v0.12.1

Backboner v0.12.1

Diff since v0.12.0

• Changed most mentions of "atom" to "point", including renaming the get_atom_displacements and get_atom_distances functions to get_displacements and get_distances respectively, with the old names still available in 0.12.x as aliases.
• Relax NNlib version

v0.12.0

Backboner v0.12.0

Diff since v0.11.4

• Remove protein submodule. (#18)
• Remove Zygote idealization extension.
• Rename every instance of the colloquial 'dihedrals' to the more correct term 'torsion_angles'.

Closed issues:

• Remove Protein submodule (#18)

v0.11.4

Backboner v0.11.4

Diff since v0.11.3

• Don't collect empty chains

v0.11.3

Backboner v0.11.3

Diff since v0.11.2

• Add get_torsional_angles function.
• Rename ChainedBonds fields internally.
• Fix backbone atom assignments.

v0.11.2

Backboner v0.11.2

Diff since v0.11.1

• Add Protein.PDBEntry function for getting a PDB entry in the form of a Vector{Protein.Chain} from the PDB without an explicit download.
• Add pdb_str macro for convenience. (e.g. pdb"1ASS")

v0.11.1

Backboner v0.11.1

Diff since v0.11.0

• Add quaternions_to_rotation_matrices and rotation_matrices_to_quaternions utility functions.

v0.11.0

Backboner v0.11.0

Diff since v0.10.1

• Support reading and writing .cif files with readchains and writechains.
• Hide methods for getting bond lengths, angles, dihedrals from bond_vectors.
• Stop exporting get_atom_displacements and get_atom_distances.
• Load proteins with Float64 by default (instead of Float32).
• Make get_dihedrals and get_bond_angles (hopefully) differentiable. (untested)
• Store the rotations of Frames as batches of rotation matrices instead of batched of quaternions.
• Remove Frame type in favor of batched multiplication.
• Make (::Frames)(coords) differentiable

v0.10.1

Backboner v0.10.1

Diff since v0.10.0

• Update to BioStructures.jl v4.0.0. (#21)

Merged pull requests:

• BioStructures.jl compat (#21) (@jgreener64)

v0.10.0

Backboner v0.10.0

Diff since v0.9.8

• Add support for residue "ins codes" (those letters next to residue numbers).
• Make Backbone{T} a subtype of AbstractVector{AbstractVector{T}}, instead of AbstractMatrix{T}.
• Only allow linear indexing of backbones.
• Remove get_bond_lengths(bond_vectors), get_bond_angles(bond_vectors), and get_dihedrals(bond_vectors) methods, in favor of only having the method for backbones, which calls _get_bond_lengths(bond_vectors), _get_bond_angles(bond_vectors), and _get_dihedrals(bond_vectors).
• Use BioStructures instead of PDBTools for writing.

Merged pull requests:

• CompatHelper: add new compat entry for Zygote in [weakdeps] at version 0.6, (keep existing compat) (#19) (@github-actions[bot])

v0.9.8

Backboner v0.9.8

Diff since v0.9.7

• Fix error in assign_oxygens!