Public Member Functions
void	Init ()

void	CreateAxeAndOrigin ()

void	DestroyAxeAndOrigin ()

void	Clear ()

void	UpdateManager ()

Private Member Functions
void	OnEnable ()

void	LateUpdateManager ()

void	keyboard ()

void	NearSpreading ()

void	SpreadCAlpha ()

void	SpreadHyperballs ()

void	SpreadSpheres ()

void	SpreadSecondaryStructure ()

void	Spreading ()

void	NarrowCAlpha ()

void	NarrowHyperballs ()

void	NarrowSpheres ()

void	NarrowSecondaryStructure ()

void	Narrowing ()

void	ResetChainPosForHyperballsAndSecondaryStructure ()

void	ResetChainPosForHyperballs ()

void	ResetChainPosForSpheres ()

void	ResetChainsPos ()

Vector3	get_com (string chain)

void	computeSpreadingVector ()

void	computeSpreadPart (out Vector3 Spread1, out Vector3 Spread2, string chain)

void	computeSpreadHelix (out Vector3 Spreadhelix, int first_atom, int last_atom, string chain)

void	goUpConstrained ()

void	goDownConstrained ()

IEnumerator	Transition ()

void	ReorientCamera ()

Private Attributes
GameObject	originPoint

GameObject	symmetryAxis

Detailed Description

Definition at line 10 of file GuidedNavigationManager.cs.

Member Function Documentation

void GuidedNavigationManager.Clear ( )

Definition at line 42 of file GuidedNavigationManager.cs.

References DestroyAxeAndOrigin(), GuidedNav.GNParameters.ghost_camera, GuidedNav.GNParameters.ghost_target, GuidedNav.GNParameters.ghost_target_instantiate, UI.UIData.guided, and GuidedNavigationOldGUI.showGuidedMenu.

Referenced by Molecule3D.clearScene(), and GuidedNavigationOldGUI.GuidedOptions().

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void GuidedNavigationManager.computeSpreadHelix	(	out Vector3	Spreadhelix,
		int	first_atom,
		int	last_atom,
		string	chain
	)

private

Computes spreading vectors for helices (third step spreading)

Parameters

Spreadhelix	Spreadhelix.
first_atom	First_atom.
last_atom	Last_atom.
chain	Chain.

Definition at line 993 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, get_com(), and GuidedNav.GNParameters.onlyTMD.

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void GuidedNavigationManager.computeSpreadingVector ( )

private

Compute spreading vectors (first step).

Definition at line 916 of file GuidedNavigationManager.cs.

References get_com(), Molecule.Model.MoleculeModel.MaxValue, Molecule.Model.MoleculeModel.MinValue, GuidedNav.GNParameters.spreadA, GuidedNav.GNParameters.spreadB, GuidedNav.GNParameters.spreadC, GuidedNav.GNParameters.spreadD, and GuidedNav.GNParameters.spreadE.

Referenced by Narrowing(), and Spreading().

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void GuidedNavigationManager.computeSpreadPart	(	out Vector3	Spread1,
		out Vector3	Spread2,
		string	chain
	)

private

Compute spreading vectors (second step).

Definition at line 948 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsChainList, Molecule.Model.MoleculeModel.atomsLocationlist, Molecule.Model.MoleculeModel.MaxValue, Molecule.Model.MoleculeModel.MinValue, Molecule.Model.MoleculeModel.residueIds, and GuidedNav.GNParameters.reslim.

Referenced by Spreading().

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void GuidedNavigationManager.CreateAxeAndOrigin ( )

Instantiate the origin and symmetry axis game objects.

Definition at line 25 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.MaxValue, and Molecule.Model.MoleculeModel.MinValue.

Referenced by GuidedNavigationOldGUI.GuidedOptions(), and Reorient.Reorient.LoadSymmetry().

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void GuidedNavigationManager.DestroyAxeAndOrigin ( )

Destroy the axis and origin game objects.

Definition at line 37 of file GuidedNavigationManager.cs.

Referenced by Clear(), and GuidedNavigationOldGUI.GuidedOptions().

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Vector3 GuidedNavigationManager.get_com ( string chain )

private

Compute center of mass.

Definition at line 879 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsChainList, Molecule.Model.MoleculeModel.atomsLocationlist, Molecule.Model.MoleculeModel.CaSplineChainList, Molecule.Model.MoleculeModel.CaSplineList, GuidedNav.GNParameters.onlyTMD, GuidedNav.GNParameters.reslim, and UI.UIData.secondarystruct.

Referenced by computeSpreadHelix(), and computeSpreadingVector().

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void GuidedNavigationManager.goDownConstrained ( )

private

Only available in "guided navigation" and specific to pentameric channels.

Constrained path for camera moving around the protein structure (second way).

Definition at line 1056 of file GuidedNavigationManager.cs.

References GuidedNav.GNParameters.isabove, GuidedNav.GNParameters.isunder, GuidedNav.GNParameters.mainCamera, Molecule.Model.MoleculeModel.MaxValue, Molecule.Model.MoleculeModel.MinValue, GuidedNav.GNParameters.nav_speed, and maxCamera.target.

Referenced by keyboard(), and LateUpdateManager().

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void GuidedNavigationManager.goUpConstrained ( )

private

Only available in "guided navigation" mode and specific to pentameric channels.

Constrained path for camera moving around the protein structure.

Definition at line 1017 of file GuidedNavigationManager.cs.

References GuidedNav.GNParameters.isabove, GuidedNav.GNParameters.isunder, GuidedNav.GNParameters.mainCamera, Molecule.Model.MoleculeModel.MaxValue, Molecule.Model.MoleculeModel.MinValue, GuidedNav.GNParameters.nav_speed, and maxCamera.target.

Referenced by keyboard(), and LateUpdateManager().

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void GuidedNavigationManager.Init ( )

Definition at line 20 of file GuidedNavigationManager.cs.

References GuidedNav.GNParameters.mainCamera.

Referenced by OnEnable(), and UpdateManager().

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void GuidedNavigationManager.keyboard ( )

private

Definition at line 219 of file GuidedNavigationManager.cs.

Referenced by LateUpdateManager().

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void GuidedNavigationManager.LateUpdateManager ( )

private

Definition at line 105 of file GuidedNavigationManager.cs.

Referenced by UpdateManager().

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void GuidedNavigationManager.NarrowCAlpha ( )

private

Narrow the chains of C-alpha traces.

Definition at line 580 of file GuidedNavigationManager.cs.

References UI.UIData.atomtype, UI.UIData.bondtype, Molecule.Model.MoleculeModel.CaSplineChainList, Molecule.View.DisplayMolecule.ChangeRepresentation(), UnityMolMain.getCurrentAtomManager(), UnityMolMain.getCurrentBondManager(), GuidedNav.GNParameters.hballs, BallUpdate.number, GenericManager.ResetPositions(), GuidedNav.GNParameters.spreadA, GuidedNav.GNParameters.spreadB, GuidedNav.GNParameters.spreadC, GuidedNav.GNParameters.spreadD, and GuidedNav.GNParameters.spreadE.

Referenced by Narrowing().

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void GuidedNavigationManager.NarrowHyperballs ( )

private

Narrow the chains when rendering hyperballs.

Definition at line 616 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsChainList, UI.UIData.atomtype, UI.UIData.bondtype, Molecule.View.DisplayMolecule.ChangeRepresentation(), UnityMolMain.getCurrentAtomManager(), UnityMolMain.getCurrentBondManager(), GuidedNav.GNParameters.hballs, BallUpdate.number, GenericManager.ResetPositions(), GuidedNav.GNParameters.spreadA, GuidedNav.GNParameters.spreadB, GuidedNav.GNParameters.spreadC, GuidedNav.GNParameters.spreadD, and GuidedNav.GNParameters.spreadE.

Referenced by Narrowing().

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void GuidedNavigationManager.Narrowing ( )

private

Narrowing chains.

Definition at line 758 of file GuidedNavigationManager.cs.

References UI.UIData.atomtype, GuidedNav.GNParameters.comp_spread, computeSpreadingVector(), NarrowCAlpha(), NarrowHyperballs(), NarrowSecondaryStructure(), NarrowSpheres(), UI.UIData.secondarystruct, and SecondaryStructureOldGUI.toggle_SEC_STRUCT.

Referenced by keyboard().

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void GuidedNavigationManager.NarrowSecondaryStructure ( )

private

Definition at line 677 of file GuidedNavigationManager.cs.

Referenced by Narrowing().

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void GuidedNavigationManager.NarrowSpheres ( )

private

Narrow the chains when rendering spheres.

Definition at line 652 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsChainList, BallUpdate.number, GuidedNav.GNParameters.sballs, GuidedNav.GNParameters.spreadA, GuidedNav.GNParameters.spreadB, GuidedNav.GNParameters.spreadC, GuidedNav.GNParameters.spreadD, and GuidedNav.GNParameters.spreadE.

Referenced by Narrowing().

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void GuidedNavigationManager.NearSpreading ( )

private

Slightly spreads the chains when the camera is near the protein structure.

Definition at line 316 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, GuidedNav.GNParameters.atomtree, AtomTree.Build(), GuidedNav.GNParameters.closeatom, GuidedNav.GNParameters.comp_spread, GuidedNav.GNParameters.distclose, AtomTree.GetClosestAtomType(), GuidedNav.GNParameters.mainCamera, GuidedNav.GNParameters.poscloseatom, GuidedNav.GNParameters.rep, ResetChainsPos(), UI.UIData.spread_tree, and Spreading().

Referenced by UpdateManager().

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void GuidedNavigationManager.OnEnable ( )

private

Definition at line 16 of file GuidedNavigationManager.cs.

References Init().

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void GuidedNavigationManager.ReorientCamera ( )

private

Definition at line 1107 of file GuidedNavigationManager.cs.

References GuidedNav.GNParameters.mainCamera, Molecule.Model.MoleculeModel.MaxValue, Molecule.Model.MoleculeModel.MinValue, GuidedNav.GNParameters.reoriented, and maxCamera.target.

Referenced by keyboard().

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void GuidedNavigationManager.ResetChainPosForHyperballs ( )

private

Resets the chains positions when rendering hyperballs.

Definition at line 807 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, GuidedNav.GNParameters.hballs, and BallUpdate.number.

Referenced by ResetChainsPos().

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void GuidedNavigationManager.ResetChainPosForHyperballsAndSecondaryStructure ( )

private

Resets the chains positions when rendering the secondary structure.

Definition at line 788 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.CaSplineList, GuidedNav.GNParameters.hballs, and BallUpdate.number.

Referenced by ResetChainsPos().

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void GuidedNavigationManager.ResetChainPosForSpheres ( )

private

Resets the chains positions when rendering spheres.

Definition at line 826 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsLocationlist, BallUpdate.number, and GuidedNav.GNParameters.sballs.

Referenced by ResetChainsPos().

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void GuidedNavigationManager.ResetChainsPos ( )

private

Resets the chains position.

Definition at line 846 of file GuidedNavigationManager.cs.

References UI.UIData.atomtype, UI.UIData.bondtype, Molecule.View.DisplayMolecule.ChangeRepresentation(), GuidedNav.GNParameters.comp_spread, SecondaryStructureManager.CreateRibbons(), SecondaryStructureManager.DestroyRibbons(), UnityMolMain.getSecondaryStructureManager(), ResetChainPosForHyperballs(), ResetChainPosForHyperballsAndSecondaryStructure(), ResetChainPosForSpheres(), UI.UIData.secondarystruct, and SecondaryStructureOldGUI.toggle_SEC_STRUCT.

Referenced by keyboard(), and NearSpreading().

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void GuidedNavigationManager.SpreadCAlpha ( )

private

Spread chains when rendering the C-alpha spline as hyperballs.

Definition at line 333 of file GuidedNavigationManager.cs.

References UI.UIData.atomtype, UI.UIData.bondtype, Molecule.Model.MoleculeModel.CaSplineChainList, Molecule.View.DisplayMolecule.ChangeRepresentation(), Molecule.View.DisplayMolecule.DestroyBonds(), GuidedNav.GNParameters.hballs, BallUpdate.number, GuidedNav.GNParameters.spreadA, GuidedNav.GNParameters.spreadB, GuidedNav.GNParameters.spreadC, GuidedNav.GNParameters.spreadD, and GuidedNav.GNParameters.spreadE.

Referenced by Spreading().

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void GuidedNavigationManager.SpreadHyperballs ( )

private

Spread chains when rendering the atoms as hyperballs.

Definition at line 363 of file GuidedNavigationManager.cs.

References Molecule.Model.MoleculeModel.atomsChainList, UI.UIData.atomtype, UI.UIData.bondtype, Molecule.View.DisplayMolecule.ChangeRepresentation(), Molecule.View.DisplayMolecule.DestroyBonds(), GuidedNav.GNParameters.hballs, BallUpdate.number, GuidedNav.GNParameters.spreadA, GuidedNav.GNParameters.spreadB, GuidedNav.GNParameters.spreadC, GuidedNav.GNParameters.spreadD, and GuidedNav.GNParameters.spreadE.

Referenced by Spreading().

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void GuidedNavigationManager.Spreading ( )

private

Spreading chains (limit: 5 chains)

Definition at line 547 of file GuidedNavigationManager.cs.

Referenced by keyboard(), and NearSpreading().

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void GuidedNavigationManager.SpreadSecondaryStructure ( )

private

Spread chains when rendering the secondary structure.

Definition at line 467 of file GuidedNavigationManager.cs.

Referenced by Spreading().

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void GuidedNavigationManager.SpreadSpheres ( )

private

Spread chains when rendering the atoms as spheres.

Definition at line 393 of file GuidedNavigationManager.cs.

Referenced by Spreading().

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IEnumerator GuidedNavigationManager.Transition ( )

private

Definition at line 1094 of file GuidedNavigationManager.cs.

References GuidedNav.GNParameters.mainCamera, GuidedNav.GNParameters.optim_target, and GuidedNav.GNParameters.transitionDuration.

void GuidedNavigationManager.UpdateManager ( )

Definition at line 51 of file GuidedNavigationManager.cs.

References UI.UIData.guided, Init(), LateUpdateManager(), GuidedNav.GNParameters.mainCamera, GuidedNav.GNParameters.monomer_jump, GuidedNav.GNParameters.navigationDown, GuidedNav.GNParameters.navigationUp, GuidedNav.GNParameters.near_spread, NearSpreading(), GuidedNav.GNParameters.panoramic, GuidedNav.GNParameters.reoriented, GuidedNav.GNParameters.reset_panoramic, and maxCamera.weight_cam.

Referenced by GuidedNavigationOldGUI.GuidedOptions().

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Member Data Documentation

GameObject GuidedNavigationManager.originPoint

private

GameObjects representing the space origin and molecule symmetry axis.

Definition at line 13 of file GuidedNavigationManager.cs.

GameObject GuidedNavigationManager.symmetryAxis

private

Definition at line 14 of file GuidedNavigationManager.cs.

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

Assets/Scripts/GuidedNavigation/GuidedNavigationManager.cs

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Function Documentation

Member Data Documentation