Class Biojs.Protein3DUniprot

Version 1.0.0.

Extends Biojs.Protein3DWS.

Defined in: Biojs.Protein3DUniprot.js.

Class Summary
Constructor Attributes	Constructor Name and Description
	Biojs.Protein3DUniprot(options) Protein viewer to show the pdb files aligned to an Uniprot Accession

Method Summary
Method Attributes	Method Name and Description
	constructor(options)
	filterAlignments(selection) Filters the alignments available for the current protein: Only PDB files containing a part of the requested region are selectable.
	getAlignmentsByPdb(pdb) Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region).
	getAlignmentsBySelection(selection) Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region).
	getCurrentAlignmentId()
	getCurrentProteinId()
	removeSelection() Removes selection in the current displayed structure.
	requestPdb(pdbId) Request and display a pdb file by means of its identifier.
	setProtein(proteinId) Get all pdb files for a given uniprot id.
	setSelection(selection) Selection of a region using the uniprot positions.

Methods borrowed from class Biojs.Protein3DWS:: getPdbId
Methods borrowed from class Biojs.Protein3D:: applyJmolCommand, changeBackgroundColor, changeControlsVisiblility, display, displayAntialias, displayColorScheme, displayNegative, displayPolar, displayPositive, displayStyle, displaySurface, displayUnPolar, getSelection, hideControls, hideNegative, hidePolar, hidePositive, hideSurface, hideUnPolar, reset, rotate, setHalosVisible, setPdb, showControls, showLoadingImage, toString, undisplay
Methods borrowed from class Biojs:: addListener, extend, getId, listen, raiseEvent, setEventHandlers, setOptions

Event Summary
Event Attributes	Event Name and Description
	onPdbSelected(actionPerformed)

Events borrowed from class Biojs.Protein3DWS:: onRequestError
Events borrowed from class Biojs.Protein3D:: onPdbLoaded, onSelection

Class Detail

Biojs.Protein3DUniprot(options)

Protein viewer to show the pdb files aligned to an Uniprot Accession
Author: John Gomez.

var instance = new Biojs.Protein3DUniprot({
		target: 'YourOwnDivId',
		proteinId: 'P07148'
});

Parameters:
{Object} options: An object with the options for the component.

Options detailed:

{string} [proteinId]

Uniprot identifier of the protein.

{string} [mapping=Biojs.Protein3DUniprot.ALIGNMENTS_UNIPROT_MAPPING]

Mapping function to obtain the protein's alignments:

Biojs.Protein3DUniprot.ALIGNMENTS_UNIPROT_MAPPING
Biojs.Protein3DUniprot.ALIGNMENTS_PDBe_MAPPING

Method Detail

constructor(options)

Parameters:
options

filterAlignments(selection)

Filters the alignments available for the current protein: Only PDB files containing a part of the requested region are selectable. The specified region is highlighted in the displayed PDB file.

// Selection of the region in the interval [100,150].
instance.filterAlignments({start: 120, end: 150});

Parameters:
{Object|Array} selection: Can be either a plain object or an array. If object, it must have the fields start and end; Where "start" is greater than or equal to "end". If array, it must contain numbers representing the positions to be selected.

{Object} getAlignmentsByPdb(pdb)

Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region).

// Get the alignments matching with bases 4, 8 and 100.
alert ( instance.getAlignmentsByPdb("2F73") );

Parameters:
{string} pdb: identifier.

Returns:: {Object} .

getAlignmentsBySelection(selection)

Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region).

// Selection of the region in the interval [100,150].
instance.setSelection({start: 120, end: 150});

// Get the alignments matching with bases 4, 8 and 100.
alert ( instance.filterAlignments([4,8,100]) );

Parameters:
{Object|Array} selection: Can be either a plain object or an array. If object, it must have the fields start and end; Where "start" is greater than or equal to "end". If array, it must contain numbers representing the positions to be selected.

getCurrentAlignmentId()

getCurrentProteinId()

removeSelection()

Removes selection in the current displayed structure.

instance.removeSelection();

requestPdb(pdbId)

Request and display a pdb file by means of its identifier.

instance.requestPdb('3t6f');

Parameters:
{string} pdbId: Pdb file identifier.

setProtein(proteinId)

Get all pdb files for a given uniprot id. Also triggers the event that a new pdb file was loaded.

instance.setProtein("P99999");

Parameters:
proteinId

setSelection(selection)

Selection of a region using the uniprot positions.

// Selection of the region in the interval [100,150].
instance.setSelection({start: 100, end: 150});

// Selection of the positions 4, 8 and 100.
instance.setSelection([4,8,100]);

Parameters:
{Object|Array} selection: Can be either a plain object or an array. If object, it must have the fields start and end; Where "start" is greater than or equal to "end". If array, it must contain numbers representing the positions to be selected.

Event Detail

onPdbSelected(actionPerformed)

instance.onPdbSelected(
   function( e ) {
      alert( "Alignment " + e.alignmentId + " selected. Start: " + e.start + " End: " + e.end );
   }
);

Parameters:
{function} actionPerformed: An function which receives an Biojs.Event object as argument.

Event object data:
{Object} source: The component which did triggered the event.
{string} pdbId: The name of the loaded file.
{string} alignmentId: Alignment identifier.
{string} start: Starting base index.
{string} end: Ending base index.

Classes

Class Biojs.Protein3DUniprot