Constructor Summary
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constructor(name: String, path: String) |
Member Summary
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Method Summary
Public Methods | ||
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atomCenter(selection: Selection): Vector3 Gets the center of the (selected) structure atoms |
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Calls dispose() method of property objects. |
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Atom iterator |
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Bond iterator |
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eachChain(callback: function(chain: ChainProxy), selection: Selection): undefined Chain iterator |
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eachEntity(callback: function(entity: Entity), type: EntityType): undefined Entity iterator |
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eachModel(callback: function(model: ModelProxy), selection: Selection): undefined Model iterator |
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eachPolymer(callback: function(polymer: Polymer), selection: Selection): undefined Polymer iterator |
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eachResidue(callback: function(residue: ResidueProxy), selection: Selection): undefined Residue iterator |
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eachResidueN(n: Integer, callback: function(residueList: ResidueProxy[])): undefined Multi-residue iterator |
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getAtomSet(selection: Boolean | Selection | BitArray): BitArray Get a set of atoms |
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getAtomSetWithinGroup(selection: Selection): BitArray Get set of all atoms within the groups of a selection |
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getAtomSetWithinPoint(point: Vector3 | AtomProxy, radius: Number): BitArray Get set of atoms around a point |
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getAtomSetWithinSelection(selection: Selection, radius: Number): BitArray Get set of atoms around a set of atoms from a selection |
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getAtomSetWithinVolume(volume: Volume, radius: Number, minValue: [type], maxValue: [type], outside: [type]): BitArray Get set of atoms within a volume |
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getBoundingBox(selection: Selection, box: Box3): Vector3 Gets the bounding box of the (selected) structure atoms |
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getChainnameCount(selection: Selection): Integer Get number of unique chainnames |
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getPrincipalAxes(selection: Selection): PrincipalAxes Gets the principal axes of the (selected) structure atoms |
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init() |
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Public Constructors
Public Members
public atomCount source
public atomSet source
public atomSetCache source
public atomSetDict source
public atomStore source
public backboneBondStore source
public biomolDict source
public bondCount source
public bondSet source
public bondStore source
public boxes source
public chainStore source
public extraData: StructureExtraData source
public frames source
public header: StructureHeader source
public id source
public modelStore source
public name source
public path source
public residueMap: ResidueMap source
public residueStore source
public rungBondStore source
public spatialHash: SpatialHash source
public title source
public get type source
public validation: Validation source
Private Members
private _ap source
private _bp source
private _cp source
private _rp source
Public Methods
public atomCenter(selection: Selection): Vector3 source
Gets the center of the (selected) structure atoms
Params:
Name | Type | Attribute | Description |
selection | Selection |
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the selection |
public dispose(): undefined source
Calls dispose() method of property objects. Unsets properties to help garbage collection.
public eachAtom(callback: function(atom: AtomProxy), selection: Selection): undefined source
Atom iterator
public eachBond(callback: function(bond: BondProxy), selection: Selection): undefined source
Bond iterator
public eachChain(callback: function(chain: ChainProxy), selection: Selection): undefined source
Chain iterator
Params:
Name | Type | Attribute | Description |
callback | function(chain: ChainProxy) | the callback |
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selection | Selection |
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the selection |
public eachEntity(callback: function(entity: Entity), type: EntityType): undefined source
Entity iterator
public eachModel(callback: function(model: ModelProxy), selection: Selection): undefined source
Model iterator
Params:
Name | Type | Attribute | Description |
callback | function(model: ModelProxy) | the callback |
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selection | Selection |
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the selection |
public eachPolymer(callback: function(polymer: Polymer), selection: Selection): undefined source
Polymer iterator
public eachResidue(callback: function(residue: ResidueProxy), selection: Selection): undefined source
Residue iterator
Params:
Name | Type | Attribute | Description |
callback | function(residue: ResidueProxy) | the callback |
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selection | Selection |
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the selection |
public eachResidueN(n: Integer, callback: function(residueList: ResidueProxy[])): undefined source
Multi-residue iterator
Params:
Name | Type | Attribute | Description |
n | Integer | window size |
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callback | function(residueList: ResidueProxy[]) | the callback |
public finalizeAtoms() source
public finalizeBonds() source
public getAtomData() source
public getAtomIndices() source
public getAtomProxy() source
public getAtomSetWithinGroup(selection: Selection): BitArray source
Get set of all atoms within the groups of a selection
Params:
Name | Type | Attribute | Description |
selection | Selection | the selection object |
public getAtomSetWithinPoint(point: Vector3 | AtomProxy, radius: Number): BitArray source
Get set of atoms around a point
public getAtomSetWithinSelection(selection: Selection, radius: Number): BitArray source
Get set of atoms around a set of atoms from a selection
public getAtomSetWithinVolume(volume: Volume, radius: Number, minValue: [type], maxValue: [type], outside: [type]): BitArray source
Get set of atoms within a volume
Params:
Name | Type | Attribute | Description |
volume | Volume | the volume |
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radius | Number | radius to select within |
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minValue | [type] | minimum value to be considered as within the volume |
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maxValue | [type] | maximum value to be considered as within the volume |
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outside | [type] | use only values falling outside of the min/max values |
public getBackboneAtomData() source
public getBackboneBondData() source
public getBackboneBondSet() source
public getBondData() source
public getBondProxy() source
public getBondSet() source
public getBoundingBox(selection: Selection, box: Box3): Vector3 source
Gets the bounding box of the (selected) structure atoms
public getChainProxy() source
public getChainnameCount(selection: Selection): Integer source
Get number of unique chainnames
Params:
Name | Type | Attribute | Description |
selection | Selection | limit count to selection |
public getModelProxy() source
public getPrincipalAxes(selection: Selection): PrincipalAxes source
Gets the principal axes of the (selected) structure atoms
Params:
Name | Type | Attribute | Description |
selection | Selection |
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the selection |