SurfaceManager Class Reference

Collaboration diagram for SurfaceManager:

Public Member Functions
void	ResetColorVertices ()
void	ResetColorVertices (Mesh mesh)
GameObject	getParentGameObject ()
void	ColorVertices ()
void	ResetBrightness ()
void	ResetColorWeight ()
void	addSurface (GameObject surface)
void	addSurfacePos (GameObject surface)
void	addSurfaceNeg (GameObject surface)
GameObject[]	getSurfaces ()
GameObject[]	getSurfacesNeg ()
GameObject[]	getSurfacesPos ()
void	DestroySurfaces ()
void	DestroyPos ()
void	DestroyNeg ()
void	ShowHideSurfaceNeg ()
void	ShowHideSurfacePos ()
void	resetSurfaceColors ()
void	updateColors ()
void	updateCut ()
void	updateTexture ()
void	RecenterSurfaces (Vector3 pos)
Texture2D	ToGray (Texture texture)
void	SetTransparentSurface (bool transparent)
void	SetTransparentSurfaceColor (Color newcolor)

Static Public Member Functions
static void	InitCutParameters ()
static void	GenerateSurface ()
static void	GenerateSurfaceBfact ()
static void	ShowHideVolumetricDensity ()
static void	ShowHideSurfaces ()
static void	SurfaceRenderUp ()
static void	usePropertiesColor ()
static void	useBFactorColor ()
static void	useChainColor ()
static void	useKyteAndDoolittleColor ()
static void	useEnglemanColor ()
static void	useEinsenbergColor ()
static void	useWhiteOctanolColor ()
static void	setBrightness (float value)
static void	setColorWeight (float value)

Static Public Attributes
static float	brightness = 1f
static float	colorWeight = 0.5f
static bool	pdbGen = false
static GameObject	pdb2den
static float	cutX = 1f
static float	cutY = 0f
static float	cutZ = 0f
static float	depthCut = 40f
static float	depthCutMin = 0
static float	depthCutMax = 0
static bool	surfaceInitialized = false
static ColorObject	SurfaceColor = new ColorObject(Color.white)
static ColorObject	SurfaceInsideColor = new ColorObject(Color.gray)
static float	surfaceThreshold = 0.5f
static int	cutMode = 0
static bool	externalSurfaceTexture = false
static string	surfaceTextureName = null
static string	m_last_extSurf_Path = null
static Texture2D	extSurf = null
static bool	volumetricDensityActivated = false
static bool	useHetatmForSurface = false
static bool	useSugarForSurface = false

Private Member Functions
void	InitTree ()
void	ColorVertices (Mesh mesh)
Color	GetClosestAtomColor (Vector3 pos)

Private Attributes
List< GameObject >	surfaceList = new List<GameObject>()
List< GameObject >	surfacePos = new List<GameObject>()
List< GameObject >	surfaceNeg = new List<GameObject>()
AtomTree	atomTree
float	bTime
float	valmin = 0
float	valmax = 0
string	bftype = ""

Static Private Attributes
static bool	slowColoring = false
static List< Vector3 >	atomLocations
static List< Color >	atomColors
static GameObject	VolumetricDensityObj = null
static VolumetricDensity	volumetricDensityscript = null

Detailed Description

Definition at line 7 of file SurfaceManager.cs.

Member Function Documentation

void SurfaceManager.addSurface

(

GameObject

surface

)

Definition at line 204 of file SurfaceManager.cs.

Referenced by OBJ.Build(), GenerateMesh.CreateSurfaceObjects(), and GenerateMesh.GM().

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void SurfaceManager.addSurfaceNeg

(

GameObject

surface

)

Definition at line 211 of file SurfaceManager.cs.

Referenced by GenerateMesh.CreateSurfaceObjects().

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void SurfaceManager.addSurfacePos

(

GameObject

surface

)

Definition at line 208 of file SurfaceManager.cs.

Referenced by GenerateMesh.CreateSurfaceObjects().

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void SurfaceManager.ColorVertices ( Mesh  mesh )

private

Definition at line 87 of file SurfaceManager.cs.

References atomColors, atomLocations, Molecule.Model.MoleculeModel.atomsColorList, Molecule.Model.MoleculeModel.atomsLocationlist, Molecule.Model.AtomModel.baseColor, Molecule.Model.MoleculeModel.BFactorList, Molecule.Model.MoleculeModel.GetAtomColor(), BFactorRep.GetBFStyle(), AtomTree.GetClosestAtomType(), Ribbons.GetColorChain(), HydrophobicScales.GetColorHydro(), BFactorRep.GetMax(), BFactorRep.GetMin(), Molecule.Model.AtomModel.GetModel(), Ribbons.InitCol(), HydrophobicScales.InitEisenberg(), HydrophobicScales.InitEngleman(), HydrophobicScales.InitKyteDoo(), HydrophobicScales.InitPhysChim(), HydrophobicScales.InitWhiteOct(), resetSurfaceColors(), slowColoring, UI.UIData.surfColBF, UI.UIData.surfColChain, UI.UIData.surfColHydroEis, UI.UIData.surfColHydroEng, UI.UIData.surfColHydroKD, UI.UIData.surfColHydroWO, UI.UIData.surfColPChim, and valmin.

Referenced by useBFactorColor(), useChainColor(), useEinsenbergColor(), useEnglemanColor(), useKyteAndDoolittleColor(), usePropertiesColor(), and useWhiteOctanolColor().

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void SurfaceManager.ColorVertices

(

)

Definition at line 172 of file SurfaceManager.cs.

References bTime, and getSurfaces().

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void SurfaceManager.DestroyNeg

(

)

Definition at line 242 of file SurfaceManager.cs.

Referenced by ElectrostaticOldGUI.Electrostatics().

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void SurfaceManager.DestroyPos

(

)

Definition at line 235 of file SurfaceManager.cs.

Referenced by ElectrostaticOldGUI.Electrostatics().

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void SurfaceManager.DestroySurfaces

(

)

Definition at line 226 of file SurfaceManager.cs.

References getSurfaces().

Referenced by Molecule.View.DisplayMolecule.ClearMemory(), ElectrostaticOldGUI.Electrostatics(), GenerateSurface(), and GenerateSurfaceBfact().

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static void SurfaceManager.GenerateSurface ( )

static

Definition at line 250 of file SurfaceManager.cs.

References DestroySurfaces(), UnityMolMain.getSurfaceManager(), PDBtoDEN.ProSurface(), Molecule.Model.MoleculeModel.surfaceFileExists, UI.UIData.toggleBfac, and PDBtoDEN.TranPDBtoDEN().

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.Surface().

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static void SurfaceManager.GenerateSurfaceBfact ( )

static

Definition at line 277 of file SurfaceManager.cs.

References DestroySurfaces(), UnityMolMain.getSurfaceManager(), PDBtoDEN.ProSurface(), Molecule.Model.MoleculeModel.surfaceFileExists, UI.UIData.toggleBfac, and PDBtoDEN.TranPDBtoDEN().

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.Surface().

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Color SurfaceManager.GetClosestAtomColor ( Vector3  pos )

private

Definition at line 148 of file SurfaceManager.cs.

References atomColors, and atomLocations.

GameObject SurfaceManager.getParentGameObject

(

)

Definition at line 167 of file SurfaceManager.cs.

Referenced by OBJ.Build(), GenerateMesh.GM(), and GenerateMesh.InitGenMesh().

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GameObject [] SurfaceManager.getSurfaces

(

)

Definition at line 214 of file SurfaceManager.cs.

Referenced by ColorVertices(), DestroySurfaces(), ReadDX.isoSurface(), ResetBrightness(), ResetColorVertices(), ResetColorWeight(), resetSurfaceColors(), UI.GUIMoleculeController.SetBfactorMenu(), UI.GUIMoleculeController.SetSurfaceMenu(), ShowHideSurfaces(), SurfaceOldGUI.Surface(), SurfaceRenderUp(), updateColors(), updateCut(), and updateTexture().

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GameObject [] SurfaceManager.getSurfacesNeg

(

)

Definition at line 218 of file SurfaceManager.cs.

Referenced by ReadDX.isoSurface(), and ShowHideSurfaceNeg().

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GameObject [] SurfaceManager.getSurfacesPos

(

)

Definition at line 221 of file SurfaceManager.cs.

Referenced by ReadDX.isoSurface(), and ShowHideSurfacePos().

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static void SurfaceManager.InitCutParameters ( )

static

Definition at line 193 of file SurfaceManager.cs.

References depthCut, depthCutMax, depthCutMin, Molecule.Model.MoleculeModel.MaxValue, and Molecule.Model.MoleculeModel.MinValue.

Referenced by Molecule3D.OnGUI().

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void SurfaceManager.InitTree ( )

private

Definition at line 68 of file SurfaceManager.cs.

References AtomTree.Build().

Referenced by useBFactorColor(), useChainColor(), useEinsenbergColor(), useEnglemanColor(), useKyteAndDoolittleColor(), usePropertiesColor(), and useWhiteOctanolColor().

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void SurfaceManager.RecenterSurfaces

(

Vector3

pos

)

Definition at line 473 of file SurfaceManager.cs.

References UnityMolMain.getElectrostaticManager(), Molecule.Model.MoleculeModel.Offset, and ElectrostaticManager.RecenterFieldLines().

Referenced by Molecule3D.OnGUI().

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void SurfaceManager.ResetBrightness

(

)

Definition at line 181 of file SurfaceManager.cs.

References brightness, and getSurfaces().

Referenced by setBrightness().

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void SurfaceManager.ResetColorVertices

(

)

Definition at line 73 of file SurfaceManager.cs.

References getSurfaces().

Referenced by updateColors().

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void SurfaceManager.ResetColorVertices

(

Mesh

mesh

)

Definition at line 79 of file SurfaceManager.cs.

void SurfaceManager.ResetColorWeight

(

)

Definition at line 187 of file SurfaceManager.cs.

References colorWeight, and getSurfaces().

Referenced by setColorWeight().

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void SurfaceManager.resetSurfaceColors

(

)

Definition at line 357 of file SurfaceManager.cs.

References UnityMolMain.getSurfaceManager(), and getSurfaces().

Referenced by ColorVertices().

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static void SurfaceManager.setBrightness ( float  value )

static

Definition at line 463 of file SurfaceManager.cs.

References brightness, UnityMolMain.getSurfaceManager(), and ResetBrightness().

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.SurfaceParams().

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static void SurfaceManager.setColorWeight ( float  value )

static

Definition at line 468 of file SurfaceManager.cs.

References colorWeight, UnityMolMain.getSurfaceManager(), and ResetColorWeight().

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.SurfaceParams().

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void SurfaceManager.SetTransparentSurface

(

bool

transparent

)

Definition at line 505 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.SurfaceParams().

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void SurfaceManager.SetTransparentSurfaceColor

(

Color

newcolor

)

Definition at line 514 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.SurfaceParams().

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void SurfaceManager.ShowHideSurfaceNeg

(

)

Definition at line 326 of file SurfaceManager.cs.

References UnityMolMain.getSurfaceManager(), and getSurfacesNeg().

Referenced by ElectrostaticOldGUI.Electrostatics().

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void SurfaceManager.ShowHideSurfacePos

(

)

Definition at line 332 of file SurfaceManager.cs.

References UnityMolMain.getSurfaceManager(), and getSurfacesPos().

Referenced by ElectrostaticOldGUI.Electrostatics().

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static void SurfaceManager.ShowHideSurfaces ( )

static

Definition at line 317 of file SurfaceManager.cs.

References UnityMolMain.getSurfaceManager(), and getSurfaces().

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.Surface().

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static void SurfaceManager.ShowHideVolumetricDensity ( )

static

Definition at line 302 of file SurfaceManager.cs.

References Volumetric.Clear(), VolumetricDensity.Init(), and volumetricDensityActivated.

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.Surface().

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static void SurfaceManager.SurfaceRenderUp ( )

static

Definition at line 338 of file SurfaceManager.cs.

References UnityMolMain.getSurfaceManager(), and getSurfaces().

Referenced by SurfaceOldGUI.SurfaceParams().

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Texture2D SurfaceManager.ToGray

(

Texture

texture

)

Return the grayscale version of a texture

Returns

Grayscale version of the texture. Texture2D.

Parameters

texture

Texture to transform. Texture.

Definition at line 489 of file SurfaceManager.cs.

Referenced by updateTexture().

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void SurfaceManager.updateColors

(

)

Definition at line 363 of file SurfaceManager.cs.

References ColorObject.color, UnityMolMain.getSurfaceManager(), getSurfaces(), and ResetColorVertices().

Referenced by SurfaceOldGUI.SurfaceParams().

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void SurfaceManager.updateCut

(

)

Definition at line 371 of file SurfaceManager.cs.

References cutX, cutY, cutZ, depthCut, UnityMolMain.getSurfaceManager(), and getSurfaces().

Referenced by SurfaceOldGUI.MoveCutPlane(), SurfaceOldGUI.SurfaceCut(), and SurfaceOldGUI.SurfaceMobileCut().

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void SurfaceManager.updateTexture

(

)

Definition at line 382 of file SurfaceManager.cs.

References UnityMolMain.getSurfaceManager(), getSurfaces(), UI.UIData.grayscalemode, and ToGray().

Referenced by SurfaceOldGUI.textureMenu().

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static void SurfaceManager.useBFactorColor ( )

static

Definition at line 415 of file SurfaceManager.cs.

References ColorVertices(), UnityMolMain.getSurfaceManager(), InitTree(), and UI.UIData.surfColBF.

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.SurfaceParams().

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static void SurfaceManager.useChainColor ( )

static

Definition at line 423 of file SurfaceManager.cs.

References ColorVertices(), UnityMolMain.getSurfaceManager(), InitTree(), and UI.UIData.surfColChain.

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.SurfaceParams().

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static void SurfaceManager.useEinsenbergColor ( )

static

Definition at line 447 of file SurfaceManager.cs.

References ColorVertices(), UnityMolMain.getSurfaceManager(), InitTree(), and UI.UIData.surfColHydroEis.

Referenced by SurfaceOldGUI.HydroMenu(), and SurfaceGUI.Start().

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static void SurfaceManager.useEnglemanColor ( )

static

Definition at line 439 of file SurfaceManager.cs.

References ColorVertices(), UnityMolMain.getSurfaceManager(), InitTree(), and UI.UIData.surfColHydroEng.

Referenced by SurfaceOldGUI.HydroMenu(), and SurfaceGUI.Start().

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static void SurfaceManager.useKyteAndDoolittleColor ( )

static

Definition at line 431 of file SurfaceManager.cs.

References ColorVertices(), UnityMolMain.getSurfaceManager(), InitTree(), and UI.UIData.surfColHydroKD.

Referenced by SurfaceOldGUI.HydroMenu(), and SurfaceGUI.Start().

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static void SurfaceManager.usePropertiesColor ( )

static

Definition at line 407 of file SurfaceManager.cs.

References ColorVertices(), UnityMolMain.getSurfaceManager(), InitTree(), and UI.UIData.surfColPChim.

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.SurfaceParams().

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static void SurfaceManager.useWhiteOctanolColor ( )

static

Definition at line 455 of file SurfaceManager.cs.

References ColorVertices(), UnityMolMain.getSurfaceManager(), InitTree(), and UI.UIData.surfColHydroWO.

Referenced by SurfaceOldGUI.HydroMenu(), and SurfaceGUI.Start().

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Member Data Documentation

List<Color> SurfaceManager.atomColors

staticprivate

Definition at line 31 of file SurfaceManager.cs.

Referenced by ColorVertices(), and GetClosestAtomColor().

List<Vector3> SurfaceManager.atomLocations

staticprivate

Definition at line 30 of file SurfaceManager.cs.

Referenced by ColorVertices(), and GetClosestAtomColor().

AtomTree SurfaceManager.atomTree

private

Definition at line 40 of file SurfaceManager.cs.

string SurfaceManager.bftype = ""

private

Definition at line 45 of file SurfaceManager.cs.

float SurfaceManager.brightness = 1f

static

Definition at line 11 of file SurfaceManager.cs.

Referenced by ResetBrightness(), setBrightness(), and SurfaceOldGUI.SurfaceParams().

float SurfaceManager.bTime

private

Definition at line 41 of file SurfaceManager.cs.

Referenced by ColorVertices().

float SurfaceManager.colorWeight = 0.5f

static

Definition at line 12 of file SurfaceManager.cs.

Referenced by ResetColorWeight(), setColorWeight(), and SurfaceOldGUI.SurfaceParams().

int SurfaceManager.cutMode = 0

static

Definition at line 53 of file SurfaceManager.cs.

Referenced by SurfaceGUI.Start(), SurfaceOldGUI.SurfaceParams(), and ElectrostaticManager.UpdateParameters().

float SurfaceManager.cutX = 1f

static

Definition at line 19 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.MoveCutPlane(), SurfaceGUI.Start(), SurfaceOldGUI.SurfaceCut(), updateCut(), and ElectrostaticManager.UpdateParameters().

float SurfaceManager.cutY = 0f

static

Definition at line 20 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.MoveCutPlane(), SurfaceGUI.Start(), SurfaceOldGUI.SurfaceCut(), updateCut(), and ElectrostaticManager.UpdateParameters().

float SurfaceManager.cutZ = 0f

static

Definition at line 21 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.MoveCutPlane(), SurfaceGUI.Start(), SurfaceOldGUI.SurfaceCut(), updateCut(), and ElectrostaticManager.UpdateParameters().

float SurfaceManager.depthCut = 40f

static

Definition at line 22 of file SurfaceManager.cs.

Referenced by InitCutParameters(), SurfaceOldGUI.MoveCutPlane(), SurfaceGUI.Start(), SurfaceOldGUI.SurfaceCut(), SurfaceOldGUI.SurfaceMobileCut(), updateCut(), and ElectrostaticManager.UpdateParameters().

float SurfaceManager.depthCutMax = 0

static

Definition at line 24 of file SurfaceManager.cs.

Referenced by InitCutParameters(), and SurfaceOldGUI.SurfaceCut().

float SurfaceManager.depthCutMin = 0

static

Definition at line 23 of file SurfaceManager.cs.

Referenced by InitCutParameters(), and SurfaceOldGUI.SurfaceCut().

bool SurfaceManager.externalSurfaceTexture = false

static

Definition at line 55 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.FileSelectedCallback().

Texture2D SurfaceManager.extSurf = null

static

Definition at line 59 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.FileSelectedCallback().

string SurfaceManager.m_last_extSurf_Path = null

static

Definition at line 58 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.FileSelectedCallback(), and SurfaceOldGUI.textureMenu().

GameObject SurfaceManager.pdb2den

static

Definition at line 15 of file SurfaceManager.cs.

bool SurfaceManager.pdbGen = false

static

Definition at line 14 of file SurfaceManager.cs.

Referenced by Molecule3D.clearScene(), and SurfaceOldGUI.openCloseSurfaceMenu().

bool SurfaceManager.slowColoring = false

staticprivate

Definition at line 29 of file SurfaceManager.cs.

Referenced by ColorVertices().

ColorObject SurfaceManager.SurfaceColor = new ColorObject(Color.white)

static

Definition at line 49 of file SurfaceManager.cs.

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.SurfaceParams().

bool SurfaceManager.surfaceInitialized = false

static

Definition at line 47 of file SurfaceManager.cs.

Referenced by OBJ.Build().

ColorObject SurfaceManager.SurfaceInsideColor = new ColorObject(Color.gray)

static

Definition at line 50 of file SurfaceManager.cs.

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.SurfaceParams().

List<GameObject> SurfaceManager.surfaceList = new List<GameObject>()

private

Definition at line 33 of file SurfaceManager.cs.

List<GameObject> SurfaceManager.surfaceNeg = new List<GameObject>()

private

Definition at line 35 of file SurfaceManager.cs.

List<GameObject> SurfaceManager.surfacePos = new List<GameObject>()

private

Definition at line 34 of file SurfaceManager.cs.

string SurfaceManager.surfaceTextureName = null

static

Definition at line 56 of file SurfaceManager.cs.

Referenced by SurfaceOldGUI.textureMenu().

float SurfaceManager.surfaceThreshold = 0.5f

static

Definition at line 52 of file SurfaceManager.cs.

Referenced by SurfaceGUI.Start(), and SurfaceOldGUI.Surface().

bool SurfaceManager.useHetatmForSurface = false

static

Definition at line 64 of file SurfaceManager.cs.

Referenced by SurfaceGUI.Start(), SurfaceOldGUI.Surface(), and PDBtoDEN.TranPDBtoDEN().

bool SurfaceManager.useSugarForSurface = false

static

Definition at line 66 of file SurfaceManager.cs.

Referenced by SurfaceGUI.Start(), SurfaceOldGUI.Surface(), and PDBtoDEN.TranPDBtoDEN().

float SurfaceManager.valmax = 0

private

Definition at line 44 of file SurfaceManager.cs.

float SurfaceManager.valmin = 0

private

Definition at line 43 of file SurfaceManager.cs.

Referenced by ColorVertices().

bool SurfaceManager.volumetricDensityActivated = false

static

Definition at line 60 of file SurfaceManager.cs.

Referenced by ShowHideVolumetricDensity().

GameObject SurfaceManager.VolumetricDensityObj = null

staticprivate

Definition at line 37 of file SurfaceManager.cs.

VolumetricDensity SurfaceManager.volumetricDensityscript = null

staticprivate

Definition at line 38 of file SurfaceManager.cs.

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

• Assets/Scripts/Surface-Electrostatic/SurfaceManager.cs