v4.2.0

• Base.copy is defined for structural elements and carries out a recursive copy of the element.
• The fields of Transformation are made concrete, which may improve performance.

v4.1.1

• PDB download functions now use HTTPS rather than FTP as the PDB will deprecate the FTP protocol.

v4.1.0

• retrievepdb now takes the format keyword argument and uses MMCIFFormat by default.
• MMTF files are no longer available to download via downloadpdb, downloadentirepdb, updatelocalpdb and downloadallobsoletepdb as the RCSB PDB no longer provides them.

v4.0.0

The package is made considerably more lightweight by moving a number of dependencies to extensions. This should make it easier for other packages to build on top of BioStructures.jl. Some types and functions are also renamed to avoid clashes, and a convenient string selection syntax is introduced.

Breaking changes

• PDB, PDBXML, MMCIF and MMTF are renamed to PDBFormat, PDBXMLFormat, MMCIFFormat and MMTFFormat respectively to avoid clashing with module names. read(fp, PDB) should be replaced with read(fp, PDBFormat), for example.
• ProteinStructure is renamed to MolecularStructure since it is not limited to representing protein structures.
• x, y, z, x!, y! and z! are no longer exported as they are common variable names. They are still available as BioStructures.x etc.
• Importing BioSequences.jl is now required to use LongAA.
• Importing BioSequences.jl and BioAlignments.jl is now required to use pairalign, superimpose!, rmsd/displacements with the superimpose option or Transformation on structural elements.
• Importing MMTF.jl is now required to use MMTFDict or writemmtf.
• Importing DSSP_jll.jl is now required to use rundssp!, rundssp or the run_dssp option with read/retrievepdb.
• Importing STRIDE_jll.jl is now required to use runstride!, runstride or the run_stride option with read/retrievepdb.

Non-breaking changes

• Support for Julia versions before 1.9 is dropped.
• A string selection syntax is introduced, allowing selections such as collectatoms(struc, sel"name CA and resnumber <= 5").
• The selectors sidechainselector, proteinselector, acidicresselector, aliphaticresselector, aromaticresselector, basicresselector, chargedresselector, neutralresselector, hydrophobicresselector, polarresselector and nonpolarresselector are added.
• PDB parsing in certain situations is now much faster.

v3.1.0

• PrecompileTools.jl is used to reduce the time to first execution of PDB file reading.

v3.0.0

• On Julia 1.9 and later the DataFrame and MetaGraph constructors are moved to package extensions in order to reduce the number of dependencies. Calling using DataFrames and using Graphs, MetaGraphs respectively is now required to access these functions.
• The file formats PDB, PDBXML, MMCIF and MMTF are no longer subtypes of BioCore.IO.FileFormat, allowing BioCore.jl to be removed as a dependency.

v2.1.0

• DSSP and STRIDE can now be run to assign secondary structure to proteins.

v2.0.0

• The required versions of BioSequences.jl and BioAlignments.jl are updated to v3 of each, with support for earlier versions being dropped. LongAminoAcidSeq is hence renamed to LongAA, an alias for LongSequence{AminoAcidAlphabet}.
• Fix bug in pdbentrylist.

v1.2.1

• Fix bug allowing reflections during structural superimposition.

v1.2.0

• firstindex and lastindex are defined for structural elements, contact maps and distance maps. This allows begin and end to be used in indexing expressions.
• Support for Julia versions before 1.6 is dropped.