Ngl Versions Save

Changed

• increased light distance from camera, to fix unlit rendering
• remove double quotes from atomnames in chemComp cif parser

Changed

• fix, moved polyfills back inside the bundle

Changed

• removed (wrongly added) ngl2.js from dist folder
• fixed chemComp cif parser not passing chainid

Added

• lazy representation parameter that only builds & updates the representation when visible
• chainname based color scheme
• BondHash class to quickly get atoms connected to an atom
• SpatialHash class to quickly get neighboring atoms/points
• XmlParser parameter to use the browser's DOMParser
• attachment (top, middle, bottom; left, center, right) for LabelRepresentation/TextBuffer
• border color and width for LabelRepresentation/TextBuffer
• colored background rectangle for LabelRepresentation/TextBuffer
• "offset" style rendering of double/triple bonds (@fredludlow)
• PubchemDatasource to load cid as sdf, pubchem://16490
• basic entity support (type, description, chain mapping; mmcif, mmtf)
• entitytype, moleculetype, chainid, polymer color schemes
• ShaderRegistry, DecompressorRegistry
• box display for "axes" representation

Changed

• ResidueindexColorMaker colorscale domain on a per chain basis
• ChainindexColorMaker colorscale domain on a per model basis
• Fixed, initial parameters for a Buffer not taken into account
• ignore bonds that are defined multiple times in PDB parser
• updated mmtf lib to v1.0
• use npm as the build system
• complete list of ion and saccharide group names

Removed

• gulp as the build system

Added

• gulp build scripts
• mmtf v0.2 support
• support for rendering double/triple bonds, enable via multipleBond Representation parameter (@fredludlow, @arose)
• stage.clicked signal (renamed from .onPicking)
• stage.hovered signal
• parsing of "chem comp" cif files
• experimental "axes" representation showing the principal axes of an atom selection
• added cone, arrow & ellipsoid buffers
• added Shape class as a simple way to add custom shapes to the scene

Changed

• reorganized everything to use es6 modules
• read bondOrder from 'pdbx_value_order' in mmcif files
• interpret 'CONECT 1529 1528 1528' as double bond in pdb files
• side Buffer/Representation parameter changed: THREE.FrontSide => "front", THREE.BackSide => "back", THREE.DoubleSide => "double"
• support for negative resno values in selections: "-5:A", "-12--8", "-12-0"
• use chemical component type (available in mmtf) for determining molecule type
• .get/setOrientation return/argument changed
• enable SDF font as the default TextBuffer class only on Chrome
• support for building using three-jsnext
• renamed radiusSegments parameter to radialSegments
• WebWorkers (for building surfaces) no longer need to load the main script file
• NGL.GET renamed to NGL.getQuery

Removed

• python-based build scripts
• closure-compiler
• stage.signals.onPicking (renamed to .clicked)
• stage.signals.atom/bond/volume/nothingPicked, use .clicked instead
• NGL.mainScriptFilePath no longer needed
• NGL.useWorker, use "useWorker" representation parameter

Changed

• fixed version in builds

Added

• orthographic camera mode
• backgroundColor parameter for Stage
• x/y/z offset parameters for labels (TextBuffer)
• OX1 atoms are recognized as part of the protein backbone
• stage.makeImage now increments the task counter
• added .isIdentity method to test if an Assembly is an identity transformation over all chains
• embedded-dev build target (@sbliven)
• support for responseType = "json" to efficiently load json data

Changed

• there is no longer a fake unitcell created when no space group information is available
• the query string is removed from urls before the determining file info (e.g. name, extension)
• fixed labelText param not working in LabelRepresentation
• enable SDF font as the default only on Chrome (fixes labels not shown on some OS/Browser)
• ignore 'given' ncs operators
• ensure that resname is upper case

Removed

• stage.setTheme removed (use new backgroundColor parameter), themes now part of GUI code
• NGL.Preferences is now part of the GUI code and removed from NGL.Stage. Setting overwritePreferences: true when instantiating an NGL.Stage object is not necessary anymore.
• removed .requestVisibility method and signal (too GUI specific, if needed, should be handled there)

Added

• Store and Proxy classes for memory efficiency
• MMTF, DXBIN, DCD files format parsers
• 'unitcell' representation
• stage.makeImage (returns Promise)
• take NCS operations into account when creating unitcell & supercell assemblies
• added multi sample antialias rendering
• added support for spinning around an axis
• use bitsets for storing selections of atoms
• Assembly and AssemblyPart classes
• stage.toggleFullscreen method
• read occupancy data when available (mmCIF, pdb, mmtf)
• occupancy color scheme
• alternate location support in selections, e.g. %B
• read insertion codes when available (mmCIF, pdb, mmtf)
• insertion code support in selections, e.g. ^A
• numeric residue name support in selections, e.g. [032]
• Queue class to handle async tasks

Changed

• fixed transformation matrix in mrc/ccp4 parser
• optimized near clipping
• Fiber class remanamed to Polymer
• more consistent fog
• use workers more sparsely due to the large overhead of creating them
• create font SDF on demand, remove asset dependency
• integrated three.js lighting into custom shaders
• MIGRATION: chainname read from auth_asym_id instead of from label_asym_id field
• DOC: clarified apache configuration for deployment
• FIX: cif parser, ignore non-displayable bonds between symmetry mates
• FIX: cif parser, struct_conn bonds not added for multiple altloc atoms
• LIB: updated signals.js
• LIB: updated promise.js
• LIB: updated three.js
• LIB: updated pako.js to pako_inflate.js (no deflation support needed)
• CODE: support loading of Blob objects in addition to File objects
• CODE: tweaked DistanceRepresentation visibility params

Removed

• zip, lzma, bzip2 decompression
• removed async.js
• mdsrv related code and documentation
• stage.exportImage (makes image and triggers download), use stage.makeImage