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AntonOresten committed Nov 26, 2023
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Expand Up @@ -22,7 +22,7 @@ Pkg.add("Backboner")

The `Protein` type wraps a vector of `Chain`s, which in turn wraps the `Backbone{4}` type (4, because it stores the positions of 4 atoms per residue: N, CA, C, O). The `Backbone{N}` type has the `N` type parameter in order to remain flexible. It allows one pass only the N, CA, and C atoms of a backbone, such that the O atom positions can added in using the `add_oxygens` function.

The package includes a `SecondaryStructure` type, which describes the secondary structure of a single residue in a chain. The secondary structure of an entire chain is described by a `Vector{Char}`, where '-' stands for coil/loop, 'H' for helix, and 'E' for strand. For assignment of secondary structure, this package uses the [AssigningSecondaryStructure.jl](https://github.com/MurrellGroup/AssigningSecondaryStructure.jl) package, which implements a simplified version of the DSSP algorithm to assign three types of secondary structure to residues: loop, helix, and strand.
The secondary structure of an entire chain is described by a `Vector{Char}`, where '-' stands for coil/loop, 'H' for helix, and 'E' for strand. For assignment of secondary structure, this package uses the [AssigningSecondaryStructure.jl](https://github.com/MurrellGroup/AssigningSecondaryStructure.jl) package, which implements a simplified version of the DSSP algorithm.

Protein backbones can be loaded from a PDB file using the `pdb_to_protein` function, which returns a `Protein` instance. Inversely, a `Protein` instance can be written to a PDB file using the `protein_to_pdb` function.

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Release notes:

  • 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.

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Registration pull request created: JuliaRegistries/General/95979

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.3.0 -m "<description of version>" 012409a603903fe90fc905b9eb3d9f76ad459751
git push origin v0.3.0

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