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.