Public Member Functions
	ControlMolecule ()

Static Public Member Functions
static void	CreateResidues ()

static void	CreateResiduesSugar2 ()

static void	CheckHiRERNAModel ()

static void	BuildHireRnaHydrogenBondsStructures ()

static void	BuildMoleculeComponents ()

static void	UpdateMoleculeCenter ()

static void	CreateSplines ()

static List< int[]>	CreateBondsList (List< float[]> atomsLocationlist, List< AtomModel > atomsTypelist)

static List< int[]>	CreateBondsListWindow (List< float[]> atomsLocationlist, List< AtomModel > atomsTypelist)

static List< int[]>	CreateBondsEPList (List< float[]> atomsLocationlist, List< AtomModel > atomsTypelist)

static void	UpdateBondsFromGameObject (ArrayList atoms)

static List< int[]>	CreateBondsCAList (List< string > caChainlist)

static string	CreateSequenceString ()

static List< int[]>	CreateBondsList_HiRERNA (List< string > atomnames)

static List< int[]>	CreateBondsCSList (List< int[]> atomsLocationlist)

Detailed Description

Definition at line 76 of file ControlMolecule.cs.

Constructor & Destructor Documentation

Molecule.Control.ControlMolecule.ControlMolecule ( )

Definition at line 78 of file ControlMolecule.cs.

Member Function Documentation

static void Molecule.Control.ControlMolecule.BuildHireRnaHydrogenBondsStructures ( )

static

Definition at line 197 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.baseIdx, UI.GUIDisplay.directorypath, File, Molecule.Model.MoleculeModel.residues, RNAView.RNAView_init(), and Molecule.Model.MoleculeModel.scale_RNA.

Referenced by Molecule3D.OnGUI().

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static void Molecule.Control.ControlMolecule.BuildMoleculeComponents ( )

static

Builds the molecule's components.

This is called after reading a PDB. It fills everything that always needs to be filled in MoleculeModel.

Definition at line 245 of file ControlMolecule.cs.

Referenced by Reorient.Reorient.LoadSymmetry(), Molecule3D.OnGUI(), and ParseData.ParsePDB.RequestPDB.ReadAnimCrd().

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static void Molecule.Control.ControlMolecule.CheckHiRERNAModel ( )

static

Checks whether the loaded PDB file follows the HiRE-RNA coarse-grain model or not.

Definition at line 186 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.atomsNamelist, UI.UIData.ffType, and UI.UIData.loadHireRNA.

static List<int[]> Molecule.Control.ControlMolecule.CreateBondsCAList ( List< string > caChainlist )

static

Creates a bond list for the carbon alpha splines.

Parameters

CaChainlist	List of string. The chain of each carbon alpha.
bond	List of bonds to create.

Definition at line 810 of file ControlMolecule.cs.

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

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static List<int[]> Molecule.Control.ControlMolecule.CreateBondsCSList ( List< int[]> atomsLocationlist )

static

Definition at line 906 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.CSidList.

Referenced by ParseData.ParsePDB.RequestPDB.ReadXGMML().

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static List<int[]> Molecule.Control.ControlMolecule.CreateBondsEPList	(	List< float[]>	atomsLocationlist,
		List< AtomModel >	atomsTypelist
	)

static

Definition at line 550 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.bondEPDict, Molecule.Model.MoleculeModel.BondListFromPDB, UI.UIData.connectivity_calc, and UI.UIData.connectivity_PDB.

Referenced by Molecule.Control.ControlMolecule.BuildMoleculeComponents(), BFactorRep.CreateBFRep(), Molecule.Control.ControlMolecule.CreateSplines(), ParseData.ParsePDB.SocketPDB.loadPDB(), and AlphaChainSmoother.ReSpline().

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static List<int[]> Molecule.Control.ControlMolecule.CreateBondsList	(	List< float[]>	atomsLocationlist,
		List< AtomModel >	atomsTypelist
	)

static

Definition at line 447 of file ControlMolecule.cs.

static List<int[]> Molecule.Control.ControlMolecule.CreateBondsList_HiRERNA ( List< string > atomnames )

static

Definition at line 836 of file ControlMolecule.cs.

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

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static List<int[]> Molecule.Control.ControlMolecule.CreateBondsListWindow	(	List< float[]>	atomsLocationlist,
		List< AtomModel >	atomsTypelist
	)

static

Definition at line 485 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.bondEPDict, Molecule.Model.MoleculeModel.BondListFromPDB, UI.UIData.connectivity_calc, and UI.UIData.connectivity_PDB.

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

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static void Molecule.Control.ControlMolecule.CreateResidues ( )

static

Definition at line 81 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.residueDictionaries, and Molecule.Model.MoleculeModel.residueIds.

Referenced by Molecule3D.OnGUI().

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static void Molecule.Control.ControlMolecule.CreateResiduesSugar2 ( )

static

Definition at line 151 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, Molecule.Model.MoleculeModel.atomsNamelist, Molecule.Model.MoleculeModel.residueDictionariesSugar, and Molecule.Model.MoleculeModel.residueIds.

static string Molecule.Control.ControlMolecule.CreateSequenceString ( )

static

Definition at line 823 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.atomsResnamelist, and Molecule.Model.MoleculeModel.residues.

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

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static void Molecule.Control.ControlMolecule.CreateSplines ( )

static

Creates the carbon alpha splines.

Parameters

alist	List of atoms.
calist	List of Carbon Alpha atoms.
caChainlist	List of carbon alpha chain.
typelist	The type of each atom.

Definition at line 387 of file ControlMolecule.cs.

Referenced by ParseData.ParsePDB.RequestPDB.ReadAnimCrd().

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static void Molecule.Control.ControlMolecule.UpdateBondsFromGameObject ( ArrayList atoms )

static

Definition at line 667 of file ControlMolecule.cs.

References StickUpdate.atomnumber1, StickUpdate.atomnumber2, Molecule.Model.MoleculeModel.atoms, Molecule.Model.MoleculeModel.atomsLocationlist, Molecule.View.DisplayBond.BondCubeStyle.BondCubeParent, and Molecule.Model.MoleculeModel.clubs.

Referenced by UI.GUIDisplay.OpenAnimationCrdCallback(), and Molecule3D.Update().

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static void Molecule.Control.ControlMolecule.UpdateMoleculeCenter ( )

static

Definition at line 291 of file ControlMolecule.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, Molecule.Model.MoleculeModel.atomsSugarLocationlist, Molecule.Model.MoleculeModel.cameraLocation, Molecule.Model.MoleculeModel.CatomsLocationlist, Molecule.Model.MoleculeModel.Center, Molecule.Model.MoleculeModel.MaxValue, Molecule.Model.MoleculeModel.MinValue, Molecule.Model.MoleculeModel.Offset, and Molecule.Model.MoleculeModel.target.

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

Assets/Scripts/Molecule/Control/ControlMolecule.cs

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation