3.2.3

Updated sequence query to support atom_site.auth_ fields.

3.2.2

Better Computation scheduling (using setImmediate alternatives instead of setTimeout).

3.2.1

Parse _pdbx_struct_mod_residue from mmCIF.

3.2.0

Fixed bug in CIFTools.
Add more robust bond computation.

3.1.6

Added support for _struct_conn mmCIF category.
Refactored geometry 3D search API and added spatial hash option.

3.1.5

Renamed Matrix4.empty and Vector4.create to Matrix4/Vector4.zero.
Added more linear algebra functions.
Removed ObjectVec3 from linear algebra.

3.1.4

Added "allAtoms" query.

3.1.3

Fixed a issue in the PDB parser where ATOM/HETATM records without temperature factor would not be parsed.

3.1.2

Fixed an assembly generation issue.

3.1.1

More robust nucleotide detection.

3.1.0

Updated density data model.
Removed the support for the DSN6 density data format.
Fixed a bug in marching cubes that sometimes added bad triangles because of a vertex index cache not being properly cleaned.
Marching cubes annotation tweak.

3.0.4

Fix in PDB CRYST1 record parsing.

3.0.3

Better low resolution mol. surfaces.
Surface laplacian smooting now supports center vertex weight.

3.0.2

Enable generating symmetry mates for the P 1 spacegroup.

3.0.1

Fixed a bug in Symmetry Mates generation.
Fixed a bug in CIF based density parsing.

3.0.0

Updated Molecule representation.
- Changed namespaces for MoleculeModel to Molecule.Model
- Molecule.Model:
  - atoms/residues/chains/... are now accessed as data.atoms/...
  - positions are now a separate table and no longer part of atoms.
  - these changes are to enable better data sharing between different models of the same molecule
- Core.Structure.DataTable is now Core.Utils.DataTable and the API has been updated
Added Core.Utils.FastMap/FastSet
- This replaces most ES6 map usage in LiteMol.

2.5.1

Updated molecular surface vertex annotation code.

2.5.0

Updated Computation API. As a result, many (especially small) computation should feel a lot more responsive.

2.4.11

Support for CIF density data.
CIFTools updated.
Support for BinaryCIF 0.3.
BinaryCIF molecules will consume less memory.

2.4.10

Detection of "single atom" nucleotides.

2.4.9

Updated sequence query to support "auth_asym_id".
Added MoleculeModel.withTransformedXYZ function.

2.4.8

Updated CIFTools.

2.4.7

Refactor ChunkedArray and ArrayBuilder to procedural style to avoid deoptimization on long runs.
CIF support has been factored out as CIFTools.js.

2.4.6

Improved BinaryCIF interger packing encoder.

2.4.5

PDB parser fix.

2.4.4

Added polymerTrace(...atomNames) query.

2.4.3

Refactored code that used "private classes" to a procedural style to avoid it from being deoptimized by garbage collector on long computations.

2.4.2

SDF parser fix.
StringPool is now "local" to avoid memory leaks.

2.4.1

A bugfix in BinaryCIF decoder.
A bugfix in mmCIF assembly parsing.

2.4.0

Refactored CIF support. The CIF access is now a lot more streamlined.
Added support for BinarCIF.
Renamed Formats.Density.BRIX to Formats.Density.DSN6

2.3.1

Adding MOL/SDF support.

2.3.0

Refactoring of "Formats" namespace to enable easier support for additional formats.
- Formats.Cif is now Formats.CIF
- Moved Formats.Cif.mmCif to Formats.Molecule.mmCIF
- Moved Formats.PDB to Formats.Molecule.PDB
- Moved Formats.CCP4/BRIX to Formats.Density.CCP4/BRIX
- Moved Formats/Field.ts to Formats/Density/Data.ts and changed the namespace to Formats.Density
- Added a "common" parsing functions for all formats supported by the Core.

2.2.7

Fixed a bug in PDB parser.

2.2.6

Fixed a bug that prevented creating of "non-interactive" molecular surfaces.

2.2.5

Added query flatten and function Fragment.find(query). (for example residuesByName('ALA').flatten(f => f.find(atomsByElement('C')))).

2.2.4

Added intersectWith query.
Fixed a problem with kD tree based queries (ambient*) in "partial contexts" (i.e. when inside "inside" query).

2.2.3

Added algebraic query support.

2.2.2

Added complement query.

2.2.1

Added additional pattern queries.

2.2.0

Added support for the BRIX density format.

2.1.15

Fix to overlaping secondary structure elements.

2.1.14

Fixes to assembly generation.

2.1.13

Refactored symmetry generation code to be slightly more readable.

2.1.12

Fixed symmetry/assembly generation that contained lower amount of entities in it's result.
Fixed secondary structure indexing in symmetry/assembly generation when the output molecule is smaller than the original.

2.1.11

Updated sequence query to work on computed models.

2.1.10

Fixed another bug in asymIds :)

2.1.9

Fixed a bug with incorrect asymIds in the symmetry mate generation.

2.1.8

Refactored queries.

2.1.7

Added C4 atom to the sidechain and backbone queries.

2.1.6

Computed molecules (assemblies) now include operator indices used.

2.1.5

Fixed a bug in the CIF parser that crashed on ' X' (i.e. string token that starts with space).

2.1.4

Added support for TURN secondary structure.

2.1.3

Assembly and symmetry generation now supports secondary structure.

2.1.2

Updated the module system (again).

2.1.1

Moved marching cubes from Visualization to Core
Added PerformanceMonitor to Utils

2.1.0

Added support for generating symmetry mates and assembly models.

2.0.1

Fixes in module support.

2.0.0

Big code refactoring.

1.3.0

Added basic support for the PDB format.
Fixed a minor bug in visualization picking code.

1.2.1

Changed the visuals' constructors to take a single object as input rather than a long list of arguments.

1.2.0

Added basic support for molecule comparison based on RMSD.

1.1.5

Added support for "full" density surfaces.

1.1.4

Added entityId property to chain table in molecule representation.
Changed entity table id to entityId.

1.1.3

Fixed a bug "atom names" queries.

1.1.2

Coloring of molecular surfaces.

1.1.1

Fixed a bug in assembly visuals.
Fixed symmetry visuals.

1.1.0

Updated Density/MarchingCubes to support vertex annotation.
Added MolecularSurface support.
Added namespace LiteMol.Visualization.Molecule.