }
543 
547  private void Spreading(){
548  computeSpreadingVector();
549  GNParameters.comp_spread+=0.1f;
550  GNParameters.comp_spread = Math.Round (GNParameters.comp_spread, 1);
551  Debug.Log("comp_spread "+GNParameters.comp_spread );
552  if(UIData.isGLIC){
553  Debug.Log ("isGLIC = true");
554  //Second step spreading
555  computeSpreadPart(out GNParameters.spreadA1, out GNParameters.spreadA2, "A");
556  computeSpreadPart(out GNParameters.spreadB1, out GNParameters.spreadB2, "B");
557  computeSpreadPart(out GNParameters.spreadC1, out GNParameters.spreadC2, "C");
558  computeSpreadPart(out GNParameters.spreadD1, out GNParameters.spreadD2, "D");
559  computeSpreadPart(out GNParameters.spreadE1, out GNParameters.spreadE2, "E");
560  }
561 
562  if(SecondaryStructureOldGUI.toggle_SEC_STRUCT){
563  SpreadSecondaryStructure();
564  }
565 
566  if(UIData.atomtype == UIData.AtomType.hyperball){
567  if(UIData.secondarystruct){
568  SpreadCAlpha();
569  }else{
570  SpreadHyperballs();
571  }
572  }
573 
574  if(UIData.atomtype == UIData.AtomType.sphere){
575  SpreadSpheres();
576  } // End if Sphere
577  }// End Spreading
578 
580  private void NarrowCAlpha(){
581  GenericManager atomManager;
582  GenericManager bondManager;
583 
584  int hballNumber;
585  string atomChain;
586  BallUpdateHB ball;
587 
588  atomManager = UnityMolMain.getCurrentAtomManager();
589  bondManager = UnityMolMain.getCurrentBondManager();
590  GNParameters.hballs = GameObject.FindObjectsOfType(typeof(BallUpdateHB)) as BallUpdateHB[];
591 
592  for (int i=0; i<GNParameters.hballs.Length; i++) {
593  hballNumber = (int)GNParameters.hballs[i].number;
594  atomChain = MoleculeModel.CaSplineChainList[hballNumber];
595  ball = GNParameters.hballs[i];
596 
597  if(atomChain == "A")
598  ball.transform.Translate(-GNParameters.spreadA);
599  if(atomChain == "B")
600  ball.transform.Translate(-GNParameters.spreadB);
601  if(atomChain == "C")
602  ball.transform.Translate(-GNParameters.spreadC);
603  if(atomChain == "D")
604  ball.transform.Translate(-GNParameters.spreadD);
605  if(atomChain == "E")
606  ball.transform.Translate(-GNParameters.spreadE);
607  }
608 
609  bondManager.ResetPositions();
610 
611  Molecule.View.DisplayMolecule.ChangeRepresentation(UIData.atomtype,UIData.bondtype);
612 
613  }
614 
616  private void NarrowHyperballs(){
617  GenericManager atomManager;
618  GenericManager bondManager;
619 
620  int hballNumber;
621  string atomChain;
622  BallUpdateHB ball;
623 
624  atomManager = UnityMolMain.getCurrentAtomManager();
625  bondManager = UnityMolMain.getCurrentBondManager();
626  GNParameters.hballs = GameObject.FindObjectsOfType(typeof(BallUpdateHB)) as BallUpdateHB[];
627 
628  for (int i=0; i<GNParameters.hballs.Length; i++) {
629  hballNumber = (int)GNParameters.hballs[i].number;
630  atomChain = MoleculeModel.atomsChainList[hballNumber];
631  ball = GNParameters.hballs[i];
632 
633  if(atomChain == "A")
634  ball.transform.Translate(-GNParameters.spreadA);
635  if(atomChain == "B")
636  ball.transform.Translate(-GNParameters.spreadB);
637  if(atomChain == "C")
638  ball.transform.Translate(-GNParameters.spreadC);
639  if(atomChain == "D")
640  ball.transform.Translate(-GNParameters.spreadD);
641  if(atomChain == "E")
642  ball.transform.Translate(-GNParameters.spreadE);
643  }
644 
645  bondManager.ResetPositions();
646 
647  Molecule.View.DisplayMolecule.ChangeRepresentation(UIData.atomtype,UIData.bondtype);
648 
649  }
650 
652  private void NarrowSpheres(){
653  int sballNumber;
654  string atomChain;
655  BallUpdateSphere ball;
656 
657  GNParameters.sballs = GameObject.FindObjectsOfType(typeof(BallUpdateSphere)) as BallUpdateSphere[];
658 
659  for (int i=0; i<GNParameters.sballs.Length; i++) {
660  sballNumber = (int)GNParameters.sballs[i].number;
661  atomChain = MoleculeModel.atomsChainList[sballNumber];
662  ball = GNParameters.sballs[i];
663 
664  if(atomChain == "A")
665  ball.transform.Translate(-GNParameters.spreadA);
666  if(atomChain == "B")
667  ball.transform.Translate(-GNParameters.spreadB);
668  if(atomChain == "C")
669  ball.transform.Translate(-GNParameters.spreadC);
670  if(atomChain == "D")
671  ball.transform.Translate(-GNParameters.spreadD);
672  if(atomChain == "E")
673  ball.transform.Translate(-GNParameters.spreadE);
674  }
675  }
676 
677  private void NarrowSecondaryStructure(){
678  GameObject[] ribA = GameObject.FindGameObjectsWithTag("RibbonObjA");
679  GameObject[] ribB = GameObject.FindGameObjectsWithTag("RibbonObjB");
680  GameObject[] ribC = GameObject.FindGameObjectsWithTag("RibbonObjC");
681  GameObject[] ribD = GameObject.FindGameObjectsWithTag("RibbonObjD");
682  GameObject[] ribE = GameObject.FindGameObjectsWithTag("RibbonObjE");
683 
684  if(GNParameters.comp_spread > 2 && UIData.isGLIC){
685 
686  if(UIData.guided){
687  ribA[0].transform.Translate(-GNParameters.spreadE1);
688  ribA[1].transform.Translate (-GNParameters.spreadE2);
689  ribB[0].transform.Translate(-GNParameters.spreadD1);
690  ribB[1].transform.Translate (-GNParameters.spreadD2);
691  ribC[0].transform.Translate(-GNParameters.spreadC1);
692  ribC[1].transform.Translate (-GNParameters.spreadC2);
693  ribD[0].transform.Translate(-GNParameters.spreadB1);
694  ribD[1].transform.Translate (-GNParameters.spreadB2);
695  ribE[0].transform.Translate(-GNParameters.spreadA1);
696  ribE[1].transform.Translate (-GNParameters.spreadA2);
697  }else{
698  ribA[0].transform.Translate(-GNParameters.spreadA1);
699  ribA[1].transform.Translate (-GNParameters.spreadA2);
700  ribB[0].transform.Translate(-GNParameters.spreadB1);
701  ribB[1].transform.Translate (-GNParameters.spreadB2);
702  ribC[0].transform.Translate(-GNParameters.spreadC1);
703  ribC[1].transform.Translate (-GNParameters.spreadC2);
704  ribD[0].transform.Translate(-GNParameters.spreadD1);
705  ribD[1].transform.Translate (-GNParameters.spreadD2);
706  ribE[0].transform.Translate(-GNParameters.spreadE1);
707  ribE[1].transform.Translate (-GNParameters.spreadE2);
708  }
709  }else{
710 
711  foreach( GameObject rib in ribC)
712  rib.transform.Translate(-GNParameters.spreadC);
713 
714  if(UIData.guided)
715  {
716  foreach( GameObject rib in ribA)
717  {
718  rib.transform.Translate(-GNParameters.spreadE);
719  }
720  foreach( GameObject rib in ribB)
721  {
722  rib.transform.Translate(-GNParameters.spreadD);
723  }
724  foreach( GameObject rib in ribD)
725  {
726  rib.transform.Translate(-GNParameters.spreadB);
727  }
728  foreach( GameObject rib in ribE)
729  {
730  rib.transform.Translate(-GNParameters.spreadA);
731  }
732  }
733  else
734  {
735  foreach( GameObject rib in ribA)
736  {
737  rib.transform.Translate(-GNParameters.spreadA);
738  }
739  foreach( GameObject rib in ribB)
740  {
741  rib.transform.Translate(-GNParameters.spreadB);
742  }
743  foreach( GameObject rib in ribD)
744  {
745  rib.transform.Translate(-GNParameters.spreadD);
746  }
747  foreach( GameObject rib in ribE)
748  {
749  rib.transform.Translate(-GNParameters.spreadE);
750  }
751  }
752  }
753  }
754 
758  private void Narrowing(){
759  computeSpreadingVector();
760  GNParameters.comp_spread-=0.1f;
761  GNParameters.comp_spread = Math.Round ((double)GNParameters.comp_spread, 1);
762 
763  Debug.Log("comp_spread" + GNParameters.comp_spread);
764 
765  if(GNParameters.comp_spread <= 0){
766  GNParameters.comp_spread = 0;
767  }else{
768 
769  if(SecondaryStructureOldGUI.toggle_SEC_STRUCT){
770  NarrowSecondaryStructure();
771  }
772 
773  if(UIData.atomtype == UIData.AtomType.hyperball){
774  if(UIData.secondarystruct){
775  NarrowCAlpha();
776  }else{
777  NarrowHyperballs();
778  }
779  } // End if Hyperballs
780 
781  if(UIData.atomtype == UIData.AtomType.sphere){
782  NarrowSpheres();
783  } // End if Sphere
784  }
785  } // End Narrowing
786 
788  private void ResetChainPosForHyperballsAndSecondaryStructure(){
789  Vector3 vectemp;
790  int hballNumber;
791 
792  vectemp = new Vector3();
793 
794  GNParameters.hballs = GameObject.FindObjectsOfType(typeof(BallUpdateHB)) as BallUpdateHB[];
795 
796  for (int i=0; i<GNParameters.hballs.Length; i++) {
797  hballNumber = (int)GNParameters.hballs[i].number;
798  vectemp.x = MoleculeModel.CaSplineList[hballNumber][0];
799  vectemp.y = MoleculeModel.CaSplineList[hballNumber][1];
800  vectemp.z = MoleculeModel.CaSplineList[hballNumber][2];
801 
802  GNParameters.hballs[i].transform.position = vectemp;
803  }
804  }
805 
807  private void ResetChainPosForHyperballs(){
808  Vector3 vectemp;
809  int hballNumber;
810 
811  vectemp = new Vector3();
812 
813  GNParameters.hballs = GameObject.FindObjectsOfType(typeof(BallUpdateHB)) as BallUpdateHB[];
814 
815  for (int i=0; i<GNParameters.hballs.Length; i++) {
816  hballNumber = (int)GNParameters.hballs[i].number;
817  vectemp.x = MoleculeModel.atomsLocationlist[hballNumber][0];
818  vectemp.y = MoleculeModel.atomsLocationlist[hballNumber][1];
819  vectemp.z = MoleculeModel.atomsLocationlist[hballNumber][2];
820 
821  GNParameters.hballs[i].transform.position = vectemp;
822  }
823  }
824 
826  private void ResetChainPosForSpheres(){
827  Vector3 vectemp;
828  int hballNumber;
829 
830  vectemp = new Vector3();
831 
832  GNParameters.sballs = GameObject.FindObjectsOfType(typeof(BallUpdateSphere)) as BallUpdateSphere[];
833  for (int i=0; i<GNParameters.sballs.Length; i++) {
834  hballNumber = (int)GNParameters.sballs[i].number;
835  vectemp.x = MoleculeModel.atomsLocationlist[hballNumber][0];
836  vectemp.y = MoleculeModel.atomsLocationlist[hballNumber][1];
837  vectemp.z = MoleculeModel.atomsLocationlist[hballNumber][2];
838 
839  GNParameters.sballs[i].transform.position = vectemp;
840  }
841  }
842 
846  private void ResetChainsPos(){
847  GNParameters.comp_spread = 0;
848 
849  if(UIData.atomtype == UIData.AtomType.hyperball){
850  // True: we are rendering only C-alpha atoms (C-alpha trace or BFactor representation)
851  if(UIData.secondarystruct)
852  {
853  ResetChainPosForHyperballsAndSecondaryStructure();
854  }
855  else
856  {
857  ResetChainPosForHyperballs();
858  }
859  } //End if hyperballs
860 
861  if(UIData.atomtype == UIData.AtomType.sphere){
862  ResetChainPosForSpheres();
863  } //End if Sphere
864 
865  if(SecondaryStructureOldGUI.toggle_SEC_STRUCT){
866  UnityMolMain.getSecondaryStructureManager().DestroyRibbons();
867  UnityMolMain.getSecondaryStructureManager().CreateRibbons();
868 
869  }
870 
871  Molecule.View.DisplayMolecule.ChangeRepresentation(UIData.atomtype,UIData.bondtype);
872 
873  }// End ResetChainsPos
874 
875 
879  private Vector3 get_com(string chain)
880  {
881  float x = 0, y = 0, z = 0;
882  float nb_atoms = 0;
883  int first_atom = 0;
884 
885  if (GNParameters.onlyTMD)
886  first_atom = GNParameters.reslim;
887 
888  if (UIData.secondarystruct) {
889  for (int i=0; i < MoleculeModel.CaSplineList.Count; i++) {
890  if(MoleculeModel.CaSplineChainList[i]== chain){
891  x += MoleculeModel.CaSplineList[i][0];
892  y += MoleculeModel.CaSplineList[i][1];
893  z += MoleculeModel.CaSplineList[i][2];
894  nb_atoms++;
895  }
896  }
897  return new Vector3(x/nb_atoms, y/nb_atoms, z/nb_atoms);
898  }
899 
900  else{
901  for (int i=first_atom; i < MoleculeModel.atomsLocationlist.Count; i++) {
902  if(MoleculeModel.atomsChainList[i]== chain){
903  x += MoleculeModel.atomsLocationlist[i][0];
904  y += MoleculeModel.atomsLocationlist[i][1];
905  z += MoleculeModel.atomsLocationlist[i][2];
906  nb_atoms++;
907  }
908  }
909  return new Vector3(x/nb_atoms, y/nb_atoms, z/nb_atoms);
910  }
911  } // End get_com
912 
916  private void computeSpreadingVector()
917  {
918  Vector3 sym_center;
919  if(MoleculeModel.MinValue.y < 0)
920  sym_center = new Vector3(0, (MoleculeModel.MaxValue.y + MoleculeModel.MinValue.y), 0);
921  else
922  sym_center = new Vector3(0, (MoleculeModel.MaxValue.y - MoleculeModel.MinValue.y), 0);
923 
924  Vector3 temp = get_com("A");
925  GNParameters.spreadA = temp - sym_center;
926  GNParameters.spreadA.Normalize();
927 
928  temp = get_com("B");
929  GNParameters.spreadB = temp - sym_center;
930  GNParameters.spreadB.Normalize();
931 
932  temp = get_com("C");
933  GNParameters.spreadC = temp - sym_center;
934  GNParameters.spreadC.Normalize();
935 
936  temp = get_com("D");
937  GNParameters.spreadD = temp - sym_center;
938  GNParameters.spreadD.Normalize();
939 
940  temp = get_com("E");
941  GNParameters.spreadE = temp - sym_center;
942  GNParameters.spreadE.Normalize();
943  }
944 
948  private void computeSpreadPart(out Vector3 Spread1, out Vector3 Spread2, string chain){
949 
950  float x1 = 0, y1 = 0, z1 = 0;
951  float x2 = 0, y2 = 0, z2 = 0;
952  float nb_atoms1 = 0;
953  float nb_atoms2 = 0;
954 
955  Vector3 sym_center;
956  if(MoleculeModel.MinValue.y < 0)
957  sym_center = new Vector3(0, (MoleculeModel.MaxValue.y + MoleculeModel.MinValue.y), 0);
958  else
959  sym_center = new Vector3(0, (MoleculeModel.MaxValue.y - MoleculeModel.MinValue.y), 0);
960 
961  for (int i=0; i < MoleculeModel.atomsLocationlist.Count; i++) {
962  if(MoleculeModel.atomsChainList[i]== chain){
963  if(MoleculeModel.residueIds[i] < GNParameters.reslim){
964  x1 += MoleculeModel.atomsLocationlist[i][0];
965  y1 += MoleculeModel.atomsLocationlist[i][1];
966  z1 += MoleculeModel.atomsLocationlist[i][2];
967  nb_atoms1++;
968  }else{
969  x2 += MoleculeModel.atomsLocationlist[i][0];
970  y2 += MoleculeModel.atomsLocationlist[i][1];
971  z2 += MoleculeModel.atomsLocationlist[i][2];
972  nb_atoms2++;
973  }
974  }
975  }
976  Vector3 temp1 = new Vector3 (x1 / nb_atoms1, y1 / nb_atoms1, z1 / nb_atoms1);
977  Spread1 = temp1 - sym_center;
978  Spread1.Normalize ();
979 
980  Vector3 temp2 = new Vector3 (x2 / nb_atoms2, y2 / nb_atoms2, z2 / nb_atoms2);
981  Spread2 = temp2 - sym_center;
982  Spread2.Normalize ();
983 
984  } //End ComputeSpreadPart
985 
993  private void computeSpreadHelix(out Vector3 Spreadhelix, int first_atom, int last_atom, string chain){
994  float x = 0, y = 0, z = 0;
995  float nb_atoms = 0;
996 
997  for (int i=first_atom; i < last_atom; i++) {
998  x += MoleculeModel.atomsLocationlist[i][0];
999  y += MoleculeModel.atomsLocationlist[i][1];
1000  z += MoleculeModel.atomsLocationlist[i][2];
1001  nb_atoms++;
1002  }
1003 
1004  Vector3 temp = new Vector3 (x / nb_atoms, y / nb_atoms, z / nb_atoms);
1005  GNParameters.onlyTMD = true;
1006  Vector3 center = get_com (chain);
1007  GNParameters.onlyTMD = false;
1008  Spreadhelix = temp - center;
1009  Spreadhelix.Normalize ();
1010 
1011  }
1012 
1017  void goUpConstrained()
1018  {
1019  Vector3 v = GNParameters.mainCamera.transform.position;
1020 
1021  //if (float.Parse(MoleculeModel.FPS) > 30)
1022  GNParameters.nav_speed = (float) Math.Sqrt(Math.Abs (MoleculeModel.MinValue.y) + Math.Abs (MoleculeModel.MaxValue.y)) * (float) Math.Sqrt(Vector3.Distance(GNParameters.mainCamera.transform.position, maxCamera.target.position));
1023  Debug.Log(GNParameters.nav_speed*0.01);
1024  GNParameters.nav_speed *= 0.02f;
1025 
1026  if ((GNParameters.mainCamera.transform.position.y >= MoleculeModel.MaxValue.y)) {
1027  GNParameters.isabove = true;
1028 
1029  GNParameters.mainCamera.transform.RotateAround(maxCamera.target.position,GNParameters.mainCamera.transform.right, 1.0f*GNParameters.nav_speed);
1030  GNParameters.mainCamera.transform.LookAt(new Vector3(0, MoleculeModel.MaxValue.y, 0));
1031  maxCamera.target.position = new Vector3(0, MoleculeModel.MaxValue.y, 0);
1032  }
1033 
1034  else if ((GNParameters.mainCamera.transform.position.y <= MoleculeModel.MinValue.y)){
1035  GNParameters.isunder = true;
1036 
1037  GNParameters.mainCamera.transform.LookAt(new Vector3(0, MoleculeModel.MinValue.y, 0));
1038 
1039  GNParameters.mainCamera.transform.RotateAround(maxCamera.target.position, GNParameters.mainCamera.transform.right, 1.0f*GNParameters.nav_speed);
1040  GNParameters.mainCamera.transform.LookAt(new Vector3(0, MoleculeModel.MinValue.y, 0));
1041 
1042  maxCamera.target.position = new Vector3(0, MoleculeModel.MinValue.y, 0);
1043 
1044  }
1045  else {
1046  v.y += GNParameters.nav_speed;
1047  GNParameters.mainCamera.transform.position = v;
1048  maxCamera.target.position = new Vector3(0, v.y, 0);
1049  }
1050  }
1051 
1056  void goDownConstrained()
1057  {
1058 
1059  Vector3 v = GNParameters.mainCamera.transform.position;
1060 
1061  GNParameters.nav_speed = (float) Math.Sqrt(Math.Abs (MoleculeModel.MinValue.y) + Math.Abs (MoleculeModel.MaxValue.y)) * (float) Math.Sqrt(Vector3.Distance(GNParameters.mainCamera.transform.position, maxCamera.target.position));
1062  Debug.Log(GNParameters.nav_speed*0.01);
1063  GNParameters.nav_speed *= 0.02f;
1064 
1065  // We are above the molecule bounding box.
1066  if ((GNParameters.mainCamera.transform.position.y >= MoleculeModel.MaxValue.y)) {
1067  GNParameters.isabove = true;
1068 
1069  GNParameters.mainCamera.transform.LookAt(new Vector3(0, MoleculeModel.MaxValue.y, 0));
1070 
1071  GNParameters.mainCamera.transform.RotateAround(maxCamera.target.position, GNParameters.mainCamera.transform.right, -1.0f*GNParameters.nav_speed);
1072  GNParameters.mainCamera.transform.LookAt(new Vector3(0, MoleculeModel.MaxValue.y, 0));
1073 
1074  maxCamera.target.position = new Vector3(0, MoleculeModel.MaxValue.y, 0);
1075  }
1076  // We are below the molecule bounding box.
1077  else if ((GNParameters.mainCamera.transform.position.y <= MoleculeModel.MinValue.y)){
1078  GNParameters.isunder = true;
1079 
1080  GNParameters.mainCamera.transform.LookAt(new Vector3(0, MoleculeModel.MinValue.y, 0));
1081 
1082  GNParameters.mainCamera.transform.RotateAround(maxCamera.target.position, GNParameters.mainCamera.transform.right, -1.0f*GNParameters.nav_speed);
1083  GNParameters.mainCamera.transform.LookAt(new Vector3(0, MoleculeModel.MinValue.y, 0));
1084  maxCamera.target.position = new Vector3(0, MoleculeModel.MinValue.y, 0);
1085 
1086  } else {
1087  v.y -= GNParameters.nav_speed;
1088  GNParameters.mainCamera.transform.position = v;
1089  maxCamera.target.position = new Vector3(0, v.y, 0);
1090 
1091  }
1092  }
1093 
1094  IEnumerator Transition()
1095  {
1096  float t = 0.0f;
1097  Vector3 startingPos = GNParameters.mainCamera.transform.position;
1098  while (t < 1.0f)
1099  {
1100  t += Time.deltaTime * (Time.timeScale/GNParameters.transitionDuration);
1101 
1102  GNParameters.mainCamera.transform.position = Vector3.Lerp(startingPos, GNParameters.optim_target, t);
1103  yield return 0;
1104  }
1105  }
1106 
1107  private void ReorientCamera()
1108  {
1109  if(GNParameters.reoriented){
1110  if ((GNParameters.mainCamera.transform.position.y >= MoleculeModel.MaxValue.y))
1111  maxCamera.target.position = new Vector3(0, MoleculeModel.MaxValue.y, 0);
1112  else if((GNParameters.mainCamera.transform.position.y <= MoleculeModel.MinValue.y))
1113  maxCamera.target.position = new Vector3(0, MoleculeModel.MinValue.y, 0);
1114  else
1115  maxCamera.target.position = new Vector3(0, GNParameters.mainCamera.transform.position.y, 0);
1116 
1117  GNParameters.mainCamera.transform.LookAt(maxCamera.target.position);
1118  GNParameters.reoriented = false;
1119  }
1120  }
1121 
1122 
1123 }
1124 
1125 
GuidedNav.GNParameters.navigationUp
static bool navigationUp
Are we moving down. Boolean set to true on key press.
Definition: GuidedNavigationParameters.cs:49
GuidedNav.GNParameters.poscloseatom
static Vector3 poscloseatom
3D coordinates of the closest atom to the camera.
Definition: GuidedNavigationParameters.cs:130
GuidedNav.GNParameters.optim_user_cam_pos
static Vector3 optim_user_cam_pos
3D coordinates of the selected best camera position.
Definition: GuidedNavigationParameters.cs:162
GuidedNav.GNParameters.ghost_target_instantiate
static bool ghost_target_instantiate
Have the game objects for camera target and position been instantiated.
Definition: GuidedNavigationParameters.cs:152
UI.UIData.optim_view
static bool optim_view
Definition: UIData.cs:203
GuidedNav.GNParameters.spreadA
static Vector3 spreadA
Spreading vectors for each chain (up to 5). Computed by GuidedNavigationManager::computeSpreadingVect...
Definition: GuidedNavigationParameters.cs:114
GuidedNavigationManager.NarrowSpheres
void NarrowSpheres()
Narrow the chains when rendering spheres.
Definition: GuidedNavigationManager.cs:652
UI.UIData.secondarystruct
static bool secondarystruct
Switch between all atoms and C-alpha trace or BFactor secondary structure representation.
Definition: UIData.cs:176
GuidedNavigationManager.ResetChainPosForSpheres
void ResetChainPosForSpheres()
Resets the chains positions when rendering spheres.
Definition: GuidedNavigationManager.cs:826
GuidedNav.GNParameters.velocity
static Vector3 velocity
Camera 3D speed during its repositioning.
Definition: GuidedNavigationParameters.cs:166
UI.UIData.newUIActivated
static bool newUIActivated
Definition: UIData.cs:163
GuidedNavigationManager.CreateAxeAndOrigin
void CreateAxeAndOrigin()
Instantiate the origin and symmetry axis game objects.
Definition: GuidedNavigationManager.cs:25
GuidedNav.GNParameters.guidedzoom
static bool guidedzoom
Should we zoom? True when the camera is not at the right distance (maxCamera.desiredDistance != maxCa...
Definition: GuidedNavigationParameters.cs:55
maxCamera.target
static Transform target
Definition: maxCamera.cs:125
GuidedNav.GNParameters.navigationDown
static bool navigationDown
Are we moving down? Boolean set to true on key press.
Definition: GuidedNavigationParameters.cs:52
GuidedNavigationManager.get_com
Vector3 get_com(string chain)
Compute center of mass.
Definition: GuidedNavigationManager.cs:879
GuidedNav.GNParameters.isunder
static bool isunder
Allows to dive into the channel when zoom in the structure from below.
Definition: GuidedNavigationParameters.cs:78
SecondaryStructureOldGUI.toggle_SEC_STRUCT
static bool toggle_SEC_STRUCT
Triggers the switch between atom and secondary structure generation and rendering.
Definition: SecondaryStructureOldGUI.cs:12
GuidedNavigationManager.computeSpreadHelix
void computeSpreadHelix(out Vector3 Spreadhelix, int first_atom, int last_atom, string chain)
Computes spreading vectors for helices (third step spreading)
Definition: GuidedNavigationManager.cs:993
GuidedNavigationManager.DestroyAxeAndOrigin
void DestroyAxeAndOrigin()
Destroy the axis and origin game objects.
Definition: GuidedNavigationManager.cs:37
maxCamera.weight_cam
static float weight_cam
Definition: maxCamera.cs:133
GuidedNavigationManager.computeSpreadPart
void computeSpreadPart(out Vector3 Spread1, out Vector3 Spread2, string chain)
Compute spreading vectors (second step).
Definition: GuidedNavigationManager.cs:948
UI.UIData.guided
static bool guided
Definition: UIData.cs:201
AtomTree.Build
static AtomTree Build()
Definition: AtomTree.cs:231
Molecule.Model.MoleculeModel.atomsChainList
static List< string > atomsChainList
The chain of each atom.
Definition: MoleculeModel.cs:161
maxCamera.currentDistance
static float currentDistance
Definition: maxCamera.cs:128
GuidedNav.GNParameters.onlyTMD
static bool onlyTMD
If true, triggers the computation of the center of mass of only the TransMembrane Domain (TMD)...
Definition: GuidedNavigationParameters.cs:139
GuidedNav.GNParameters.optim_target
static Vector3 optim_target
3D coordinates of the target.
Definition: GuidedNavigationParameters.cs:155
GuidedNav.GNParameters.panoramic
static bool panoramic
Activates/Deactivate the panoramic view (immersive camera positioning).
Definition: GuidedNavigationParameters.cs:64
Molecule.Model.MoleculeModel.residueIds
static List< int > residueIds
The residue identifiers.
Definition: MoleculeModel.cs:151
GuidedNavigationManager.NarrowHyperballs
void NarrowHyperballs()
Narrow the chains when rendering hyperballs.
Definition: GuidedNavigationManager.cs:616
GuidedNavigationManager.goDownConstrained
void goDownConstrained()
Only available in "guided navigation" and specific to pentameric channels.
Definition: GuidedNavigationManager.cs:1056
GuidedNav.GNParameters.ghost_target
static GameObject ghost_target
Reference to the sphere primitive representing the camera target.
Definition: GuidedNavigationParameters.cs:146
GuidedNav.GNParameters.next_right
static bool next_right
Jump to the next monomer on the right.
Definition: GuidedNavigationParameters.cs:94
GuidedNavigationManager.originPoint
GameObject originPoint
GameObjects representing the space origin and molecule symmetry axis.
Definition: GuidedNavigationManager.cs:13
GuidedNavigationManager.NearSpreading
void NearSpreading()
Slightly spreads the chains when the camera is near the protein structure.
Definition: GuidedNavigationManager.cs:316
GuidedNavigationManager.goUpConstrained
void goUpConstrained()
Only available in "guided navigation" mode and specific to pentameric channels.
Definition: GuidedNavigationManager.cs:1017
GenericManager.ResetPositions
abstract void ResetPositions()
AtomTree.GetClosestAtomType
string GetClosestAtomType(Vector3 pos)
Definition: AtomTree.cs:151
GuidedNavigationManager.ResetChainsPos
void ResetChainsPos()
Resets the chains position.
Definition: GuidedNavigationManager.cs:846
BallUpdate.number
long number
Definition: BallUpdate.cs:84
GuidedNavigationManager.SpreadHyperballs
void SpreadHyperballs()
Spread chains when rendering the atoms as hyperballs.
Definition: GuidedNavigationManager.cs:363
GuidedNavigationManager.NarrowCAlpha
void NarrowCAlpha()
Narrow the chains of C-alpha traces.
Definition: GuidedNavigationManager.cs:580
GuidedNav.GNParameters.monomer_jump
static bool monomer_jump
Enter or exit jump navigation Triggered by key press (see GuidedNavigationManager::UpdateManager) ...
Definition: GuidedNavigationParameters.cs:89
GuidedNavigationManager.SpreadSpheres
void SpreadSpheres()
Spread chains when rendering the atoms as spheres.
Definition: GuidedNavigationManager.cs:393
Molecule.Model.MoleculeModel.CaSplineList
static List< float[]> CaSplineList
The coordinates of each Carbon alpha in the CA-Spline.
Definition: MoleculeModel.cs:99
GuidedNav.GNParameters.hballs
static BallUpdateHB[] hballs
List of all hyperballs mono behavior scripts Filled when spreading, narrowing or resetting chains pos...
Definition: GuidedNavigationParameters.cs:107
UI.UIData
!WiP Includes FLAGS of GUI.
Definition: UIData.cs:78
GuidedNav.GNParameters.next_left
static bool next_left
Jump to the next monomer on the left.
Definition: GuidedNavigationParameters.cs:99
UnityMolMain.getSecondaryStructureManager
static SecondaryStructureManager getSecondaryStructureManager()
Definition: UnityMolMain.cs:34
GuidedNav.GNParameters.mainCamera
static GameObject mainCamera
Reference to the scene camera.
Definition: GuidedNavigationParameters.cs:172
GuidedNav
The GNParameters class regroups settings used for Guided Navigation and GLIC spreading.
Definition: GuidedNavigationParameters.cs:8
Molecule.View.DisplayMolecule.ChangeRepresentation
static void ChangeRepresentation(UIData.AtomType newAtomType, UIData.BondType newBondType=UIData.BondType.nobond)
Definition: DisplayMolecule.cs:230
maxCamera.desiredDistance
static float desiredDistance
Definition: maxCamera.cs:129
UI.UIData.isGLIC
static bool isGLIC
Definition: UIData.cs:189
GuidedNav.GNParameters.reset_panoramic
static bool reset_panoramic
When true, triggers the transition from panoramic view to normal view.
Definition: GuidedNavigationParameters.cs:68
GuidedNavigationManager.SpreadSecondaryStructure
void SpreadSecondaryStructure()
Spread chains when rendering the secondary structure.
Definition: GuidedNavigationManager.cs:467
Molecule.Model.MoleculeModel.MaxValue
static Vector3 MaxValue
The "biggest" corner of the bounding box that encloses the molecule.
Definition: MoleculeModel.cs:343
Molecule.Model.MoleculeModel.CaSplineChainList
static List< string > CaSplineChainList
The chain of each carbon alpha in the CA-Spline.
Definition: MoleculeModel.cs:241
UI.UIData.bondtype
static BondType bondtype
Definition: UIData.cs:141
GuidedNavigationManager.Narrowing
void Narrowing()
Narrowing chains.
Definition: GuidedNavigationManager.cs:758
GuidedNav.GNParameters.optim_cam_position
static Vector3[] optim_cam_position
3D coordinates of the 4 best camera positions.
Definition: GuidedNavigationParameters.cs:158
GuidedNavigationManager.SpreadCAlpha
void SpreadCAlpha()
Spread chains when rendering the C-alpha spline as hyperballs.
Definition: GuidedNavigationManager.cs:333
GuidedNav.GNParameters.distclose
static float distclose
Distance between the camera and the closest atom.
Definition: GuidedNavigationParameters.cs:133
Molecule.Model.MoleculeModel.existingChain
static List< string > existingChain
List of the chains existing in the molecule.
Definition: MoleculeModel.cs:181
Molecule.Model.MoleculeModel.MinValue
static Vector3 MinValue
The "smallest" corner of the bounding box that encloses the molecule.
Definition: MoleculeModel.cs:338
maxCamera.zoomRate
static int zoomRate
Definition: maxCamera.cs:94
GuidedNav.GNParameters.near_spread
static bool near_spread
Activate/Deactivate the spreading relative the closeness of the camera to the molecule.
Definition: GuidedNavigationParameters.cs:136
GuidedNav.GNParameters.reoriented
static bool reoriented
When true, triggers the camera repositioning inside the molecule bounding box.
Definition: GuidedNavigationParameters.cs:60
UI.UIData.atomtype
static AtomType atomtype
Definition: UIData.cs:139
GuidedNav.GNParameters.ghost_camera
static GameObject ghost_camera
Reference to the sphere primitive representing the camera ending position.
Definition: GuidedNavigationParameters.cs:149
GuidedNav.GNParameters.comp_spread
static double comp_spread
Current distance of spreading.
Definition: GuidedNavigationParameters.cs:121
UnityMolMain.getCurrentBondManager
static GenericManager getCurrentBondManager()
Definition: UnityMolMain.cs:54
GuidedNavigationManager.ResetChainPosForHyperballs
void ResetChainPosForHyperballs()
Resets the chains positions when rendering hyperballs.
Definition: GuidedNavigationManager.cs:807
UI.UIData.spread_tree
static bool spread_tree
Definition: UIData.cs:190
GuidedNav.GNParameters.closeatom
static float[] closeatom
3D coordinates of the closest atom to the camera.
Definition: GuidedNavigationParameters.cs:127
GuidedNav.GNParameters.sballs
static BallUpdateSphere[] sballs
List of all spheres mono behavior scripts.
Definition: GuidedNavigationParameters.cs:111
GuidedNav.GNParameters.isabove
static bool isabove
Allows to dive into the channel when zoom in the structure from above.
Definition: GuidedNavigationParameters.cs:73
GuidedNavigationManager.Spreading
void Spreading()
Spreading chains (limit: 5 chains)
Definition: GuidedNavigationManager.cs:547
maxCamera.cameraStop
static bool cameraStop
Definition: maxCamera.cs:88
GuidedNav.GNParameters.reslim
static int reslim
Number of the first residue outside of the GLIC transmembrane domain.
Definition: GuidedNavigationParameters.cs:176
GuidedNavigationManager.ResetChainPosForHyperballsAndSecondaryStructure
void ResetChainPosForHyperballsAndSecondaryStructure()
Resets the chains positions when rendering the secondary structure.
Definition: GuidedNavigationManager.cs:788
UI
Definition: GUIDisplay.cs:66
UnityMolMain.getCurrentAtomManager
static GenericManager getCurrentAtomManager()
Definition: UnityMolMain.cs:50
Molecule.Model.MoleculeModel.atomsLocationlist
static List< float[]> atomsLocationlist
The coordinates of each atom.
Definition: MoleculeModel.cs:79
GuidedNavigationManager.computeSpreadingVector
void computeSpreadingVector()
Compute spreading vectors (first step).
Definition: GuidedNavigationManager.cs:916