Inheritance diagram for Molecule.Model.MoleculeModel:

Collaboration diagram for Molecule.Model.MoleculeModel:

Public Member Functions
	MoleculeModel ()

Static Public Member Functions
static Color	GetAtomColor (string atomType)

Static Public Attributes
static string	sequence = ""

static List< float[]>	atomsLocationlist = new List<float[]>()

static List< Vector3 >	atomsIMDSimulationLocationlist

static List< float[]>	CatomsLocationlist = new List<float[]>()

static List< float[]>	backupCatomsLocationlist = new List<float[]>()

static List< float[]>	CaSplineList = new List<float[]>()

static List< AtomModel >	atomsTypelist = new List<AtomModel>()

static List< string >	atomsNamelist = new List<string>()

static List< int >	atomsNumberList = new List<int>()

static List< string >	atomsSugarNamelist = new List<string>()

static List< string >	atomsSugarResnamelist = new List<string>()

static List< string >	sugarResname

static List< float[]>	atomsSugarLocationlist = new List<float[]>()

static List< string >	resSugarChainList = new List<string>()

static List< int[]>	bondEPSugarList = new List<int[]>()

static List< AtomModel >	atomsSugarTypelist = new List<AtomModel>()

static List< int[]>	BondListFromPDB = new List<int[]>()

static List< string >	atomHetTypeList = new List<string>()

static List< string >	existingName = new List<string>()

static List< string >	atomsResnamelist = new List<string>()

static List< string >	existingRes = new List<string>()

static List< int >	residueIds = new List<int>()

static Dictionary< int, ArrayList >	residues = new Dictionary<int, ArrayList>()

static List< string >	atomsChainList = new List<string>()

static List< string >	resChainList = new List<string>()

static List< string >	resChainList2 = new List<string>()

static int	firstresnb = new int()

static List< string >	existingChain = new List<string>()

static List< Color >	atomsColorList = new List<Color>()

static List< float >	atomsLocalScaleList = new List<float>()

static List< int >	splits = new List<int>()

static List< int[]>	bondList = new List<int[]>()

static List< int[]>	bondEPList = new List<int[]>()

static Dictionary< int, List< int > >	bondEPDict = new Dictionary<int, List<int>>()

static List< int[]>	CSidList = new List<int[]>()

static List< string[]>	CSSGDList = new List<string[]>()

static List< float[]>	CSRadiusList = new List<float[]>()

static List< string[]>	CSColorList = new List<string[]>()

static List< string[]>	CSLabelList = new List<string[]>()

static List< List< Vector3 > >	FieldLineList = null

static List< int[]>	bondCAList =new List<int[]>()

static List< AtomModel >	CaSplineTypeList = new List<AtomModel>()

static List< string >	CaSplineChainList = new List<string>()

static List< string >	backupCaSplineChainList = new List<string>()

static List< float >	BFactorList = new List<float>()

static Dictionary< int, int[]>	atomsForEllipsoidsPerResidue = new Dictionary<int, int[]>()

static Dictionary< int, int >	atomsForEllipsoidsOrientationPerResidue = new Dictionary<int, int>()

static List< int >	baseIdx = new List<int>()

static List< float >	scale_RNA = new List<float>()

static List< GameObject >	ellipsoids = new List<GameObject>()

static Dictionary< int, GameObject >	ellipsoidsPerResidue = new Dictionary<int, GameObject>()

static List< GameObject >	bondsForReplacedAtoms = new List<GameObject>()

static List< Dictionary< string, Vector3 > >	residueDictionaries

static List< Dictionary< string, Vector3 > >	residueDictionariesSugar

static List< float[]>	ssHelixList = new List<float[]> ()

static List< float[]>	ssStrandList = new List<float[]> ()

static List< string >	helixChainList = new List<string>()

static List< string >	strandChainList = new List<string> ()

static Vector3	target =new Vector3(0f,0f,0f)

static Vector3	cameraLocation =new Vector3(10f,10f,10f)

static Vector3	Offset =new Vector3(0f,0f,0f)

static Vector3	Center =new Vector3(0f,0f,0f)

static Vector3	MinValue = new Vector3(0f,0f,0f)

static Vector3	MaxValue = new Vector3(0f,0f,0f)

static ColorObject	oxygenColor = new ColorObject(new Color(0.827f,0.294f,0.333f,1f))

static ColorObject	carbonColor = new ColorObject(new Color(0.282f,0.6f,0.498f,1f))

static ColorObject	nitrogenColor = new ColorObject(new Color(0.443f,0.662f,0.882f,1f))

static ColorObject	hydrogenColor = new ColorObject(Color.white)

static ColorObject	sulphurColor = new ColorObject(new Color(1f,0.839f,0.325f,1f))

static ColorObject	phosphorusColor = new ColorObject(new Color(0.960f,0.521f,0.313f,1f))

static ColorObject	unknownColor = new ColorObject(new Color(1f,0.4f,1f,1f))

static string	oxygenNumber ="0"

static string	carbonNumber ="0"

static string	nitrogenNumber ="0"

static string	hydrogenNumber ="0"

static string	sulphurNumber ="0"

static string	phosphorusNumber ="0"

static string	unknownNumber ="0"

static Dictionary< string, GameObject[]>	atomsByChar = new Dictionary<string, GameObject[]>()

static ArrayList	atoms = new ArrayList()

static GameObject[]	clubs

static Vector3	vo =new Vector3(0.66f,0.66f,0.66f)

static Vector3	vc =new Vector3(0.86f,0.86f,0.86f)

static Vector3	vn =new Vector3(0.80f,0.80f,0.80f)

static Vector3	vh =new Vector3(0.78f,0.78f,0.78f)

static Vector3	vs =new Vector3(1.04f,1.04f,1.04f)

static Vector3	vp =new Vector3(1.30f,1.30f,1.30f)

static Vector3	vno =new Vector3(1f,1f,1f)

static float	oxygenScale =100f

static float	carbonScale =100f

static float	nitrogenScale =100f

static float	hydrogenScale =100f

static float	sulphurScale =100f

static float	phosphorusScale =100f

static float	unknownScale =100f

static long	atomsnumber =0

static long	bondsnumber =0

static string	FPS =""

static Particle[]	p

static Particle[]	fieldlinep

static string	newtooltip

static bool	fieldLineFileExists =false

static bool	dxFileExists = false

static bool	surfaceFileExists =false

static bool	networkLoaded = false

static Vector3[]	vertices

Detailed Description

Definition at line 71 of file MoleculeModel.cs.

Constructor & Destructor Documentation

Molecule.Model.MoleculeModel.MoleculeModel ( )

Definition at line 441 of file MoleculeModel.cs.

Member Function Documentation

static Color Molecule.Model.MoleculeModel.GetAtomColor ( string atomType )

static

Definition at line 356 of file MoleculeModel.cs.

References ColorObject.color.

Referenced by Selections.clearSelection(), SurfaceManager.ColorVertices(), ParseData.ParsePDB.RequestPDB.ReadAnimTop(), and ParsePDB.ReadPDB2().

Here is the caller graph for this function:

Member Data Documentation

List<string> Molecule.Model.MoleculeModel.atomHetTypeList = new List<string>()

static

Definition at line 130 of file MoleculeModel.cs.

Referenced by ParsePDB.ReadPDB2(), and PDBtoDEN.TranPDBtoDEN().

ArrayList Molecule.Model.MoleculeModel.atoms = new ArrayList()

static

Definition at line 392 of file MoleculeModel.cs.

Dictionary<string, GameObject[]> Molecule.Model.MoleculeModel.atomsByChar = new Dictionary<string, GameObject[]>()

static

Definition at line 391 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayMolecule.AddPhysics(), and Molecule.View.DisplayMolecule.DeletePhysics().

List<string> Molecule.Model.MoleculeModel.atomsChainList = new List<string>()

static

List<Color> Molecule.Model.MoleculeModel.atomsColorList = new List<Color>()

static

The color of each atom.

Definition at line 186 of file MoleculeModel.cs.

Referenced by AtomTree.Build(), DepthCueing.BuildColorList(), AmbientOcclusion.BuildColorList(), SurfaceManager.ColorVertices(), DepthCueing.Darken(), Molecule.View.DisplayAtom.AtomParticleStyle.DisplayAtomParticle(), HBallManager.ManagePhysics(), AmbientOcclusion.Occlude(), ParseData.ParsePDB.RequestPDB.ReadAnimTop(), ParsePDB.ReadPDB2(), CubeManager.ResetColors(), LineManager.ResetColors(), CubeBondManager.ResetColors(), HStickManager.ResetColors(), SphereManager.ResetColors(), StickUpdate.ResetColors(), HStickMeshManager.ResetColors(), HBallManager.ResetColors(), DepthCueing.Revert(), AmbientOcclusion.Revert(), CubeManager.SetColor(), HBallMeshManager.SetColor(), SphereManager.SetColor(), HBallManager.SetColor(), BondCubeUpdate.Start(), and StickUpdate.Start().

Dictionary<int, int> Molecule.Model.MoleculeModel.atomsForEllipsoidsOrientationPerResidue = new Dictionary<int, int>()

static

Definition at line 268 of file MoleculeModel.cs.

Referenced by HBallManager.computeEllipsoidOrientation(), HBallManager.findAtoms(), and HBallManager.UpdateEllipsoids().

Dictionary<int, int[]> Molecule.Model.MoleculeModel.atomsForEllipsoidsPerResidue = new Dictionary<int, int[]>()

static

The atoms per ellipsoids per residue for HiRERNA rendering Key is the residue id Value is an array of atom ids (3 in any case) parameterizing the ellipsoid

Definition at line 266 of file MoleculeModel.cs.

Referenced by HBallManager.ActivateBases(), HBallManager.computeEllipsoidNormal(), HBallManager.computeEllipsoidPosition(), HBallManager.DeactivateBases(), and HBallManager.findAtoms().

List<Vector3> Molecule.Model.MoleculeModel.atomsIMDSimulationLocationlist

static

The coordinates of each atom, simulated through an IMD simulation.

List of float[3].

Definition at line 84 of file MoleculeModel.cs.

Referenced by RNAView.computeEnergyForBasePair(), ArtemisManager.connect(), RNAView.ENewPlane(), SnapshotManager.generateSnapshot(), ArtemisThreadedClient.mainProc(), LineManager.ResetIMDSimulationPositions(), HStickManager.ResetIMDSimulationPositions(), HStickMeshManager.ResetIMDSimulationPositions(), CubeManager.ResetIMDSimulationPositions(), SphereManager.ResetIMDSimulationPositions(), HBallMeshManager.ResetIMDSimulationPositions(), and HBallManager.ResetIMDSimulationPositions().

List<float> Molecule.Model.MoleculeModel.atomsLocalScaleList = new List<float>()

static

Definition at line 188 of file MoleculeModel.cs.

Referenced by Molecule3D.clearScene(), ParsePDB.ReadPDB2(), HStickManager.ResetRadii(), HStickMeshManager.ResetRadii(), CubeManager.ResetRadii(), SphereManager.ResetRadii(), HBallMeshManager.ResetRadii(), HBallManager.ResetRadii(), CubeManager.SetRadii(), SphereManager.SetRadii(), HBallMeshManager.SetRadii(), and HBallManager.SetRadii().

List<float[]> Molecule.Model.MoleculeModel.atomsLocationlist = new List<float[]>()

static

The coordinates of each atom.

List of float[4].

Definition at line 79 of file MoleculeModel.cs.

List<string> Molecule.Model.MoleculeModel.atomsNamelist = new List<string>()

static

The name of each atom.

E.g.: O, N, C, H1, H2, etc. List of strings.

Definition at line 109 of file MoleculeModel.cs.

long Molecule.Model.MoleculeModel.atomsnumber =0

static

Definition at line 418 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildMoleculeComponents(), ArtemisManager.connect(), BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomMethodByCube(), Molecule.View.DisplayAtom.AtomSphereStyle.DisplayAtomMethodBySphere(), ParseData.ParsePDB.SocketPDB.loadPDB(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), UI.GUIMoleculeController.RenderHelp(), and AlphaChainSmoother.ReSpline().

List<int> Molecule.Model.MoleculeModel.atomsNumberList = new List<int>()

static

The number of each atoms (in the PDB file)

Definition at line 115 of file MoleculeModel.cs.

Referenced by AtomTree.Build(), ParsePDB.ReadPDB2(), and ClickAtom.Update().

List<string> Molecule.Model.MoleculeModel.atomsResnamelist = new List<string>()

static

The name of the residue to which each atom belongs.

E.g.: ALA, LEU, ASP, etc. List of strings.

Definition at line 141 of file MoleculeModel.cs.

Referenced by AtomTree.Build(), Molecule.Control.ControlMolecule.CreateSequenceString(), HBallManager.findAtoms(), HBallManager.GenerateEllipsoids(), SnapshotManager.generateSnapshot(), SugarManager.Hide_No_Sugar_Hyperballs(), Reorient.Reorient.LoadSymmetry(), ParseData.ParsePDB.RequestPDB.ReadAnimTop(), ParsePDB.ReadPDB2(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), RingBlending.RingBlending(), CubeManager.SetColor(), HBallMeshManager.SetColor(), SphereManager.SetColor(), HBallManager.SetColor(), CubeManager.SetRadii(), SphereManager.SetRadii(), HBallManager.SetRadii(), HBallManager.SetTexture(), SugarManager.show_HyperBalls_Sugar(), SugarRibbons.SugarRibbons(), PDBtoDEN.TranPDBtoDEN(), and ClickAtom.Update().

List<float[]> Molecule.Model.MoleculeModel.atomsSugarLocationlist = new List<float[]>()

static

Definition at line 122 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildMoleculeComponents(), Molecule.Control.ControlMolecule.CreateSplines(), ParseData.ParsePDB.SocketPDB.loadPDB(), ParsePDB.ReadPDB2(), SugarRibbons.SugarRibbons(), and Molecule.Control.ControlMolecule.UpdateMoleculeCenter().

List<string> Molecule.Model.MoleculeModel.atomsSugarNamelist = new List<string>()

static

Definition at line 117 of file MoleculeModel.cs.

Referenced by ParsePDB.ReadPDB2(), and SugarRibbons.SugarRibbons().

List<string> Molecule.Model.MoleculeModel.atomsSugarResnamelist = new List<string>()

static

Definition at line 118 of file MoleculeModel.cs.

Referenced by ParsePDB.ReadPDB2(), and SugarRibbons.SugarRibbons().

List<AtomModel> Molecule.Model.MoleculeModel.atomsSugarTypelist = new List<AtomModel>()

static

Definition at line 125 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildMoleculeComponents(), Molecule.Control.ControlMolecule.CreateSplines(), ParseData.ParsePDB.SocketPDB.loadPDB(), and ParsePDB.ReadPDB2().

List<AtomModel> Molecule.Model.MoleculeModel.atomsTypelist = new List<AtomModel>()

static

The type of each atom.

List of AtomModel.

Definition at line 104 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomParticleStyle.AtomListByAxisOrder(), Molecule.View.DisplayAtom.AtomCubeStyle.AtomListByAxisOrder(), AtomTree.Build(), Molecule.Control.ControlMolecule.BuildMoleculeComponents(), Selections.clearSelection(), BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomMethodByCube(), Molecule.View.DisplayAtom.AtomMeshStyle.DisplayAtoms(), Molecule.View.DisplayAtom.AtomSphereStyle.DisplayAtoms(), Molecule.View.DisplayBond.BondMeshStyle.DisplayBondsMethodByMesh(), HBallManager.findBonds(), SugarManager.Hide_No_Sugar_Hyperballs(), QuadAtoms.Init(), ParseData.ParsePDB.SocketPDB.loadPDB(), Reorient.Reorient.LoadSymmetry(), ParseData.ParsePDB.RequestPDB.ReadAnimTop(), ParsePDB.ReadPDB2(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), HStickManager.ResetRadii(), HStickMeshManager.ResetRadii(), CubeManager.ResetRadii(), SphereManager.ResetRadii(), HBallMeshManager.ResetRadii(), HBallManager.ResetRadii(), AlphaChainSmoother.ReSpline(), HBallMeshManager.SetColor(), SugarManager.show_HyperBalls_Sugar(), LineManager.showHydrogens(), CubeBondManager.showHydrogens(), HStickMeshManager.showHydrogens(), ShurikenParticleManager.showHydrogens(), HStickManager.showHydrogens(), HBallMeshManager.showHydrogens(), PDBtoDEN.TranPDBtoDEN(), and ClickAtom.Update().

List<string> Molecule.Model.MoleculeModel.backupCaSplineChainList = new List<string>()

static

Sometimes inside pdbs lists are not sorted, and residues mixed So I had to create this list to sort residues index by chain ID.

Backup CaSplineChainList (chain of each carbon alpha in the CA-Spline). Used in ReSpline and BfactorRep

Definition at line 254 of file MoleculeModel.cs.

Referenced by BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), and AlphaChainSmoother.ReSpline().

List<float[]> Molecule.Model.MoleculeModel.backupCatomsLocationlist = new List<float[]>()

static

Backup of the coordinates of each Carbon alpha.

List of float[3].

Definition at line 94 of file MoleculeModel.cs.

Referenced by BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), and Reorient.Reorient.LoadSymmetry().

List<int> Molecule.Model.MoleculeModel.baseIdx = new List<int>()

static

The index (in tables) of the base extremity.

Definition at line 273 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildHireRnaHydrogenBondsStructures(), and RNAView.computeEnergyForBasePair().

List<float> Molecule.Model.MoleculeModel.BFactorList = new List<float>()

static

Bfactor of each atom.

Definition at line 259 of file MoleculeModel.cs.

Referenced by AtomTree.Build(), SurfaceManager.ColorVertices(), BFactorRep.CreateBFRep(), ParseData.ParsePDB.RequestPDB.ReadAnimTop(), ParsePDB.ReadPDB2(), and PDBtoDEN.TranPDBtoDEN().

List<int[]> Molecule.Model.MoleculeModel.bondCAList =new List<int[]>()

static

The bonds between carbon alpha in the CA-Spline.

Each element of this list is an int[2] where: int[0] is the index of the first CA, int[1] is the second one.

Definition at line 231 of file MoleculeModel.cs.

Referenced by BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), Molecule.View.DisplayBond.BondMeshStyle.DisplayBonds(), Molecule.View.DisplayBond.BondCubeStyle.DisplayBonds(), Molecule.View.DisplayBond.BondTubeStyle.DisplayBonds(), Molecule.View.DisplayBond.BondLineStyle.DisplayBonds(), and AlphaChainSmoother.ReSpline().

Dictionary<int, List<int> > Molecule.Model.MoleculeModel.bondEPDict = new Dictionary<int, List<int>>()

static

Dictionary of every bounded atoms (which atoms whith which atoms).

Definition at line 213 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.CreateBondsEPList(), and Molecule.Control.ControlMolecule.CreateBondsListWindow().

List<int[]> Molecule.Model.MoleculeModel.bondEPList = new List<int[]>()

static

The bonds between atoms.

Each element of this list is an int[2] where: int[0] is the index of the first atom, int[1] is the second one.

Definition at line 208 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildMoleculeComponents(), BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), Molecule.View.DisplayBond.BondMeshStyle.DisplayBonds(), Molecule.View.DisplayBond.BondCubeStyle.DisplayBonds(), Molecule.View.DisplayBond.BondTubeStyle.DisplayBonds(), Molecule.View.DisplayBond.BondParticleStyle.DisplayBonds(), Molecule.View.DisplayBond.BondLineStyle.DisplayBonds(), HStickMeshManager.hideBondForAtom(), ParseData.ParsePDB.SocketPDB.loadPDB(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), HStickMeshManager.ResetColors(), HStickManager.ResetIMDSimulationPositions(), HStickMeshManager.ResetIMDSimulationPositions(), HStickMeshManager.ResetPositions(), HStickMeshManager.ResetRadii(), HStickMeshManager.ResetVisibility(), AlphaChainSmoother.ReSpline(), RingBlending.RingBlending(), HStickMeshManager.showHydrogens(), and SugarRibbons.SugarRibbons().

List<int[]> Molecule.Model.MoleculeModel.bondEPSugarList = new List<int[]>()

static

Definition at line 124 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildMoleculeComponents(), Molecule.Control.ControlMolecule.CreateSplines(), ParseData.ParsePDB.SocketPDB.loadPDB(), and SugarRibbons.SugarRibbons().

List<int[]> Molecule.Model.MoleculeModel.bondList = new List<int[]>()

static

Not used anymore.

The bonds between atoms. Each element of this list is an int[2] where: int[0] is the index of the first atom, int[1] is the second one.

Definition at line 201 of file MoleculeModel.cs.

List<int[]> Molecule.Model.MoleculeModel.BondListFromPDB = new List<int[]>()

static

Definition at line 128 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.CreateBondsEPList(), Molecule.Control.ControlMolecule.CreateBondsListWindow(), and ParsePDB.ReadPDB2().

List<GameObject> Molecule.Model.MoleculeModel.bondsForReplacedAtoms = new List<GameObject>()

static

Definition at line 290 of file MoleculeModel.cs.

Referenced by HBallManager.ActivateBases(), HBallManager.DeactivateBases(), and HBallManager.findBonds().

long Molecule.Model.MoleculeModel.bondsnumber =0

static

Definition at line 419 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildMoleculeComponents(), BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), Molecule.View.DisplayBond.BondMeshStyle.DisplayBonds(), Molecule.View.DisplayBond.BondTubeStyle.DisplayBonds(), Molecule.View.DisplayBond.BondLineStyle.DisplayBonds(), ParseData.ParsePDB.SocketPDB.loadPDB(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), UI.GUIMoleculeController.RenderHelp(), and AlphaChainSmoother.ReSpline().

Vector3 Molecule.Model.MoleculeModel.cameraLocation =new Vector3(10f,10f,10f)

static

Definition at line 322 of file MoleculeModel.cs.

Referenced by ParseData.ParsePDB.SocketPDB.loadPDB(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), maxCamera.ToCenter(), and Molecule.Control.ControlMolecule.UpdateMoleculeCenter().

ColorObject Molecule.Model.MoleculeModel.carbonColor = new ColorObject(new Color(0.282f,0.6f,0.498f,1f))

static

Definition at line 347 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), Molecule.Model.AtomModel.InitHiRERNA(), UI.GUIDisplay.SetAtomColor(), and PDBtoDEN.TranPDBtoDEN().

string Molecule.Model.MoleculeModel.carbonNumber ="0"

static

Definition at line 369 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.AtomScales(), and Molecule.Control.ControlMolecule.BuildMoleculeComponents().

float Molecule.Model.MoleculeModel.carbonScale =100f

static

Definition at line 409 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.AtomCubeStyle(), Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle(), and Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB().

List<string> Molecule.Model.MoleculeModel.CaSplineChainList = new List<string>()

static

The chain of each carbon alpha in the CA-Spline.

Definition at line 241 of file MoleculeModel.cs.

Referenced by BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), GuidedNavigationManager.get_com(), GuidedNavigationManager.NarrowCAlpha(), ParseData.ParsePDB.RequestPDB.ReadAnimTop(), ParsePDB.ReadPDB2(), AlphaChainSmoother.ReSpline(), and GuidedNavigationManager.SpreadCAlpha().

List<float[]> Molecule.Model.MoleculeModel.CaSplineList = new List<float[]>()

static

The coordinates of each Carbon alpha in the CA-Spline.

List of float[3].

Definition at line 99 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle(), BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomMethodByCube(), Molecule.View.DisplayAtom.AtomParticleStyle.DisplayAtoms(), Molecule.View.DisplayAtom.AtomSphereStyle.DisplayAtoms(), GuidedNavigationManager.get_com(), GuidedNavigationManager.ResetChainPosForHyperballsAndSecondaryStructure(), and AlphaChainSmoother.ReSpline().

List<AtomModel> Molecule.Model.MoleculeModel.CaSplineTypeList = new List<AtomModel>()

static

Type of each carbon alpha in the CA-Spline.

List of AtomModel.

Definition at line 236 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomParticleStyle.AtomListByAxisOrder(), Molecule.View.DisplayAtom.AtomCubeStyle.AtomListByAxisOrder(), BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomMethodByCube(), Molecule.View.DisplayAtom.AtomSphereStyle.DisplayAtoms(), and AlphaChainSmoother.ReSpline().

List<float[]> Molecule.Model.MoleculeModel.CatomsLocationlist = new List<float[]>()

static

The coordinates of each Carbon alpha.

List of float[3].

Definition at line 89 of file MoleculeModel.cs.

Referenced by SecondaryStructureOldGUI.ChooseStructure_BF(), Molecule.Control.ControlMolecule.CreateSplines(), Reorient.Reorient.LoadSymmetry(), ParseData.ParsePDB.RequestPDB.ReadAnimCrd(), ParsePDB.ReadPDB2(), AlphaChainSmoother.ReSpline(), and Molecule.Control.ControlMolecule.UpdateMoleculeCenter().

Vector3 Molecule.Model.MoleculeModel.Center =new Vector3(0f,0f,0f)

static

The barycenter of the molecule.

Vector3.

Definition at line 333 of file MoleculeModel.cs.

Referenced by GeometryBuffer.PopulateMeshes(), and Molecule.Control.ControlMolecule.UpdateMoleculeCenter().

GameObject [] Molecule.Model.MoleculeModel.clubs

static

Definition at line 394 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.UpdateBondsFromGameObject().

List<string[]> Molecule.Model.MoleculeModel.CSColorList = new List<string[]>()

static

Definition at line 218 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB(), Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), and ParseData.ParsePDB.RequestPDB.ReadXGMML().

List<int[]> Molecule.Model.MoleculeModel.CSidList = new List<int[]>()

static

Definition at line 215 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.CreateBondsCSList(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), and ClickAtom.Update().

List<string[]> Molecule.Model.MoleculeModel.CSLabelList = new List<string[]>()

static

Definition at line 219 of file MoleculeModel.cs.

Referenced by ParseData.ParsePDB.RequestPDB.ReadXGMML(), and ClickAtom.Update().

List<float[]> Molecule.Model.MoleculeModel.CSRadiusList = new List<float[]>()

static

Definition at line 217 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB(), Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), and ClickAtom.Update().

List<string[]> Molecule.Model.MoleculeModel.CSSGDList = new List<string[]>()

static

Definition at line 216 of file MoleculeModel.cs.

Referenced by ParseData.ParsePDB.RequestPDB.ReadXGMML(), and ClickAtom.Update().

bool Molecule.Model.MoleculeModel.dxFileExists = false

static

Definition at line 431 of file MoleculeModel.cs.

Referenced by ElectrostaticOldGUI.Electrostatics(), ParsePDB.LoadPDBRequest2(), and UI.LoadTypeGUI.MainFun().

List<GameObject> Molecule.Model.MoleculeModel.ellipsoids = new List<GameObject>()

static

Contiguous (really?) list of ellipsoids

Definition at line 283 of file MoleculeModel.cs.

Referenced by HBallManager.ActivateEllipsoids(), HBallManager.DeactivateEllipsoids(), HBallManager.DestroyAll(), HBallManager.GenerateEllipsoids(), and HBallManager.SetTexture().

Dictionary<int, GameObject> Molecule.Model.MoleculeModel.ellipsoidsPerResidue = new Dictionary<int, GameObject>()

static

The ellipsoids per residue.

Definition at line 288 of file MoleculeModel.cs.

Referenced by HBallManager.computeEllipsoidOrientation(), HBallManager.GenerateEllipsoids(), and HBallManager.UpdateEllipsoids().

List<string> Molecule.Model.MoleculeModel.existingChain = new List<string>()

static

List of the chains existing in the molecule.

Definition at line 181 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.ChainsMenu(), Molecule3D.clearScene(), Ribbons.CreateSSlist(), GuidedNavigationManager.LateUpdateManager(), and ParsePDB.ReadPDB2().

List<string> Molecule.Model.MoleculeModel.existingName = new List<string>()

static

List of the names existing in the molecule.

Definition at line 136 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.AtomsExtendedMenu(), Molecule3D.clearScene(), and ParsePDB.ReadPDB2().

List<string> Molecule.Model.MoleculeModel.existingRes = new List<string>()

static

List of the residues existing in the molecule.

Definition at line 146 of file MoleculeModel.cs.

Referenced by Molecule3D.clearScene(), and UI.GUIDisplay.ResiduesMenu().

bool Molecule.Model.MoleculeModel.fieldLineFileExists =false

static

Definition at line 429 of file MoleculeModel.cs.

Referenced by ElectrostaticManager.DestroyFieldLines(), FieldLineStyle.DisplayFieldLine(), ElectrostaticOldGUI.Electrostatics(), RepresentationOldGUI.HyperballStyle(), ToolsGUI.Interact(), and ParsePDB.LoadPDBRequest2().

List<List<Vector3> > Molecule.Model.MoleculeModel.FieldLineList = null

static

Definition at line 221 of file MoleculeModel.cs.

Referenced by FieldLineStyle.DisplayFieldLine(), ParsePDB.LoadJsonRequest(), ParseData.ParsePDB.RequestPDB.LoadJsonWWW(), and ParsePDB.LoadPDBRequest2().

Particle [] Molecule.Model.MoleculeModel.fieldlinep

static

Definition at line 425 of file MoleculeModel.cs.

int Molecule.Model.MoleculeModel.firstresnb = new int()

static

First residue number in pdb.

Definition at line 176 of file MoleculeModel.cs.

Referenced by Ribbons.CreateRibbons(), and ParsePDB.ReadPDB2().

string Molecule.Model.MoleculeModel.FPS =""

static

Definition at line 421 of file MoleculeModel.cs.

List<string> Molecule.Model.MoleculeModel.helixChainList = new List<string>()

static

The helix chain list (extract from the pdb).

Definition at line 314 of file MoleculeModel.cs.

Referenced by Ribbons.FindHelix(), and ParsePDB.ReadPDB2().

ColorObject Molecule.Model.MoleculeModel.hydrogenColor = new ColorObject(Color.white)

static

Definition at line 349 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), UI.GUIDisplay.SetAtomColor(), and PDBtoDEN.TranPDBtoDEN().

string Molecule.Model.MoleculeModel.hydrogenNumber ="0"

static

Definition at line 371 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.AtomScales(), and Molecule.Control.ControlMolecule.BuildMoleculeComponents().

float Molecule.Model.MoleculeModel.hydrogenScale =100f

static

Definition at line 411 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.AtomCubeStyle(), Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle(), and Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB().

Vector3 Molecule.Model.MoleculeModel.MaxValue = new Vector3(0f,0f,0f)

static

The "biggest" corner of the bounding box that encloses the molecule.

Definition at line 343 of file MoleculeModel.cs.

Referenced by AtomTree.Build(), GuidedNavigationManager.computeSpreadingVector(), GuidedNavigationManager.computeSpreadPart(), GuidedNavigationManager.CreateAxeAndOrigin(), GuidedNavigationManager.goDownConstrained(), GuidedNavigationManager.goUpConstrained(), SurfaceManager.InitCutParameters(), GuidedNavigationManager.keyboard(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), GuidedNavigationManager.ReorientCamera(), PDBtoDEN.TranPDBtoDEN(), and Molecule.Control.ControlMolecule.UpdateMoleculeCenter().

Vector3 Molecule.Model.MoleculeModel.MinValue = new Vector3(0f,0f,0f)

static

The "smallest" corner of the bounding box that encloses the molecule.

Definition at line 338 of file MoleculeModel.cs.

Referenced by AmbientOcclusion.AmbientOcclusion(), AtomTree.Build(), GuidedNavigationManager.computeSpreadingVector(), GuidedNavigationManager.computeSpreadPart(), GuidedNavigationManager.CreateAxeAndOrigin(), GuidedNavigationManager.goDownConstrained(), GuidedNavigationManager.goUpConstrained(), VolumetricDensity.Init(), SurfaceManager.InitCutParameters(), GuidedNavigationManager.keyboard(), Reorient.Reorient.LoadSymmetry(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), GuidedNavigationManager.ReorientCamera(), PDBtoDEN.TranPDBtoDEN(), and Molecule.Control.ControlMolecule.UpdateMoleculeCenter().

bool Molecule.Model.MoleculeModel.networkLoaded = false

static

Definition at line 436 of file MoleculeModel.cs.

Referenced by RepresentationOldGUI.HyperballStyle(), Molecule3D.OnGUI(), ParseData.ParsePDB.RequestPDB.ReadAnimCrd(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), and HBallManager.Update().

string Molecule.Model.MoleculeModel.newtooltip

static

Definition at line 427 of file MoleculeModel.cs.

Referenced by AdvancedOptionsOldGUI.AdvOptions(), RepresentationOldGUI.AtomMenu(), UI.GUIDisplay.AtomScales(), UI.GUIDisplay.AtomsExtendedMenu(), RepresentationOldGUI.AtomStyle(), AdvancedOptionsOldGUI.BackColor(), AdvancedOptionsOldGUI.Background(), AdvancedOptionsOldGUI.BackGroundControl(), RepresentationOldGUI.Bond(), UI.GUIDisplay.ChainsMenu(), SecondaryStructureOldGUI.ChooseSmoothness_BF(), SecondaryStructureOldGUI.ChooseStructure_BF(), AdvancedOptionsOldGUI.Effects(), ElectrostaticOldGUI.Electrostatics(), ElectrostaticOldGUI.FieldLines(), UI.GUIMoleculeController.LabelSlider(), ColorPicker.loadColor(), AdvancedOptionsOldGUI.LoadScreenShot(), Reorient.Reorient.LoadSymmetry(), UI.LoadTypeGUI.MainFun(), RepresentationOldGUI.Metaphor(), RepresentationOldGUI.MetaphorControl(), Molecule3D.OnGUI(), UI.GUIDisplay.PanelsMenu(), RepresentationOldGUI.PhysicalChoice(), RepresentationOldGUI.RenderingParameters(), UI.GUIDisplay.ResiduesMenu(), RepresentationOldGUI.SetAtomStyle(), SurfaceOldGUI.Surface(), SurfaceOldGUI.SurfaceParams(), and SurfaceOldGUI.textureMenu().

ColorObject Molecule.Model.MoleculeModel.nitrogenColor = new ColorObject(new Color(0.443f,0.662f,0.882f,1f))

static

Definition at line 348 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), UI.GUIDisplay.SetAtomColor(), and PDBtoDEN.TranPDBtoDEN().

string Molecule.Model.MoleculeModel.nitrogenNumber ="0"

static

Definition at line 370 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.AtomScales(), and Molecule.Control.ControlMolecule.BuildMoleculeComponents().

float Molecule.Model.MoleculeModel.nitrogenScale =100f

static

Definition at line 410 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.AtomCubeStyle(), Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle(), and Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB().

Vector3 Molecule.Model.MoleculeModel.Offset =new Vector3(0f,0f,0f)

static

The offset for the molecule.

The original barycenter of the molecule + this = (0,0,0). Vector3. Also used for density grids.

Definition at line 328 of file MoleculeModel.cs.

Referenced by AdvancedOptionsOldGUI.AdvOptions(), ParseData.ParsePDB.SocketPDB.loadPDB(), ParsePDB.LoadPDBRequest2(), GeometryBuffer.PopulateMeshes(), ParseData.ParsePDB.RequestPDB.ReadAnimCrd(), ElectrostaticManager.ReadDxFile(), ParseData.ParsePDB.RequestPDB.ReadPDBReaction(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), ElectrostaticManager.RecenterFieldLines(), SurfaceManager.RecenterSurfaces(), ClickAtom.Update(), and Molecule.Control.ControlMolecule.UpdateMoleculeCenter().

ColorObject Molecule.Model.MoleculeModel.oxygenColor = new ColorObject(new Color(0.827f,0.294f,0.333f,1f))

static

Definition at line 346 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), Molecule.Model.AtomModel.InitHiRERNA(), UI.GUIDisplay.SetAtomColor(), and PDBtoDEN.TranPDBtoDEN().

string Molecule.Model.MoleculeModel.oxygenNumber ="0"

static

Definition at line 368 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.AtomScales(), and Molecule.Control.ControlMolecule.BuildMoleculeComponents().

float Molecule.Model.MoleculeModel.oxygenScale =100f

static

Definition at line 408 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.AtomCubeStyle(), Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle(), and Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB().

Particle [] Molecule.Model.MoleculeModel.p

static

Definition at line 423 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle(), Molecule.View.DisplayAtom.AtomParticleStyle.CreateParticleBall(), and ShurikenParticleManager.Init().

ColorObject Molecule.Model.MoleculeModel.phosphorusColor = new ColorObject(new Color(0.960f,0.521f,0.313f,1f))

static

Definition at line 351 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), Molecule.Model.AtomModel.InitHiRERNA(), UI.GUIDisplay.SetAtomColor(), and PDBtoDEN.TranPDBtoDEN().

string Molecule.Model.MoleculeModel.phosphorusNumber ="0"

static

Definition at line 375 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.AtomScales(), and Molecule.Control.ControlMolecule.BuildMoleculeComponents().

float Molecule.Model.MoleculeModel.phosphorusScale =100f

static

Definition at line 415 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.AtomCubeStyle(), Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle(), and Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB().

List<string> Molecule.Model.MoleculeModel.resChainList = new List<string>()

static

The chain of each residue (only work if residues are numbered by chain).

Definition at line 166 of file MoleculeModel.cs.

Referenced by SugarRibbons.create_Bond(), SugarRibbons.generateBiggerCycleMesh(), ParsePDB.ReadPDB2(), and SugarRibbons.SugarRibbons().

List<string> Molecule.Model.MoleculeModel.resChainList2 = new List<string>()

static

The chain of each residue.

Definition at line 171 of file MoleculeModel.cs.

Referenced by Ribbons.ComputeNbRes(), Ribbons.CreateRibbons(), and ParsePDB.ReadPDB2().

List<Dictionary<string, Vector3> > Molecule.Model.MoleculeModel.residueDictionaries

static

Definition at line 292 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.CreateResidues(), Ribbons.CreateRibbons(), and Reorient.Reorient.LoadSymmetry().

List<Dictionary<string, Vector3> > Molecule.Model.MoleculeModel.residueDictionariesSugar

static

Definition at line 293 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.CreateResiduesSugar2().

List<int> Molecule.Model.MoleculeModel.residueIds = new List<int>()

static

The residue identifiers.

One per atom.

Definition at line 151 of file MoleculeModel.cs.

Referenced by Molecule3D.clearScene(), GuidedNavigationManager.computeSpreadPart(), BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateResidues(), Molecule.Control.ControlMolecule.CreateResiduesSugar2(), SnapshotManager.generateSnapshot(), Reorient.Reorient.LoadSymmetry(), ParsePDB.ReadPDB2(), AlphaChainSmoother.ReSpline(), GuidedNavigationManager.SpreadSpheres(), and ClickAtom.Update().

Dictionary<int, ArrayList> Molecule.Model.MoleculeModel.residues = new Dictionary<int, ArrayList>()

static

The residues.

Keys: residue IDs. Values: list of atoms IDs.

Definition at line 156 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildHireRnaHydrogenBondsStructures(), Molecule3D.clearScene(), Molecule.Control.ControlMolecule.CreateSequenceString(), HBallManager.findAtoms(), RNAView.findHbonds(), HBallManager.GenerateEllipsoids(), ParsePDB.ReadPDB2(), and Selections.selectResidue().

List<string> Molecule.Model.MoleculeModel.resSugarChainList = new List<string>()

static

Definition at line 123 of file MoleculeModel.cs.

Referenced by ParsePDB.ReadPDB2(), and SugarRibbons.SugarRibbons().

List<float> Molecule.Model.MoleculeModel.scale_RNA = new List<float>()

static

RNA Scale parameters

Definition at line 278 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.BuildHireRnaHydrogenBondsStructures(), RNAView.Ehbond(), and RNAView.NewPlane().

string Molecule.Model.MoleculeModel.sequence = ""

static

Definition at line 72 of file MoleculeModel.cs.

Referenced by Molecule.Control.ControlMolecule.CreateSplines(), and VARNABillboard.generateFileInThread().

List<int> Molecule.Model.MoleculeModel.splits = new List<int>()

static

Terminal residue number of each subunits.

Definition at line 193 of file MoleculeModel.cs.

Referenced by Ribbons.CreateRibbons(), and ParsePDB.ReadPDB2().

List<float[]> Molecule.Model.MoleculeModel.ssHelixList = new List<float[]> ()

static

List of informations about each helix (extract from the pdb) float[0] is the first residue of each helix float[1] is the last residue of each helix float[2] the length of each helix float[3] the class of each helix

Definition at line 302 of file MoleculeModel.cs.

Referenced by Ribbons.CreateRibbons(), Ribbons.FindHelix(), and ParsePDB.ReadPDB2().

List<float[]> Molecule.Model.MoleculeModel.ssStrandList = new List<float[]> ()

static

First and last residue of each strand (extract from the pdb) float[0] is the first residue of each strand float[1] is the last residue of each strand

Definition at line 309 of file MoleculeModel.cs.

Referenced by Ribbons.CreateRibbons(), Ribbons.FindStrand(), and ParsePDB.ReadPDB2().

List<string> Molecule.Model.MoleculeModel.strandChainList = new List<string> ()

static

The strand chain list (extract from the pdb).

Definition at line 319 of file MoleculeModel.cs.

Referenced by Ribbons.FindStrand(), and ParsePDB.ReadPDB2().

List<string> Molecule.Model.MoleculeModel.sugarResname

static

Initial value:

= new List<string> {"ABE","ACE","ALT","API","ARA","DHA","FRU","FUC","GAL",
            "GLC","GUL","IDO","DKN","KDO","MAN","NEG","RHA","RIB","SIA","TAG","TAL","XYL",
            "GLA","FUL","GLB","NAG","NDG","BMA","MMA","A2G","AAL","BGC"}

Definition at line 119 of file MoleculeModel.cs.

Referenced by SugarManager.Hide_No_Sugar_Hyperballs(), ParsePDB.ReadPDB2(), SugarManager.show_HyperBalls_Sugar(), and PDBtoDEN.TranPDBtoDEN().

ColorObject Molecule.Model.MoleculeModel.sulphurColor = new ColorObject(new Color(1f,0.839f,0.325f,1f))

static

Definition at line 350 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), UI.GUIDisplay.SetAtomColor(), and PDBtoDEN.TranPDBtoDEN().

string Molecule.Model.MoleculeModel.sulphurNumber ="0"

static

Definition at line 372 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.AtomScales(), and Molecule.Control.ControlMolecule.BuildMoleculeComponents().

float Molecule.Model.MoleculeModel.sulphurScale =100f

static

Definition at line 412 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.AtomCubeStyle(), Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle(), and Molecule.View.DisplayAtom.AtomCubeStyle.CreateAtomHB().

bool Molecule.Model.MoleculeModel.surfaceFileExists =false

static

Definition at line 433 of file MoleculeModel.cs.

Referenced by ElectrostaticOldGUI.Electrostatics(), SurfaceManager.GenerateSurface(), SurfaceManager.GenerateSurfaceBfact(), RepresentationOldGUI.HyperballStyle(), ToolsGUI.Interact(), Molecule3D.loadFile(), ParsePDB.LoadPDBRequest2(), and SurfaceOldGUI.Surface().

Vector3 Molecule.Model.MoleculeModel.target =new Vector3(0f,0f,0f)

static

Definition at line 321 of file MoleculeModel.cs.

Referenced by ParseData.ParsePDB.SocketPDB.loadPDB(), ParseData.ParsePDB.RequestPDB.ReadXGMML(), Molecule3D.SetCenter(), ClickAtom.Update(), and Molecule.Control.ControlMolecule.UpdateMoleculeCenter().

ColorObject Molecule.Model.MoleculeModel.unknownColor = new ColorObject(new Color(1f,0.4f,1f,1f))

static

Definition at line 352 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.DisplayAtomCube(), UI.GUIDisplay.SetAtomColor(), and PDBtoDEN.TranPDBtoDEN().

string Molecule.Model.MoleculeModel.unknownNumber ="0"

static

Definition at line 376 of file MoleculeModel.cs.

Referenced by UI.GUIDisplay.AtomScales(), and Molecule.Control.ControlMolecule.BuildMoleculeComponents().

float Molecule.Model.MoleculeModel.unknownScale =100f

static

Definition at line 416 of file MoleculeModel.cs.

Referenced by Molecule.View.DisplayAtom.AtomCubeStyle.AtomCubeStyle(), and Molecule.View.DisplayAtom.AtomParticleStyle.AtomParticleStyle().

Vector3 Molecule.Model.MoleculeModel.vc =new Vector3(0.86f,0.86f,0.86f)

static

Definition at line 399 of file MoleculeModel.cs.

Vector3 [] Molecule.Model.MoleculeModel.vertices

static

Definition at line 438 of file MoleculeModel.cs.

Referenced by GenerateMesh.GM(), and GeometryBuffer.PopulateMeshes().

Vector3 Molecule.Model.MoleculeModel.vh =new Vector3(0.78f,0.78f,0.78f)

static

Definition at line 401 of file MoleculeModel.cs.

Vector3 Molecule.Model.MoleculeModel.vn =new Vector3(0.80f,0.80f,0.80f)

static

Definition at line 400 of file MoleculeModel.cs.

Vector3 Molecule.Model.MoleculeModel.vno =new Vector3(1f,1f,1f)

static

Definition at line 406 of file MoleculeModel.cs.

Vector3 Molecule.Model.MoleculeModel.vo =new Vector3(0.66f,0.66f,0.66f)

static

Definition at line 398 of file MoleculeModel.cs.

Vector3 Molecule.Model.MoleculeModel.vp =new Vector3(1.30f,1.30f,1.30f)

static

Definition at line 405 of file MoleculeModel.cs.

Vector3 Molecule.Model.MoleculeModel.vs =new Vector3(1.04f,1.04f,1.04f)

static

Definition at line 402 of file MoleculeModel.cs.

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

Assets/Scripts/Molecule/Model/MoleculeModel.cs

Public Member Functions

Static Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation