Part of the SMCRA data structure, UnityMolModel stores the chains of the structure as a dictionary <string,UnityMolChain>. It also stores the bonds as UnityMolBonds A list of UnityMolAtom of the model is provided to loop over all atoms quickly More...

Public Member Functions
	UnityMolModel (Dictionary< string, UnityMolChain > dictChains, string nameModel)
	UnityMolModel constructor taking chain dictionary as arg More...

	UnityMolModel (List< UnityMolChain > listChains, string nameModel)
	UnityMolModel constructor taking chain list as arg, all the chains are inserted into the _chains dictionary More...

	UnityMolModel (UnityMolChain newChain, string nameModel)
	UnityMolModel constructor taking one chain as arg, the chain is inserted into the chains dictionary More...

void	ComputeCenterOfGravityCSharp ()
	Computes the center of gravity of the model More...

static void	computeCenterOfGravity (int N, float[] positions, float[] minmaxcog)

void	ComputeCenterOfGravity ()

void	CenterAtoms ()
	Fills UnityMol.position using UnityMolAtom.oriposition and the centerOfGravity computed with ComputeCenterOfGravity() More...

void	fillIdAtoms ()
	Fills idInAllAtoms field More...

UnityMolAtom	getAtomWithID (int idAtom)

List< UnityMolAtom >	ToAtomList ()

UnityMolSelection	ToSelection ()

bool	hasHydrogens ()

Vector3 []	getAllPositions ()

Static Public Member Functions
static Vector3	ComputeCenterOfGravityCSharp (Vector3[] positions)
	Computes the center of gravity of the provided Vector3 array More...

static Vector3	ComputeCenterOfGravity (Vector3[] positions)

Public Attributes
UnityMolStructure	structure
	Store all the chains of the model More...

Dictionary< string, UnityMolChain >	chains
	Store all the chains of the model More...

string	name
	Name of the model More...

UnityMolBonds	bonds
	Bonds of the model, contains a dictionary of <UnityMolAtoms,UnityMolAtom[]> More...

List< UnityMolAtom >	allAtoms
	Stores a reference to all the atoms of the model More...

Vector3	centerOfGravity
	Center of gravity of the model More...

Vector3	maximumPositions
	Maximum position in x, y and z More...

Vector3	minimumPositions
	Minimum position in x, y and z More...

List< Int2 >	customChemBonds = new List<Int2>()
	Custom chemical bonds read in a PDB file More...

FieldLinesReader	fieldLinesR
	FieldLines Json file reader to be passed to UnityMolRepresentation More...

Detailed Description

Part of the SMCRA data structure, UnityMolModel stores the chains of the structure as a dictionary <string,UnityMolChain>. It also stores the bonds as UnityMolBonds A list of UnityMolAtom of the model is provided to loop over all atoms quickly

Constructor & Destructor Documentation

◆ UnityMolModel() [1/3]

UMol.UnityMolModel.UnityMolModel	(	Dictionary< string, UnityMolChain >	dictChains,
		string	nameModel
	)

UnityMolModel constructor taking chain dictionary as arg

◆ UnityMolModel() [2/3]

UMol.UnityMolModel.UnityMolModel	(	List< UnityMolChain >	listChains,
		string	nameModel
	)

UnityMolModel constructor taking chain list as arg, all the chains are inserted into the _chains dictionary

◆ UnityMolModel() [3/3]

UMol.UnityMolModel.UnityMolModel	(	UnityMolChain	newChain,
		string	nameModel
	)

UnityMolModel constructor taking one chain as arg, the chain is inserted into the chains dictionary

Member Function Documentation

◆ CenterAtoms()

void UMol.UnityMolModel.CenterAtoms ( )

Fills UnityMol.position using UnityMolAtom.oriposition and the centerOfGravity computed with ComputeCenterOfGravity()

◆ computeCenterOfGravity()

static void UMol.UnityMolModel.computeCenterOfGravity	(	int	N,
		float []	positions,
		float []	minmaxcog
	)

◆ ComputeCenterOfGravity() [1/2]

void UMol.UnityMolModel.ComputeCenterOfGravity ( )

◆ ComputeCenterOfGravity() [2/2]

static Vector3 UMol.UnityMolModel.ComputeCenterOfGravity ( Vector3 [] positions )

static

◆ ComputeCenterOfGravityCSharp() [1/2]

void UMol.UnityMolModel.ComputeCenterOfGravityCSharp ( )

Computes the center of gravity of the model

◆ ComputeCenterOfGravityCSharp() [2/2]

static Vector3 UMol.UnityMolModel.ComputeCenterOfGravityCSharp ( Vector3 [] positions )

static

Computes the center of gravity of the provided Vector3 array

◆ fillIdAtoms()

void UMol.UnityMolModel.fillIdAtoms ( )

Fills idInAllAtoms field

◆ getAllPositions()

Vector3 [] UMol.UnityMolModel.getAllPositions ( )

◆ getAtomWithID()

UnityMolAtom UMol.UnityMolModel.getAtomWithID ( int idAtom )

◆ hasHydrogens()

bool UMol.UnityMolModel.hasHydrogens ( )

◆ ToAtomList()

List<UnityMolAtom> UMol.UnityMolModel.ToAtomList ( )

◆ ToSelection()

UnityMolSelection UMol.UnityMolModel.ToSelection ( )

Member Data Documentation

◆ allAtoms

List<UnityMolAtom> UMol.UnityMolModel.allAtoms

Stores a reference to all the atoms of the model

◆ bonds

UnityMolBonds UMol.UnityMolModel.bonds

Bonds of the model, contains a dictionary of <UnityMolAtoms,UnityMolAtom[]>

◆ centerOfGravity

Vector3 UMol.UnityMolModel.centerOfGravity

Center of gravity of the model

◆ chains

Dictionary<string, UnityMolChain> UMol.UnityMolModel.chains

Store all the chains of the model

◆ customChemBonds

List<Int2> UMol.UnityMolModel.customChemBonds = new List<Int2>()

Custom chemical bonds read in a PDB file

◆ fieldLinesR

FieldLinesReader UMol.UnityMolModel.fieldLinesR

FieldLines Json file reader to be passed to UnityMolRepresentation

◆ maximumPositions

Vector3 UMol.UnityMolModel.maximumPositions

Maximum position in x, y and z

◆ minimumPositions

Vector3 UMol.UnityMolModel.minimumPositions

Minimum position in x, y and z

◆ name

string UMol.UnityMolModel.name

Name of the model

◆ structure

UnityMolStructure UMol.UnityMolModel.structure