SugarRibbons Class Reference

Collaboration diagram for SugarRibbons:

Public Member Functions
	SugarRibbons (bool SugarOnly)
List< List< GameObject > >	createSugarRibs (float RibbonsThickness, bool sugarOnly, float thickness_Little, float thickness_BIG, float thickness_bond_6_C1_C4, float thickness_6_other, float thickness_bond_5, float lighter_color_factor_ring, float lighter_color_factor_bond, int color_mode_ring, int color_mode_bond, ColorObject bondcolor, ColorObject ringcolor, float OxySphereSize, ColorObject OxySphereColor)
void	changeColor (int which)
Vector3	calcMidPoint (Vector3 a, Vector3 b)
List< Vector3 >	enlargeMesh (int i, float scaling)
GameObject	CreateOxygenSphere (int pos, int res, int sugartype=0)
List< GameObject >	ShowOxySphere (int colortype)
GameObject	CreateSugarRibbonsObj (Mesh mesh, string res="", string chain="", string tag="SugarRibbons", int id=0)
List< List< GameObject > >	createSugarRibbons ()
void	updateColorBond (List< GameObject > objs, ColorObject newColor)
void	updateColorRing (List< GameObject > objs, ColorObject newColor)
void	updateColorBond (List< GameObject > objs, int type)
void	updateColorRing (List< GameObject > objs, int type)
Color	lightColor (Color color, float correctionFactor=0.35f)
void	cleanup ()

Static Public Member Functions
static void	Solve (Mesh mesh)

Public Attributes
List< Mesh >	CycleMesh = new List<Mesh>()
List< Mesh >	CycleBIGMesh = new List<Mesh>()
List< Mesh >	meshesRingUp =new List<Mesh>()
List< Mesh >	meshesRingDown = new List<Mesh>()
List< Mesh >	meshesSideRing = new List<Mesh> ()
List< Mesh >	meshesBIGRingUp =new List<Mesh>()
List< Mesh >	meshesBIGRingDown = new List<Mesh>()
List< Mesh >	meshesBIGSideRing = new List<Mesh> ()
List< Mesh >	meshesBondUp = new List<Mesh>()
List< Mesh >	meshesBondDown = new List<Mesh>()
List< Mesh >	meshesBondSide = new List<Mesh>()
List< GraphVertex >	molAsGraph = new List<GraphVertex>()
List< List< int > >	cycles = new List<List<int>>()
List< string >	residueslist = new List<string>()
List< int >	residuesNumberlist = new List<int>()
List< Vector3 >	barylist = new List<Vector3>()
List< Vector3 >	vertices = new List<Vector3>()
List< Color32 >	colors = new List<Color32>()
List< Vector3 >	normals = new List<Vector3>()
List< int >	triangles = new List<int>()
float	THICKNESS
float	THICKNESS_LITTLE_MESH
float	THICKNESS_BIG_MESH
float	THICKNESS_BOND_6_C1_C4
float	THICKNESS_BOND_6_OTHER
float	THICKNESS_BOND_5
float	LIGHTER_COLOR_FACTOR_RING
float	LIGHTER_COLOR_FACTOR_BOND
float	OXYSPHERESIZE
bool	SUGAR_ONLY
int	COLOR_MODE_RING
int	COLOR_MODE_BOND
int	SUGAR =0
int	CHAIN =1
int	PICKER =2
ColorObject	BONDCOLOR
ColorObject	RINGCOLOR
ColorObject	OXYSPHERECOLOR
int	nbRes
List< string >	sugarResname = new List<string>()
List< float[]>	atomsLocationlist = new List<float[]>()
List< string >	atomsResnamelist = new List<string>()
List< string >	atomsNamelist = new List<string>()
List< string >	resChainList = new List<string>()
List< int[]>	bondEPList = new List<int[]>()
Dictionary< int, List< int > >	connectivityList = new Dictionary<int, List<int>>()
Dictionary< int, Dictionary< int, int[]> >	MeshIndexForAtom = new Dictionary<int, Dictionary<int, int[]>>()
Dictionary< int, string >	res_for_bond = new Dictionary<int, string>()

Static Public Attributes
static float[]	wideness = {1f, 2f, 1f}

Private Member Functions
Vector3	LinearComb (float scalar0, Vector3 vector0, float scalar1, Vector3 vector1)
Vector3	float3toVector3 (float[] point)
void	generateCycleMesh2 ()
List< Vector3 >	makeFlatVertex (List< Vector3 > verticeEn)
void	generateBiggerCycleMesh (float scaling=0.60f)
void	generateRibbonsMesh (Mesh centralMesh, int resnumber, float thicknessCenter=1f, bool center=true)
void	create_Bond ()
void	debugline (Vector3 a, Vector3 b)
void	CalculBarycenter ()
Vector3	calculMeshBarycenter (Mesh mesh)
Vector3	calculMidPoint (Vector3 a, Vector3 b)
int	findRingAtomIndex (int ringIndex, int AtomNumber)
Vector3	CycleAtomToVector3 (int index_res, int number)
Vector3	calcullittleRibbonsControlPoint (Vector3 a, Vector3 b, float size=0.7f)
void	createDebugSphere (Vector3 point, Color color, float size=1f)
Vector3	calculMeanNormalMesh (Mesh mesh)
int[]	invertTrianglesMesh (Mesh mesh)
int[]	generateTriangleSide (Mesh mesh)

Detailed Description

Definition at line 8 of file SugarRibbons.cs.

Constructor & Destructor Documentation

SugarRibbons.SugarRibbons

(

bool

SugarOnly

)

Definition at line 89 of file SugarRibbons.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.atomsResnamelist, Molecule.Model.MoleculeModel.atomsSugarLocationlist, Molecule.Model.MoleculeModel.atomsSugarNamelist, Molecule.Model.MoleculeModel.atomsSugarResnamelist, Molecule.Model.MoleculeModel.bondEPList, Molecule.Model.MoleculeModel.bondEPSugarList, CalculBarycenter(), GraphVertex.coordinate, GraphVertex.id, Molecule.Model.MoleculeModel.resChainList, GraphVertex.resname, Molecule.Model.MoleculeModel.resSugarChainList, and GraphVertex.type.

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Member Function Documentation

Vector3 SugarRibbons.calcMidPoint	(	Vector3	a,
		Vector3	b
	)

Definition at line 283 of file SugarRibbons.cs.

Referenced by enlargeMesh().

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void SugarRibbons.CalculBarycenter ( )

private

Definition at line 984 of file SugarRibbons.cs.

Referenced by SugarRibbons().

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Vector3 SugarRibbons.calcullittleRibbonsControlPoint ( Vector3  a, Vector3  b, float  size = 0.7f  )

private

Definition at line 1050 of file SugarRibbons.cs.

Referenced by makeFlatVertex().

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Vector3 SugarRibbons.calculMeanNormalMesh ( Mesh  mesh )

private

Definition at line 1072 of file SugarRibbons.cs.

Referenced by generateRibbonsMesh().

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Vector3 SugarRibbons.calculMeshBarycenter ( Mesh  mesh )

private

Definition at line 1007 of file SugarRibbons.cs.

Vector3 SugarRibbons.calculMidPoint ( Vector3  a, Vector3  b  )

private

Definition at line 1024 of file SugarRibbons.cs.

void SugarRibbons.changeColor

(

int

which

)

Definition at line 217 of file SugarRibbons.cs.

void SugarRibbons.cleanup

(

)

Definition at line 1126 of file SugarRibbons.cs.

Referenced by SugarManager.DestroySugarRibs().

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void SugarRibbons.create_Bond ( )

private

Definition at line 533 of file SugarRibbons.cs.

References UI.GUIDisplay.ChainColorDict, ColorObject.color, UI.GUIDisplay.colorByResiduesDict, findRingAtomIndex(), lightColor(), and Molecule.Model.MoleculeModel.resChainList.

Referenced by createSugarRibbons().

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void SugarRibbons.createDebugSphere ( Vector3  point, Color  color, float  size = 1f  )

private

Definition at line 1062 of file SugarRibbons.cs.

GameObject SugarRibbons.CreateOxygenSphere	(	int	pos,
		int	res,
		int	sugartype = 0
	)

Definition at line 701 of file SugarRibbons.cs.

References UI.GUIDisplay.ChainColorDict, and UI.GUIDisplay.colorByResiduesDict.

Referenced by ShowOxySphere().

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List<List<GameObject> > SugarRibbons.createSugarRibbons

(

)

Definition at line 847 of file SugarRibbons.cs.

References create_Bond(), CreateSugarRibbonsObj(), generateBiggerCycleMesh(), generateCycleMesh2(), and generateRibbonsMesh().

Referenced by createSugarRibs().

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GameObject SugarRibbons.CreateSugarRibbonsObj	(	Mesh	mesh,
		string	res = "",
		string	chain = "",
		string	tag = "SugarRibbons",
		int	id = 0
	)

For each mesh, we create Two mesh (to have a ribbon with tchickness)

Parameters

mesh	Mesh.
res	Res.

Definition at line 744 of file SugarRibbons.cs.

References Solve().

Referenced by createSugarRibbons().

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List<List<GameObject> > SugarRibbons.createSugarRibs	(	float	RibbonsThickness,
		bool	sugarOnly,
		float	thickness_Little,
		float	thickness_BIG,
		float	thickness_bond_6_C1_C4,
		float	thickness_6_other,
		float	thickness_bond_5,
		float	lighter_color_factor_ring,
		float	lighter_color_factor_bond,
		int	color_mode_ring,
		int	color_mode_bond,
		ColorObject	bondcolor,
		ColorObject	ringcolor,
		float	OxySphereSize,
		ColorObject	OxySphereColor
	)

Definition at line 189 of file SugarRibbons.cs.

References createSugarRibbons().

Referenced by SugarManager.CreateSugarRibs().

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Vector3 SugarRibbons.CycleAtomToVector3 ( int  index_res, int  number  )

private

Definition at line 1041 of file SugarRibbons.cs.

Referenced by enlargeMesh(), and generateCycleMesh2().

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void SugarRibbons.debugline ( Vector3  a, Vector3  b  )

private

Definition at line 831 of file SugarRibbons.cs.

List<Vector3> SugarRibbons.enlargeMesh	(	int	i,
		float	scaling
	)

Definition at line 287 of file SugarRibbons.cs.

References calcMidPoint(), and CycleAtomToVector3().

Referenced by generateBiggerCycleMesh().

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int SugarRibbons.findRingAtomIndex ( int  ringIndex, int  AtomNumber  )

private

Definition at line 1033 of file SugarRibbons.cs.

Referenced by create_Bond().

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Vector3 SugarRibbons.float3toVector3 ( float[]  point )

private

Definition at line 72 of file SugarRibbons.cs.

void SugarRibbons.generateBiggerCycleMesh ( float  scaling = 0.60f )

private

Definition at line 393 of file SugarRibbons.cs.

References UI.GUIDisplay.ChainColorDict, ColorObject.color, UI.GUIDisplay.colorByResiduesDict, enlargeMesh(), lightColor(), makeFlatVertex(), and Molecule.Model.MoleculeModel.resChainList.

Referenced by createSugarRibbons().

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void SugarRibbons.generateCycleMesh2 ( )

private

Definition at line 240 of file SugarRibbons.cs.

References UI.GUIDisplay.colorByResiduesDict, and CycleAtomToVector3().

Referenced by createSugarRibbons().

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void SugarRibbons.generateRibbonsMesh ( Mesh  centralMesh, int  resnumber, float  thicknessCenter = 1f, bool  center = true  )

private

Definition at line 457 of file SugarRibbons.cs.

References calculMeanNormalMesh(), UI.GUIDisplay.colorByResiduesDict, generateTriangleSide(), and invertTrianglesMesh().

Referenced by createSugarRibbons().

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int [] SugarRibbons.generateTriangleSide ( Mesh  mesh )

private

Definition at line 1103 of file SugarRibbons.cs.

Referenced by generateRibbonsMesh().

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int [] SugarRibbons.invertTrianglesMesh ( Mesh  mesh )

private

Definition at line 1092 of file SugarRibbons.cs.

Referenced by generateRibbonsMesh().

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Color SugarRibbons.lightColor	(	Color	color,
		float	correctionFactor = 0.35f
	)

Definition at line 1118 of file SugarRibbons.cs.

Referenced by create_Bond(), generateBiggerCycleMesh(), updateColorBond(), and updateColorRing().

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Vector3 SugarRibbons.LinearComb ( float  scalar0, Vector3  vector0, float  scalar1, Vector3  vector1  )

private

Definition at line 38 of file SugarRibbons.cs.

List<Vector3> SugarRibbons.makeFlatVertex ( List< Vector3 >  verticeEn )

private

Definition at line 356 of file SugarRibbons.cs.

References calcullittleRibbonsControlPoint().

Referenced by generateBiggerCycleMesh().

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List<GameObject> SugarRibbons.ShowOxySphere

(

int

colortype

)

Definition at line 724 of file SugarRibbons.cs.

References CreateOxygenSphere().

Referenced by SugarManager.ResetSugarRibbons(), and SugarManager.ShowOxySphere().

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static void SugarRibbons.Solve ( Mesh  mesh )

static

Definition at line 773 of file SugarRibbons.cs.

Referenced by CreateSugarRibbonsObj().

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void SugarRibbons.updateColorBond	(	List< GameObject >	objs,
		ColorObject	newColor
	)

Definition at line 890 of file SugarRibbons.cs.

References ColorObject.color, and lightColor().

Referenced by SugarManager.UpdateSugarRibsBondColor().

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void SugarRibbons.updateColorBond	(	List< GameObject >	objs,
		int	type
	)

Definition at line 910 of file SugarRibbons.cs.

References UI.GUIDisplay.ChainColorDict, UI.GUIDisplay.colorByResiduesDict, and lightColor().

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void SugarRibbons.updateColorRing	(	List< GameObject >	objs,
		ColorObject	newColor
	)

Definition at line 899 of file SugarRibbons.cs.

References ColorObject.color, and lightColor().

Referenced by SugarManager.UpdateSugarRibsRingColor().

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void SugarRibbons.updateColorRing	(	List< GameObject >	objs,
		int	type
	)

Definition at line 960 of file SugarRibbons.cs.

References UI.GUIDisplay.ChainColorDict, UI.GUIDisplay.colorByResiduesDict, and lightColor().

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Member Data Documentation

List<float[]> SugarRibbons.atomsLocationlist = new List<float[]>()

Definition at line 78 of file SugarRibbons.cs.

List<string> SugarRibbons.atomsNamelist = new List<string>()

Definition at line 80 of file SugarRibbons.cs.

List<string> SugarRibbons.atomsResnamelist = new List<string>()

Definition at line 79 of file SugarRibbons.cs.

List<Vector3> SugarRibbons.barylist = new List<Vector3>()

Definition at line 35 of file SugarRibbons.cs.

ColorObject SugarRibbons.BONDCOLOR

Definition at line 62 of file SugarRibbons.cs.

List<int[]> SugarRibbons.bondEPList = new List<int[]>()

Definition at line 82 of file SugarRibbons.cs.

int SugarRibbons.CHAIN =1

Definition at line 60 of file SugarRibbons.cs.

int SugarRibbons.COLOR_MODE_BOND

Definition at line 58 of file SugarRibbons.cs.

int SugarRibbons.COLOR_MODE_RING

Definition at line 57 of file SugarRibbons.cs.

List<Color32> SugarRibbons.colors = new List<Color32>()

Definition at line 43 of file SugarRibbons.cs.

Dictionary<int,List<int> > SugarRibbons.connectivityList = new Dictionary<int, List<int>>()

Definition at line 84 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.CycleBIGMesh = new List<Mesh>()

Definition at line 13 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.CycleMesh = new List<Mesh>()

Definition at line 12 of file SugarRibbons.cs.

List<List<int> > SugarRibbons.cycles = new List<List<int>>()

Definition at line 31 of file SugarRibbons.cs.

float SugarRibbons.LIGHTER_COLOR_FACTOR_BOND

Definition at line 54 of file SugarRibbons.cs.

Referenced by SugarOldGUI.ColorTuneMenu().

float SugarRibbons.LIGHTER_COLOR_FACTOR_RING

Definition at line 53 of file SugarRibbons.cs.

Referenced by SugarOldGUI.ColorTuneMenu().

List<Mesh> SugarRibbons.meshesBIGRingDown = new List<Mesh>()

Definition at line 21 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.meshesBIGRingUp =new List<Mesh>()

Definition at line 20 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.meshesBIGSideRing = new List<Mesh> ()

Definition at line 22 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.meshesBondDown = new List<Mesh>()

Definition at line 26 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.meshesBondSide = new List<Mesh>()

Definition at line 27 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.meshesBondUp = new List<Mesh>()

Definition at line 25 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.meshesRingDown = new List<Mesh>()

Definition at line 17 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.meshesRingUp =new List<Mesh>()

Definition at line 16 of file SugarRibbons.cs.

List<Mesh> SugarRibbons.meshesSideRing = new List<Mesh> ()

Definition at line 18 of file SugarRibbons.cs.

Dictionary<int, Dictionary<int, int[]> > SugarRibbons.MeshIndexForAtom = new Dictionary<int, Dictionary<int, int[]>>()

Definition at line 85 of file SugarRibbons.cs.

List<GraphVertex> SugarRibbons.molAsGraph = new List<GraphVertex>()

Definition at line 30 of file SugarRibbons.cs.

int SugarRibbons.nbRes

Definition at line 68 of file SugarRibbons.cs.

List<Vector3> SugarRibbons.normals = new List<Vector3>()

Definition at line 44 of file SugarRibbons.cs.

ColorObject SugarRibbons.OXYSPHERECOLOR

Definition at line 64 of file SugarRibbons.cs.

float SugarRibbons.OXYSPHERESIZE

Definition at line 55 of file SugarRibbons.cs.

Referenced by SugarOldGUI.SugarRibbonsTune().

int SugarRibbons.PICKER =2

Definition at line 61 of file SugarRibbons.cs.

Dictionary<int, string> SugarRibbons.res_for_bond = new Dictionary<int, string>()

Definition at line 86 of file SugarRibbons.cs.

List<string> SugarRibbons.resChainList = new List<string>()

Definition at line 81 of file SugarRibbons.cs.

List<string> SugarRibbons.residueslist = new List<string>()

Definition at line 32 of file SugarRibbons.cs.

List<int> SugarRibbons.residuesNumberlist = new List<int>()

Definition at line 33 of file SugarRibbons.cs.

ColorObject SugarRibbons.RINGCOLOR

Definition at line 63 of file SugarRibbons.cs.

int SugarRibbons.SUGAR =0

Definition at line 59 of file SugarRibbons.cs.

bool SugarRibbons.SUGAR_ONLY

Definition at line 56 of file SugarRibbons.cs.

List<string> SugarRibbons.sugarResname = new List<string>()

Definition at line 69 of file SugarRibbons.cs.

float SugarRibbons.THICKNESS

Definition at line 47 of file SugarRibbons.cs.

float SugarRibbons.THICKNESS_BIG_MESH

Definition at line 49 of file SugarRibbons.cs.

float SugarRibbons.THICKNESS_BOND_5

Definition at line 52 of file SugarRibbons.cs.

float SugarRibbons.THICKNESS_BOND_6_C1_C4

Definition at line 50 of file SugarRibbons.cs.

float SugarRibbons.THICKNESS_BOND_6_OTHER

Definition at line 51 of file SugarRibbons.cs.

float SugarRibbons.THICKNESS_LITTLE_MESH

Definition at line 48 of file SugarRibbons.cs.

List<int> SugarRibbons.triangles = new List<int>()

Definition at line 45 of file SugarRibbons.cs.

List<Vector3> SugarRibbons.vertices = new List<Vector3>()

Definition at line 42 of file SugarRibbons.cs.

float [] SugarRibbons.wideness = {1f, 2f, 1f}

static

Definition at line 66 of file SugarRibbons.cs.

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

• Assets/Scripts/Sugar/SugarRibbons.cs