HBallManager Class Reference

Inheritance diagram for HBallManager:

Collaboration diagram for HBallManager:

Public Member Functions
bool	ellipsoidViewEnabled ()
override void	Init ()
override void	DestroyAll ()
override void	ToggleDistanceCueing (bool enabling)
void	SetTexture (Texture texture, List< string > atom, string residue="All", string chain="All")
void	SetTexture (string resource_name, List< string > atom, string residue="All", string chain="All")
void	SetTexture (Texture texture, int atomNum)
void	SetTexture (string resource_name, int atomNum)
override void	SetColor (Color col, List< string > atom, string residue="All", string chain="All")
override void	SetColor (Color col, int atomNum)
override void	SetRadii (List< string > atom, string residue="All", string chain="All")
override void	SetRadii (int id)
Color	GetColor (Vector3 pos)
override GameObject	GetBall (int id)
override void	ResetPositions ()
override void	ResetIMDSimulationPositions ()
override void	ResetRadii ()
void	CreateMouseOversIMDSimulation ()
void	DestroyMouseOversIMDSimulation ()
override void	DisableRenderers ()
override void	EnableRenderers ()
override void	EnableShadows ()
override void	DisableShadows ()
Vector3	computeEllipsoidPosition (int residueId)
Vector3	computeEllipsoidNormal (int residueId)
Vector3	computeEllipsoidOrientation (int residueId)
void	findAtoms ()
void	findBonds ()
void	UpdateEllipsoids ()
void	GenerateEllipsoids ()
void	ActivateBases ()
void	DeactivateBases ()
void	ActivateEllipsoids ()
void	DeactivateEllipsoids ()
void	RenderEllipsoids ()
void	RenderAtoms ()
void	SwitchRendering ()
void	ResetShininess ()
SingleAtomSelection	getClosestAtomGameObject (Vector3 position)
override void	showHydrogens (bool hide)

Static Public Attributes
static string[]	allowedAtomsForPosition = {"CY", "C1", "U1", "G1", "G2", "A1", "A2"}
static BallUpdateHB[]	hballs
static bool	xgmml = false
static float	depthFactor = 1.0f
static float	brightness = 1.0f
static float	shininess = 0.0f
static bool	resetBrightness = false
static bool	resetShininess = false
static bool	ellipsoidView = false
static bool	ellipsoidsInitialized = false

Private Member Functions
void	ResetColors ()
void	MoveNetworkNodes ()
void	CreateMouseOvers ()
void	DestroyMouseOvers ()
void	ExitInteractive ()
void	StartPhysicsManagement ()
void	ManagePhysics ()
void	ResetBrightness ()
void	Update ()

Private Attributes
GameObject[]	hballsGameObjects

Static Private Attributes
static float	oldDepthFactor = 1.0f
static bool	mouseOvers = false
static bool	wasInteractiveColored = false

Additional Inherited Members
Public Attributes inherited from GenericManager
bool	isInit = false

Detailed Description

Definition at line 72 of file HBallManager.cs.

Member Function Documentation

void HBallManager.ActivateBases

(

)

Definition at line 1289 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsForEllipsoidsPerResidue, Molecule.Model.MoleculeModel.atomsNamelist, and Molecule.Model.MoleculeModel.bondsForReplacedAtoms.

Referenced by RenderAtoms().

Here is the caller graph for this function:

void HBallManager.ActivateEllipsoids

(

)

Definition at line 1346 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.ellipsoids.

Referenced by RenderEllipsoids().

Here is the caller graph for this function:

Vector3 HBallManager.computeEllipsoidNormal

(

int

residueId

)

Compute the plane normal for an ellipsoid (given a residue)

Returns

The ellipsoid normal.

Parameters

residueId

Residue identifier.

Definition at line 1092 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsForEllipsoidsPerResidue.

Referenced by UpdateEllipsoids().

Here is the caller graph for this function:

Vector3 HBallManager.computeEllipsoidOrientation

(

int

residueId

)

Definition at line 1118 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsForEllipsoidsOrientationPerResidue, and Molecule.Model.MoleculeModel.ellipsoidsPerResidue.

Vector3 HBallManager.computeEllipsoidPosition

(

int

residueId

)

Compute an ellipsoid position based on its associated atoms

Returns

The ellipsoid position.

Parameters

residueId

Residue identifier.

Definition at line 1068 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsForEllipsoidsPerResidue, and Molecule.Model.MoleculeModel.atomsNamelist.

Referenced by UpdateEllipsoids().

Here is the caller graph for this function:

void HBallManager.CreateMouseOvers ( )

private

Creates the mouse overs, needed when interactive mode is triggered.

Definition at line 843 of file HBallManager.cs.

Referenced by Update().

Here is the caller graph for this function:

void HBallManager.CreateMouseOversIMDSimulation

(

)

Implements GenericAtomManager.

Definition at line 870 of file HBallManager.cs.

References MouseOverMoleculeIMDSimulation.setAtomId().

Referenced by EnableRenderers().

Here is the call graph for this function:

Here is the caller graph for this function:

void HBallManager.DeactivateBases

(

)

Definition at line 1316 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsForEllipsoidsPerResidue, Molecule.Model.MoleculeModel.atomsNamelist, and Molecule.Model.MoleculeModel.bondsForReplacedAtoms.

Referenced by RenderEllipsoids().

Here is the caller graph for this function:

void HBallManager.DeactivateEllipsoids

(

)

Definition at line 1356 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.ellipsoids.

Referenced by DisableRenderers(), GenerateEllipsoids(), and RenderAtoms().

Here is the caller graph for this function:

override void HBallManager.DestroyAll ( )

virtual

Disable and destroys all the Hyperballs and Sticks.

Implements GenericManager.

Definition at line 123 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.ellipsoids, and GenericManager.isInit.

Referenced by Molecule.View.DisplayMolecule.DestroyAllAtomsAndBonds().

Here is the caller graph for this function:

void HBallManager.DestroyMouseOvers ( )

private

Destroys the mouse overs, needed when interactive mode is turned off.

Definition at line 854 of file HBallManager.cs.

Referenced by Update().

Here is the caller graph for this function:

void HBallManager.DestroyMouseOversIMDSimulation

(

)

Implements GenericAtomManager.

Definition at line 878 of file HBallManager.cs.

Referenced by DisableRenderers().

Here is the caller graph for this function:

override void HBallManager.DisableRenderers ( )

virtual

Disables the renderers for the entire set of balls and sticks.

Implements GenericManager.

Definition at line 922 of file HBallManager.cs.

References UI.UIData.atomtype, DeactivateEllipsoids(), DestroyMouseOversIMDSimulation(), and UI.GUIMoleculeController.toggle_IMD.

Here is the call graph for this function:

override void HBallManager.DisableShadows ( )

virtual

Implements GenericManager.

Definition at line 974 of file HBallManager.cs.

bool HBallManager.ellipsoidViewEnabled

(

)

Definition at line 92 of file HBallManager.cs.

References ellipsoidView.

Referenced by HiRERNAOldGUI.HiRERNAMenu().

Here is the caller graph for this function:

override void HBallManager.EnableRenderers ( )

virtual

Enables the renderers for the entire set of balls and sticks.

Implements GenericManager.

Definition at line 945 of file HBallManager.cs.

References CreateMouseOversIMDSimulation(), UnityMolMain.setCurrentAtomManager(), and UI.GUIMoleculeController.toggle_IMD.

Here is the call graph for this function:

override void HBallManager.EnableShadows ( )

virtual

Implements GenericManager.

Definition at line 965 of file HBallManager.cs.

void HBallManager.ExitInteractive ( )

private

Definition at line 861 of file HBallManager.cs.

References ResetColors(), and ResetPositions().

Referenced by Update().

Here is the call graph for this function:

Here is the caller graph for this function:

void HBallManager.findAtoms

(

)

Find atoms used to compute the ellipsoid plane

Definition at line 1126 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsForEllipsoidsOrientationPerResidue, Molecule.Model.MoleculeModel.atomsForEllipsoidsPerResidue, Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.atomsResnamelist, and Molecule.Model.MoleculeModel.residues.

Referenced by GenerateEllipsoids(), and SetTexture().

Here is the caller graph for this function:

void HBallManager.findBonds

(

)

Find bonds to be hidden to render ellipsoids

Definition at line 1194 of file HBallManager.cs.

References StickUpdate.atomnumber1, StickUpdate.atomnumber2, Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.atomsTypelist, and Molecule.Model.MoleculeModel.bondsForReplacedAtoms.

Referenced by GenerateEllipsoids().

Here is the caller graph for this function:

void HBallManager.GenerateEllipsoids

(

)

Generates the ellipsoids based on coarse-grain model

Definition at line 1234 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsResnamelist, DeactivateEllipsoids(), Molecule.Model.MoleculeModel.ellipsoids, Molecule.Model.MoleculeModel.ellipsoidsPerResidue, findAtoms(), findBonds(), Molecule.Model.MoleculeModel.residues, and UpdateEllipsoids().

Referenced by Update().

Here is the call graph for this function:

Here is the caller graph for this function:

override GameObject HBallManager.GetBall ( int  id )

virtual

Gets the GameObject from hballs at the position "id".

Returns

The ball.

Parameters

id	Identifier.

Implements GenericManager.

Definition at line 750 of file HBallManager.cs.

SingleAtomSelection HBallManager.getClosestAtomGameObject

(

Vector3

position

)

Implements GenericAtomManager.

Definition at line 1405 of file HBallManager.cs.

References SingleAtomSelection.go, BallUpdate.number, and SingleAtomSelection.pdbIndex.

Color HBallManager.GetColor

(

Vector3

pos

)

Gets the color of the atom at the location "pos".

Returns

The color.

Parameters

pos

Position.

Definition at line 734 of file HBallManager.cs.

override void HBallManager.Init ( )

virtual

Initalizes this instance.

Implements GenericManager.

Definition at line 99 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atoms, UI.GUIDisplay.file_extension, GenericManager.isInit, BallUpdate.resetColors, and BallUpdate.resetRadii.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), and ResetPositions().

Here is the caller graph for this function:

void HBallManager.ManagePhysics ( )

private

Manages the rigidbody physics.

Mostly just creates rigid bodies, spring joints, and sets a few parameters.

Definition at line 898 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsColorList, BallUpdate.number, and UI.UIData.toggleGray.

Referenced by Update().

Here is the caller graph for this function:

void HBallManager.MoveNetworkNodes ( )

private

Moves the network nodes when the depth factor is changed.

Definition at line 758 of file HBallManager.cs.

References BallUpdateHB.z.

Referenced by Update().

Here is the caller graph for this function:

void HBallManager.RenderAtoms

(

)

Definition at line 1373 of file HBallManager.cs.

References ActivateBases(), and DeactivateEllipsoids().

Referenced by SwitchRendering().

Here is the call graph for this function:

Here is the caller graph for this function:

void HBallManager.RenderEllipsoids

(

)

Definition at line 1366 of file HBallManager.cs.

References ActivateEllipsoids(), and DeactivateBases().

Referenced by SwitchRendering().

Here is the call graph for this function:

Here is the caller graph for this function:

void HBallManager.ResetBrightness ( )

private

Definition at line 986 of file HBallManager.cs.

References HStickManager.resetBrightness, and HStickMeshManager.resetBrightness.

Referenced by Update().

Here is the caller graph for this function:

void HBallManager.ResetColors ( )

private

Resets the colors of all balls and sticks.

Uses the colors set in BallUpdateHB and StickUpdate objects. Whose classes probably ought to be renamed.

Definition at line 420 of file HBallManager.cs.

References BallUpdate.atomcolor, Molecule.Model.MoleculeModel.atomsColorList, UI.UIData.atomtype, BallUpdate.bondsReadyToBeReset, BallUpdate.number, BallUpdate.resetColors, and UI.UIData.secondarystruct.

Referenced by ExitInteractive(), and Update().

Here is the caller graph for this function:

override void HBallManager.ResetIMDSimulationPositions ( )

virtual

Resets the positions of all balls.

(Useful after interactive mode)

Implements GenericManager.

Definition at line 783 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsIMDSimulationLocationlist.

override void HBallManager.ResetPositions ( )

virtual

Resets the positions of all balls.

(Useful after interactive mode)

Implements GenericManager.

Definition at line 766 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, UI.UIData.atomtype, BallUpdate.bondsReadyToBeReset, UI.UIData.bondtype, Molecule.View.DisplayMolecule.ChangeRepresentation(), and Init().

Referenced by ExitInteractive(), UI.LoadTypeGUI.MainFun(), and Molecule3D.SetCenter().

Here is the call graph for this function:

Here is the caller graph for this function:

override void HBallManager.ResetRadii ( )

virtual

Resets the radii of all balls when it is changed via the GUI.

Implements GenericManager.

Definition at line 793 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsLocalScaleList, Molecule.Model.MoleculeModel.atomsTypelist, UI.UIData.atomtype, RepresentationOldGUI.globalRadius, SecondaryStructureOldGUI.highBFradius, UI.GUIDisplay.newScale, BallUpdate.number, BallUpdate.oldRadiusFactor, BallUpdate.radiusFactor, BallUpdate.rayon, UI.UIData.secondarystruct, and SecondaryStructureOldGUI.structType.

Referenced by Update().

Here is the caller graph for this function:

void HBallManager.ResetShininess

(

)

Definition at line 1393 of file HBallManager.cs.

References HStickManager.resetShininess, HStickMeshManager.resetShininess, HStickManager.shininess, HStickMeshManager.shininess, and shininess.

Referenced by Update().

Here is the caller graph for this function:

override void HBallManager.SetColor ( Color  col, List< string >  atom, string  residue = "All", string  chain = "All"  )

virtual

Sets the color of atoms.

Parameters

col	Color.
atom	Atom type.
residue	Residue.
chain	Chain.

Implements GenericManager.

Definition at line 453 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsChainList, Molecule.Model.MoleculeModel.atomsColorList, Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.atomsResnamelist, BallUpdate.number, UI.GUIDisplay.quickSelection, and BallUpdate.resetColors.

override void HBallManager.SetColor ( Color  col, int  atomNum  )

virtual

Sets the color of a specific atom.

(Atom selection)

Parameters

col	Color.
atomNum	Atom number.

Implements GenericManager.

Definition at line 581 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsColorList, and BallUpdate.resetColors.

override void HBallManager.SetRadii ( List< string >  atom, string  residue = "All", string  chain = "All"  )

virtual

Changes the scale of the atoms.

Parameters

atom	Atom type.
residue	Residue.
chain	Chain.

Implements GenericManager.

Definition at line 601 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsChainList, Molecule.Model.MoleculeModel.atomsLocalScaleList, Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.atomsResnamelist, BallUpdate.bondsReadyToBeReset, UI.GUIDisplay.newScale, BallUpdate.number, UI.GUIDisplay.quickSelection, and BallUpdate.resetRadii.

override void HBallManager.SetRadii ( int  id )

virtual

Changes the scale for Atom selection.

Parameters

id	Identifier of the selected atom.

Implements GenericManager.

Definition at line 716 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsLocalScaleList, BallUpdate.bondsReadyToBeReset, UI.GUIDisplay.newScale, and BallUpdate.resetRadii.

void HBallManager.SetTexture	(	Texture	texture,
		List< string >	atom,
		string	residue = "All",
		string	chain = "All"
	)

Sets the texture of atoms.

Parameters

texture	Texture.
atom	Atom type.
residue	Residue.
chain	Chain.

Definition at line 242 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsChainList, Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.atomsResnamelist, BallUpdate.bondsReadyToBeReset, Molecule.Model.MoleculeModel.ellipsoids, findAtoms(), BallUpdate.number, UI.GUIDisplay.quickSelection, and BallUpdateHB.SetTexture().

Referenced by UI.GUIDisplay.AtomScales(), UI.GUIDisplay.FileSelectedCallback(), SetTexture(), and UI.GUIDisplay.SetTexturePanel().

Here is the call graph for this function:

Here is the caller graph for this function:

void HBallManager.SetTexture	(	string	resource_name,
		List< string >	atom,
		string	residue = "All",
		string	chain = "All"
	)

Sets the texture of one atom.

Parameters

resource_name	Path of the texture.
atom	Atom type.
residue	Residue.
chain	Chain.

Definition at line 378 of file HBallManager.cs.

References SetTexture().

Here is the call graph for this function:

void HBallManager.SetTexture	(	Texture	texture,
		int	atomNum
	)

Sets the MatCap texture for one atom.

Parameters

tex	Texture to use. Texture.
atomNum	Number of the atom. Int.

Definition at line 392 of file HBallManager.cs.

References BallUpdate.bondsReadyToBeReset, and BallUpdateHB.SetTexture().

Here is the call graph for this function:

void HBallManager.SetTexture	(	string	resource_name,
		int	atomNum
	)

Sets the MatCap texture for one atom.

Parameters

resource_name	Path of the texture to use. String.
atomNum	Number of the atom. Int.

Definition at line 410 of file HBallManager.cs.

References SetTexture().

Here is the call graph for this function:

override void HBallManager.showHydrogens ( bool  hide )

virtual

Implements GenericManager.

Definition at line 1429 of file HBallManager.cs.

void HBallManager.StartPhysicsManagement ( )

private

Definition at line 886 of file HBallManager.cs.

Referenced by Update().

Here is the caller graph for this function:

void HBallManager.SwitchRendering

(

)

Definition at line 1380 of file HBallManager.cs.

References ellipsoidView, RenderAtoms(), and RenderEllipsoids().

Referenced by HiRERNAOldGUI.HiRERNAMenu().

Here is the call graph for this function:

Here is the caller graph for this function:

override void HBallManager.ToggleDistanceCueing ( bool  enabling )

virtual

Initializes the list of sticks.

Implements GenericManager.

Definition at line 182 of file HBallManager.cs.

References UI.UIData.bondtype.

void HBallManager.Update ( )

private

Definition at line 996 of file HBallManager.cs.

References HStickManager.adjustRadii, UI.UIData.atomtype, UI.UIData.bondtype, CreateMouseOvers(), depthFactor, DestroyMouseOvers(), ExitInteractive(), UI.UIData.ffType, GenerateEllipsoids(), UI.UIData.isFileLoaded, UI.UIData.isHBallLoaded, ManagePhysics(), MoveNetworkNodes(), Molecule.Model.MoleculeModel.networkLoaded, BallUpdate.oldRadiusFactor, StickUpdate.oldscale, StickUpdate.oldshrink, BallUpdate.radiusFactor, ResetBrightness(), BallUpdate.resetColors, ResetColors(), BallUpdate.resetRadii, ResetRadii(), ResetShininess(), StickUpdate.scale, StickUpdate.shrink, StartPhysicsManagement(), UI.GUIMoleculeController.toggle_IMD, UI.GUIMoleculeController.toggle_NA_INTERACTIVE, and UpdateEllipsoids().

Here is the call graph for this function:

void HBallManager.UpdateEllipsoids

(

)

Definition at line 1215 of file HBallManager.cs.

References Molecule.Model.MoleculeModel.atomsForEllipsoidsOrientationPerResidue, computeEllipsoidNormal(), computeEllipsoidPosition(), and Molecule.Model.MoleculeModel.ellipsoidsPerResidue.

Referenced by GenerateEllipsoids(), and Update().

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

string [] HBallManager.allowedAtomsForPosition = {"CY", "C1", "U1", "G1", "G2", "A1", "A2"}

static

Definition at line 74 of file HBallManager.cs.

float HBallManager.brightness = 1.0f

static

Definition at line 82 of file HBallManager.cs.

Referenced by RepresentationOldGUI.AtomMenu(), AtomsGUI.Brightness(), HStickMeshManager.ResetBrightness(), and HStickManager.ResetBrightness().

float HBallManager.depthFactor = 1.0f

static

Definition at line 81 of file HBallManager.cs.

Referenced by Molecule3D.Update(), and Update().

bool HBallManager.ellipsoidsInitialized = false

static

Definition at line 91 of file HBallManager.cs.

bool HBallManager.ellipsoidView = false

static

Definition at line 90 of file HBallManager.cs.

Referenced by ellipsoidViewEnabled(), and SwitchRendering().

BallUpdateHB [] HBallManager.hballs

static

Definition at line 77 of file HBallManager.cs.

Referenced by SugarManager.Hide_No_Sugar_Hyperballs(), and SugarManager.show_HyperBalls_Sugar().

GameObject [] HBallManager.hballsGameObjects

private

Definition at line 78 of file HBallManager.cs.

bool HBallManager.mouseOvers = false

staticprivate

Definition at line 87 of file HBallManager.cs.

float HBallManager.oldDepthFactor = 1.0f

staticprivate

Definition at line 86 of file HBallManager.cs.

bool HBallManager.resetBrightness = false

static

Definition at line 84 of file HBallManager.cs.

Referenced by RepresentationOldGUI.AtomMenu(), and AtomsGUI.Brightness().

bool HBallManager.resetShininess = false

static

Definition at line 85 of file HBallManager.cs.

Referenced by RepresentationOldGUI.RenderingParameters().

float HBallManager.shininess = 0.0f

static

Definition at line 83 of file HBallManager.cs.

Referenced by RepresentationOldGUI.RenderingParameters(), and ResetShininess().

bool HBallManager.wasInteractiveColored = false

staticprivate

Definition at line 88 of file HBallManager.cs.

bool HBallManager.xgmml = false

static

Definition at line 80 of file HBallManager.cs.

---

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

• Assets/Scripts/Molecule/View/HBallManager.cs