v0.8.0

Backboner v0.8.0

Diff since v0.7.1

• Add is_knotted function for checking if a backbone contains a knot.

Merged pull requests:

• Overhaul and add knot detection algorithm (#16) (@anton083)
• Update knots.jl (#17) (@anton083)

v0.7.1

Backboner v0.7.1

Diff since v0.7.0

• Add Frames constructor for rotation matrices

Merged pull requests:

• Add Frames constructor for rotation matrices (#14) (@anton083)

Closed issues:

• Frames where rotations are in matrix form. (#13)

v0.7.0

Backboner v0.7.0

Diff since v0.6.0

• Add Frames type for working with e.g. rotations and locations of protein residue backbone triangles, using the Kabsch algorithm

Merged pull requests:

• Update proteindata (#11) (@anton083)
• Add Frames (#12) (@anton083)

v0.6.0

Backboner v0.6.0

Diff since v0.5.0

• Add matrix type parameter to Backbone
• Remove secondary assignment functions
• Remove idealization code (might make a package using a coordinate gradient approach)
• Add resnums field to Protein.Chain
• Probably more stuff that I missed

v0.5.0

Backboner v0.5.0

Diff since v0.4.0

v0.4.0

Backboner v0.4.0

Diff since v0.3.1

Merged pull requests:

• Add dihedrals (#9) (@anton083)

v0.3.1

Backboner v0.3.1

Diff since v0.3.0

• When estimating oxygen atom positions, the last oxygen atom is now put on the same plane as the N, Ca, and C atoms of the last residue.

v0.3.0

Backboner v0.3.0

Diff since v0.2.0

• Added documentation (incomplete).
• Added Residue type with fields: index, backbone (the entire backbone of the parent chain), aa (amino acid), and ss (secondary structure).
• Added the backbone_atom_coords function to get the coordinates of the backbone atoms of a residue, represented by a 3x4 matrix.
• Added aavector field to Chain.
• Chain is now a subtype of AbstractVector{Residue}.
• The add_oxygens function no longer removes the last residue of a Backbone{3} when creating the Backbone{4}. Instead, it selects a random orientation for the oxygen atom of the last residue.
• Secondary structure of chains are now represented by Chars according to the standard for DSSP classification.
• Removed SecondaryStructure type.

v0.2.0

Release notes:

• Changed the name of the missing/unassigned/mixed secondary structure type instance from MiSSing to Unassigned (breaking change) ... that's it lol

v0.1.0

Release notes:

• Added Backbone{N} type for storing coordinates of atoms in a backbone with N atoms per residue.
  • Added constructors for creating a backbone from residue locations and rotation matrices or quaternions
  • Added locs_and_rots function for converting backbone to locations of residues and their rotation_matrices.
  • Added add_oxygens function for estimating the oxygen positions in a backbone, based on the N, CA, and C positions.
• Added Chain type for wrapping a backbone with additional information such as chain name and secondary structure.
• Added Protein type for wrapping a vector of chains and allowing for accessing chains by name instead of just index in vector.
• Added SecondaryStructure type with singleton instances Loop, Helix, and Strand for filling secondary structure vectors of chains.
• Added assign_secondary_structure! function for assigning secondary structure to the chains of a protein.
• Added IO functions for reading PDB files and loading them into proteins, and vice versa.
• Added atom_coord_matrix function for getting all coordinates of a certain atom in a backbone.