UnityMol  0.9.6-875
UnityMol viewer / In developement
Public Member Functions | Static Public Member Functions | Public Attributes | Properties | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
Molecule3D Class Reference
+ Inheritance diagram for Molecule3D:
+ Collaboration diagram for Molecule3D:

Public Member Functions

void OnDisable ()
 
void Display ()
 
void loadFile ()
 
void SetFOV (float angle)
 
void ToNotParticle ()
 
void ToParticle ()
 

Static Public Member Functions

static void clearScene ()
 

Public Attributes

GUIDisplay gUIDisplay
 
IPEndPoint _ipep
 
ArrayList clubLocationalist =new ArrayList()
 
float sensitivityX = 1.5F
 
float sensitivityY = 1.5F
 
float minimumX = -360F
 
float maximumX = 360F
 
float minimumY = -60F
 
float maximumY = 60F
 
string location
 
Vector2 directoryScroll = new Vector2()
 
Vector2 fileScroll = new Vector2()
 
GUISkin mySkin
 
int polop = 0
 
int masque = 0
 
bool fileLoadingFinished =false
 
float default_near_clip_plane
 
float default_near_plane_length
 

Properties

UIData.AtomType PreviousAtomType [get]
 
UIData.BondType PreviousBondType [get]
 

Private Member Functions

void Awake ()
 
void Start ()
 
void OnGUI ()
 
void Update ()
 
float transition (float val, float newVal, float deltaVal)
 
void OpenMenuOperate ()
 
void HiddenOperate ()
 
void KeyOperate ()
 
void MouseOperate ()
 
void SetCenter (int mode)
 

Private Attributes

bool fontInitialized = false
 
Skybox camSky
 
RequestPDB requestPDB
 
Boolean isControl =false
 
float rotationXX = 0F
 
float rotationYY = 0F
 
GameObject toggleNewUI
 
GameObject scenecontroller
 
float default_fov_angle
 
float default_fov_angle_rad
 
float angle_rad
 
Camera camera
 
UIData.AtomType previous_AtomType = UIData.AtomType.noatom
 
UIData.BondType previous_BondType = UIData.BondType.nobond
 

Static Private Attributes

static GameObject LocCamera
 

Detailed Description

Definition at line 82 of file Molecule3D.cs.

Member Function Documentation

void Molecule3D.Awake ( )
private

Definition at line 256 of file Molecule3D.cs.

static void Molecule3D.clearScene ( )
static

Clears the scene.

Usually performed before loaded a new file.

Definition at line 156 of file Molecule3D.cs.

References Molecule.Model.MoleculeModel.atomsLocalScaleList, GuidedNavigationManager.Clear(), Molecule.View.DisplayMolecule.ClearMemory(), SugarManager.ColorationModeBond, SugarManager.ColorationModeRing, ArtemisManager.disconnect(), Molecule.Model.MoleculeModel.existingChain, Molecule.Model.MoleculeModel.existingName, Molecule.Model.MoleculeModel.existingRes, UnityMolMain.getArtemisManager(), UnityMolMain.getGuidedNavigationManager(), UnityMolMain.getVRPNManager(), RepresentationOldGUI.globalRadius, UI.UIData.hasMoleculeDisplay, UI.GUIDisplay.id, UI.UIData.isCubeLoaded, ParseData.ParsePDB.RequestPDB.isDone, UI.UIData.isFileLoaded, UI.UIData.isHBallLoaded, UI.UIData.isMoleculeDisplayed, UI.UIData.isParticlesInitialized, UI.UIData.isSphereLoaded, UI.UIData.loadHireRNA, SurfaceManager.pdbGen, DepthCueing.reset, AmbientOcclusion.reset, Molecule.Model.MoleculeModel.residueIds, Molecule.Model.MoleculeModel.residues, UI.UIData.secondarystruct, UI.GUIMoleculeController.toggle_HIDE_HYDROGEN, UI.GUIMoleculeController.toggle_NA_HIDE, UI.GUIMoleculeController.toggle_NA_INTERACTIVE, UI.GUIMoleculeController.toggle_NA_MEASURE, SugarOldGUI.toggle_OXYGEN, SugarOldGUI.toggle_RING_BLENDING, and SugarOldGUI.toggle_TWISTER.

Referenced by BackendManager.downloadSessionFile(), LoadGUI.Fetch(), OnDisable(), UI.GUIDisplay.OpenAnimationCrdCallback(), UI.GUIDisplay.OpenAnimationTopCallback(), LoadGUI.OpenFileCallback(), and UI.GUIDisplay.OpenReactionCallback().

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void Molecule3D.Display ( )

Definition at line 292 of file Molecule3D.cs.

References UI.UIData.atomtype, UI.UIData.bondtype, and Molecule.View.DisplayMolecule.ChangeRepresentation().

Referenced by OnGUI().

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void Molecule3D.HiddenOperate ( )
private

Hides the GUI and enables a sort of "full-screen" mode, as in GUI-less, not as opposed to windowed.

Helps quite a bit with performance, or at least with CPU load.

UIData.hiddenUI && UIData.hiddenUIbutFPS && !UIData.hiddenCamera) {

Definition at line 718 of file Molecule3D.cs.

References UI.UIData.hiddenUI.

Referenced by Update().

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void Molecule3D.KeyOperate ( )
private

For keyboard control.

Definition at line 753 of file Molecule3D.cs.

References UI.UIData.bondtype, Molecule.View.DisplayMolecule.ChangeRepresentation(), ScreenShot.open, UI.UIData.switchmode, UI.GUIMoleculeController.toggle_NA_MAXCAM, and ToNotParticle().

Referenced by Update().

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void Molecule3D.loadFile ( )

Definition at line 410 of file Molecule3D.cs.

References UI.UIData.atomtype, UI.UIData.bondtype, UI.UIData.fetchPDBFile, UI.GUIDisplay.file_base_name, UI.GUIDisplay.file_extension, RepresentationOldGUI.globalRadius, UI.UIData.hasMoleculeDisplay, UI.UIData.init_molecule, UI.UIData.isFileLoaded, UI.UIData.isMoleculeDisplayed, UI.UIData.isOpenFile, RepresentationOldGUI.linkScale, ParseData.ParsePDB.RequestPDB.LoadAnimCrd(), ParseData.ParsePDB.RequestPDB.LoadAnimTop(), ParseData.ParsePDB.RequestPDB.LoadPDBReaction(), ParseData.ParsePDB.RequestPDB.LoadXGMML(), UI.GUIDisplay.pdbID, UI.GUIDisplay.pdbServer, UI.GUIDisplay.proxyPort, UI.GUIDisplay.proxyServer, UI.GUIMoleculeController.showAtomMenu, RepresentationOldGUI.shrink, and Molecule.Model.MoleculeModel.surfaceFileExists.

Referenced by OnGUI().

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void Molecule3D.MouseOperate ( )
private

Sets the center of the scene on : The original center ('R' key) The targeted atom ('T' key)

Camera controls with mouse inputs.

Definition at line 852 of file Molecule3D.cs.

References sensitivityX, sensitivityY, UI.UIData.switchmode, UI.GUIMoleculeController.toggle_NA_MAXCAM, ToNotParticle(), and ToParticle().

Referenced by Update().

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void Molecule3D.OnDisable ( )

Definition at line 148 of file Molecule3D.cs.

References clearScene().

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void Molecule3D.OnGUI ( )
private

Definition at line 298 of file Molecule3D.cs.

References Molecule.View.DisplayMolecule.AddPhysics(), UI.UIData.atomtype, UI.UIData.backGroundIs, UI.UIData.bondtype, Molecule.Control.ControlMolecule.BuildHireRnaHydrogenBondsStructures(), Molecule.Control.ControlMolecule.BuildMoleculeComponents(), Molecule.View.DisplayMolecule.ChangeRepresentation(), UI.UIData.changeStructure, Molecule.Control.ControlMolecule.CreateResidues(), Molecule.View.DisplayMolecule.DeletePhysics(), Display(), UI.GUIDisplay.Display(), ElectrostaticManager.DisplayFieldLines(), UI.UIData.EnableUpdate, UI.GUIMoleculeController.FileBrowser_show, UnityMolMain.getElectrostaticManager(), UnityMolMain.getSurfaceManager(), UI.UIData.hiddenUI, UI.UIData.hiddenUIbutFPS, SurfaceManager.InitCutParameters(), UI.UIData.interactive, UI.UIData.isFileLoaded, UI.UIData.isGLIC, UI.UIData.isMoleculeDisplayed, UI.UIData.isOpenFile, UI.UIData.isParticlesInitialized, loadFile(), UI.UIData.loadHireRNA, UI.GUIDisplay.m_fileBrowser, UI.GUIMoleculeController.m_fileBrowser, mySkin, Molecule.Model.MoleculeModel.networkLoaded, Molecule.Model.MoleculeModel.newtooltip, ImprovedFileBrowser.OnGUI(), UI.GUIDisplay.pdbID, SurfaceManager.RecenterSurfaces(), UI.UIData.resetInteractive, UI.GUIMoleculeController.SetAtomsExtended(), SetCenter(), UI.GUIMoleculeController.SetChains(), Rectangles.SetFontSize(), UI.GUIMoleculeController.SetPanels(), UI.GUIMoleculeController.SetResidues(), UI.GUIMoleculeController.showAtomsExtendedMenu, UI.GUIMoleculeController.showChainsMenu, UI.GUIMoleculeController.showPanelsMenu, UI.GUIMoleculeController.showResiduesMenu, and UI.GUIMoleculeController.toggle_INFOS.

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void Molecule3D.OpenMenuOperate ( )
private

Switch back to the particle mode.

('Delete' key)

Definition at line 689 of file Molecule3D.cs.

References Molecule.View.DisplayMolecule.ChangeRepresentation(), and UI.UIData.openAllMenu.

Referenced by Update().

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void Molecule3D.SetCenter ( int  mode)
private

Sets the center of the scene on the original center or on an atom.

Parameters
modeSetting mode (0 for original center, 1 for atom center). Int.

Definition at line 893 of file Molecule3D.cs.

References UI.UIData.atomtype, HBallManager.ResetPositions(), Molecule.Model.MoleculeModel.target, and maxCamera.ToCenter().

Referenced by OnGUI().

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void Molecule3D.SetFOV ( float  angle)

Definition at line 697 of file Molecule3D.cs.

Referenced by RepresentationOldGUI.HyperballStyle().

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void Molecule3D.Start ( )
private

Definition at line 270 of file Molecule3D.cs.

References UnityMolMain.getElectrostaticManager(), Molecule.View.DisplayMolecule.GetManagers(), ElectrostaticManager.Init(), Molecule.Model.AtomModel.InitAtomic(), UnityMolMain.setCurrentAtomManager(), and UnityMolMain.setCurrentBondManager().

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void Molecule3D.ToNotParticle ( )

Switch the protein representation to Hyperball.

Used in switch mode (LOD).

Definition at line 920 of file Molecule3D.cs.

References UI.UIData.atomtype, UI.UIData.bondtype, Molecule.View.DisplayMolecule.ChangeRepresentation(), previous_AtomType, and previous_BondType.

Referenced by KeyOperate(), maxCamera.LateUpdate(), and MouseOperate().

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void Molecule3D.ToParticle ( )

Switch the protein representation to Particle.

Used in switch mode (LOD).

Definition at line 931 of file Molecule3D.cs.

References UI.UIData.atomtype, UI.UIData.bondtype, Molecule.View.DisplayMolecule.ChangeRepresentation(), previous_AtomType, and previous_BondType.

Referenced by maxCamera.joypadOperate(), maxCamera.LateUpdate(), and MouseOperate().

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float Molecule3D.transition ( float  val,
float  newVal,
float  deltaVal 
)
private

Make the transition between metaphors.

Parameters
valValue.
newValNew value.
deltaValDelta value.

Definition at line 680 of file Molecule3D.cs.

Referenced by Update().

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void Molecule3D.Update ( )
private

Definition at line 498 of file Molecule3D.cs.

References Molecule.Model.Reaction.acount, Molecule.Model.Reaction.affichage, Molecule.Model.Reaction.animation, Molecule.Model.MoleculeModel.atoms, UI.UIData.bondtype, UI.UIData.cameraStop2, Molecule.View.DisplayMolecule.ChangeRepresentation(), ColorObject.color, Molecule.Model.Reaction.coord, Molecule.Model.Reaction.count, Molecule.Model.Reaction.current, RepresentationOldGUI.deltaRadius, RepresentationOldGUI.deltaScale, RepresentationOldGUI.deltaShrink, HStickManager.depthFactor, HBallManager.depthFactor, UI.GUIMoleculeController.depthfactor, BallUpdateHB.drag, UI.GUIMoleculeController.drag, ElectrostaticManager.EnergyGrayColor, BallUpdateHB.EnergyGrayColor, Molecule.Model.Reaction.forward, UnityMolMain.getElectrostaticManager(), RepresentationOldGUI.globalRadius, HiddenOperate(), Molecule.Model.Reaction.isReaction, Molecule.Model.Reaction.isReady, KeyOperate(), RepresentationOldGUI.linkScale, MouseOperate(), RepresentationOldGUI.newGlobalRadius, RepresentationOldGUI.newScale, RepresentationOldGUI.newShrink, OpenMenuOperate(), BallUpdate.radiusFactor, StickUpdate.radiusFactor, LineManager.ResetPositions(), HStickManager.ResetPositions(), HStickMeshManager.ResetPositions(), CubeBondManager.ResetPositions(), HBallMeshManager.resetRadii, HStickMeshManager.resetScale, HStickMeshManager.resetShrink, LineUpdate.scale, StickUpdate.scale, UI.GUIMoleculeController.showAtomMenu, RepresentationOldGUI.showAtomType, RepresentationOldGUI.showBondType, RepresentationOldGUI.showHyperballsMenu, RepresentationOldGUI.shrink, StickUpdate.shrink, BallUpdateHB.spring, UI.GUIMoleculeController.spring, UI.GUIMoleculeController.toggle_HB_TRANS, RepresentationOldGUI.transDelta, transition(), RepresentationOldGUI.transMETAPHOR, ElectrostaticManager.update(), and Molecule.Control.ControlMolecule.UpdateBondsFromGameObject().

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Member Data Documentation

IPEndPoint Molecule3D._ipep

Definition at line 91 of file Molecule3D.cs.

float Molecule3D.angle_rad
private

Definition at line 127 of file Molecule3D.cs.

Camera Molecule3D.camera
private

Definition at line 129 of file Molecule3D.cs.

Skybox Molecule3D.camSky
private

Definition at line 87 of file Molecule3D.cs.

ArrayList Molecule3D.clubLocationalist =new ArrayList()

Definition at line 92 of file Molecule3D.cs.

float Molecule3D.default_fov_angle
private

Definition at line 118 of file Molecule3D.cs.

float Molecule3D.default_fov_angle_rad
private

Definition at line 119 of file Molecule3D.cs.

float Molecule3D.default_near_clip_plane

Definition at line 122 of file Molecule3D.cs.

float Molecule3D.default_near_plane_length

Definition at line 124 of file Molecule3D.cs.

Vector2 Molecule3D.directoryScroll = new Vector2()

Definition at line 102 of file Molecule3D.cs.

bool Molecule3D.fileLoadingFinished =false

Definition at line 115 of file Molecule3D.cs.

Vector2 Molecule3D.fileScroll = new Vector2()

Definition at line 103 of file Molecule3D.cs.

bool Molecule3D.fontInitialized = false
private

Definition at line 84 of file Molecule3D.cs.

GUIDisplay Molecule3D.gUIDisplay

Definition at line 88 of file Molecule3D.cs.

Boolean Molecule3D.isControl =false
private

Definition at line 90 of file Molecule3D.cs.

string Molecule3D.location

Definition at line 101 of file Molecule3D.cs.

GameObject Molecule3D.LocCamera
staticprivate

Definition at line 86 of file Molecule3D.cs.

int Molecule3D.masque = 0

Definition at line 110 of file Molecule3D.cs.

float Molecule3D.maximumX = 360F

Definition at line 96 of file Molecule3D.cs.

float Molecule3D.maximumY = 60F

Definition at line 98 of file Molecule3D.cs.

float Molecule3D.minimumX = -360F

Definition at line 95 of file Molecule3D.cs.

float Molecule3D.minimumY = -60F

Definition at line 97 of file Molecule3D.cs.

GUISkin Molecule3D.mySkin

Definition at line 106 of file Molecule3D.cs.

Referenced by OnGUI().

int Molecule3D.polop = 0

Definition at line 109 of file Molecule3D.cs.

UIData.AtomType Molecule3D.previous_AtomType = UIData.AtomType.noatom
private

Definition at line 134 of file Molecule3D.cs.

Referenced by ToNotParticle(), and ToParticle().

UIData.BondType Molecule3D.previous_BondType = UIData.BondType.nobond
private

Definition at line 141 of file Molecule3D.cs.

Referenced by ToNotParticle(), and ToParticle().

RequestPDB Molecule3D.requestPDB
private

Definition at line 89 of file Molecule3D.cs.

float Molecule3D.rotationXX = 0F
private

Definition at line 99 of file Molecule3D.cs.

float Molecule3D.rotationYY = 0F
private

Definition at line 100 of file Molecule3D.cs.

GameObject Molecule3D.scenecontroller
private

Definition at line 112 of file Molecule3D.cs.

float Molecule3D.sensitivityX = 1.5F

Definition at line 93 of file Molecule3D.cs.

Referenced by MouseOperate().

float Molecule3D.sensitivityY = 1.5F

Definition at line 94 of file Molecule3D.cs.

Referenced by MouseOperate().

GameObject Molecule3D.toggleNewUI
private

Definition at line 104 of file Molecule3D.cs.

Property Documentation

UIData.AtomType Molecule3D.PreviousAtomType
get

Definition at line 135 of file Molecule3D.cs.

Referenced by RepresentationOldGUI.SetAtomStyle().

UIData.BondType Molecule3D.PreviousBondType
get

Definition at line 142 of file Molecule3D.cs.

The documentation for this class was generated from the following file: