v0.11.0

• The required versions of BioSequences.jl and BioAlignments.jl are updated to v2 of each, with support for earlier versions being dropped. AminoAcidSequence is hence renamed to LongAminoAcidSeq.
• threeletter_to_aa, a lookup table of amino acids, is re-exported from BioSymbols.

v0.10.1

• Change compatibility bounds for new DataFrames.jl release.

v0.10.0

• Change keyword argument names pdb_dir to dir and file_format to format for downloadpdb, downloadentirepdb, updatelocalpdb, downloadallobsoletepdb and retrievepdb.
• Remove readpdb, which has the same functionality as read.
• API reference section, more docstrings, links to related software and interactive Bio3DView.jl examples in documentation.

v0.9.4

• Change compatibility bounds for new RecipesBase.jl and CodecZlib.jl releases.

v0.9.3

• Change compatibility bounds for new RecipesBase.jl release.

v0.9.2

• Improvements to performance throughout the package. Some functions are made up to 5 times faster.

v0.9.1

• Fix documentation build.

v0.9.0

• A reader and writer are added for the MMTF file format, building on top of MMTF.jl. The interface is the same as for PDB and mmCIF files, with files either being read into the standard hierarchical structure or a MMTFDict. Gzipped files are supported. PDB, mmCIF and MMTF files can be interconverted.
• The expand_disordered flag is added to collectatoms, collectresidues, countatoms, countresidues, coordarray, writepdb, writemmcif, writemmtf and DataFrame. It determines whether disordered atoms and residues are expanded to include all entries. By default it is false except for the output functions, i.e. the last four above, where it is true by default.
• The pdbextension dictionary is changed to remove leading dots in the values.
• Improved file writing of empty elements.
• Examples are split off into a separate section in the documentation.
• A benchmark suite is added to track performance.

v0.8.0

• Superimposition of structural elements is supported using the Kabsch algorithm. New functions are superimpose!, Transformation, applytransform! and applytransform.
• rmsd and displacements carry out superimposition by default, with the relevant keyword arguments available. Setting superimpose to false prevents this. rmsdatoms and dispatoms respectively determine which atoms to calculate the property for.
• The trivial allselector, which selects all atoms or residues, is added.
• The backbone oxygen "O" is added to backboneatomnames.
• Compatible bounds of package dependencies are added to Project.toml.

v0.7.0

• MetaGraph from MetaGraphs.jl is extended to create graphs of contacting elements in a molecular structure, giving access to all the graph analysis tools in LightGraphs.jl.
• DataFrame from DataFrames.jl is extended to allow creation of data frames from lists of atoms or residues.
• pairalign from BioAlignments.jl is extended to produce pairwise alignments from structural elements.
• AminoAcidSequence now takes any element type and has the gaps keyword argument.
• Documentation example of interoperability with NearestNeighbors.jl.
• Parametric types used more extensively internally.