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Change Log

All notable changes to this project will be documented in this file, following the suggestions of Keep a CHANGELOG. This project adheres to Semantic Versioning.

[v2.4.0]

  • Summary of changes from v2.3.0

Added

  • Reinstated the PLY parser

Changed

  • Default to bcif format instead of mmtf in RCSB and PDBe data providers

[v2.3.0]

  • Summary of changes from v2.2.2

Added

  • Support binary CIF files
  • Parse connectivity from PDBe updated mmCif format
  • PDBe as new datasource

Changed

  • RCSB provider now defaults to binary CIF download instead of deprecated MMTF format
  • Upgrade Three.js dependency to v0.158. Upgrade dependencies to resolve issues reported by npm audit
  • Dev: replace Jest test runner with Vitest

Removed

  • .PLY parser has been removed due its reliance on primitives unavailable in newest Three.js versions

[v2.2.2]

  • Summary of changes from v2.2.0

Changed

  • Fix coreCif (elements with charges), mmCif (handle chem_comp block) files parsing
  • Fix Colormaker class after v2.2.0 change in bundling

[v2.2.0]

  • Summary of changes from v2.1.1

Added

  • Pymol mouse bindings: add focus scroll #992

Changed

  • Remove support for Internet Explorer #993
  • Add inferBonds loading parameter #977

[v2.1.1]

  • Summary of changes from v2.0.0

Changed

  • Inline getAllowedContour result #988
  • Fix calculate chain names #979
  • Fix pdbwriter model format #984
  • Reworked structure.refreshed signal and logic on updates #942
  • Housekeeping for github actions #976
  • Fix CL1 atom type guess #959
  • Typescript delarations #958
  • Fix pdbqt #957
  • molfile v3000 #955
  • Fix typing of CylinderBuffer #906
  • Fix sdf atom names #949
  • Fix unecessary structure disposal #941
  • Housekeeping #929

[v2.0.0]

  • Stable release

Added

  • Alphafold Datasource (@fredricj)

Changed

  • Enable three.js treeshaking in build config (@milot-mirdita)
  • Stable angle calculation in dihedral histrogram representation
  • Fix atom name writing in PdbWriter

[v.2.0.0.dev.40]

Added

  • color management
  • Export many more types (representations, params)
  • support coloring atoms or bonds by external data

Changed

  • default surface type is 'av'
  • numerous Typescript fixes, typos etc
  • build system fixes and dependency updates
  • fix CylinderImpostor bugs

[v.2.0.0.dev.39]

Added

  • allow writing of partial PDB structure
  • more typescript declarations
  • CallbackTrajectory class and example

Changed

  • catch errors thrown from sprintfjs in label format

[v.2.0.0.dev.38]

Added

  • contour option for volume surfaces (electron density maps)
  • buble, for transpiling some ES2015 features (e.g. classes, arrow functions, ...)
  • volume slice representation including interpolation support
  • xplor/cns volume file parser
  • colorVolume parameter for surface representation of volume data
  • voxelSize parameter for volume file parser
  • support for non orthogonal cell in cube file parser
  • dsn6/brix volume file parser
  • psf topology/structure file parser
  • wwPDB validation report xml parser, representation and colorschemes
  • support for picking Shape objects, Volume slices, Contact bonds
  • scroll mouse behavior to change far/near clipping and fog
  • label primitive for Shape class
  • support for reversing color schemes with colorReverse parameter
  • independent component movement via .setPosition, .setRotation, .setScale, .setTransform
  • bonded and ring selection language keywords
  • resname list to selection language, [ALA,GLU]

Changed

  • renamed volume parameter in molecular surface representation to colorVolume
  • renamed colormaker classes from colorMaker to colormaker, i.e. removed camel case
  • renamed ColormakerRegistry.getTypes to .getSchemes
  • colormaker subclasses now auto-register with ColormakerRegistry
  • refactored buffer classes to use a data object as input
  • refactored picking to be more general
  • replaced PickingData with PickingProxy
  • updated three.js to r85
  • updated chroma.js to 1.3.3
  • replaced utils/bitset with utils/bitarray
  • tweaked aminoacid keywords in selection language to follow rasmol/jmol, vmd

Removed

  • stage/component.centerView method, use .autoView instead
  • GidPool, picking handled by Picker objects
  • deprecated use of # for element selection, use _ instead

v0.9.3 - 2016-10-14

Changed

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

v0.9.2 - 2016-10-06

Changed

  • fix, moved polyfills back inside the bundle

v0.9.1 - 2016-10-06

Changed

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

v0.9.0 - 2016-10-05

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

v0.8 - 2016-07-22

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

v0.7.1a - 2016-06-02

Changed

  • fixed version in builds

v0.7.1 - 2016-06-02

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)

v0.7 - 2016-05-08

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

v0.6 - 2015-10-12

Added

  • MIGRATION: Stage.loadFile signature changed, now returns a Promise and does not accept callbacks
  • MIGRATION: moved trajectory server into its own repository: MDSrv
  • ADD: Support for MOL2 and SDF files
  • ADD: Support for DX files
  • ADD: Support for PQR files
  • ADD: ExampleRegistry singleton
  • ADD: PluginRegistry singleton
  • ADD: Datasource class to use instead of hard-coded paths
  • ADD: GidPool
  • ADD: simple xml parser
  • ADD: APBS plugin to load PQR and DX file, simple GUI
  • ADD: bond and surface picking
  • ADD: User-defined color schemes (API)
  • GUI: VirtualList and VirtualTable
  • GUI: re-sizable sidebar (contents still need to be made responsive)
  • WIP: scripting API

Changed

  • EXAMPLES: general fixes and enhancements
  • DOC: moved installation and development information into the README
  • GUI/DOC: Higher color contrast for GUI and documentation pages
  • CODE: qunit updated
  • CODE: moved logical units of code into their own files
  • CODE: speeded up secondary structure assignment from PDB/mmCIF files; fixed bugs leading to wrong assignment
  • CODE: element color scheme now uses colorValue parameter to color carbon elements
  • CODE: script and assets paths are now configurable
  • CODE: more forgiving pdb parsing wrt to model records
  • CODE: helper function for re-ordering atoms
  • CODE: enhancements to handling Web Workers (WorkerPool, lazy Worker creation)
  • CODE: enhancements to volume triangulation (limit to given box, skip empty parts)
  • CODE: all *Buffer classes now inherit from Buffer and share common code
  • CODE: BufferAttributes can be re-used or grown
  • CODE: moved Buffer-specific code out of Representation class
  • CODE: molecular surface enhancements (color by atom, filter by atom)
  • CODE: nicer clipping of meshes and impostors (unlit interior to make them appear solid)
  • CODE: optimized kdtree building
  • CODE: clearer atomnames handling for fiber creation
  • CODE: Color handling code refactored exposing more parameters
  • CODE: Basic support for async creation of representations (so far used for molecular surfaces and volume triangulation)
  • CODE: chunked data loading and parsing via streamer class
  • CODE: faster autobonding of large residues (e.g. hydrated lipids)
  • CODE: WebWorker support while using development and build files
  • CODE: WebWorker used for decompression, parsing and surface generation
  • FIX: Issue #7
  • FIX: residues at the end of fibers may not require all backbone atoms
  • FIX: standard compatible atom names when writing pdb files
  • FIX: origin coordinates not used/read from mrc header

Removed

  • DEL: removed FragFit plugins

v0.5 - 2015-30-04

Added

  • Initial release