diff --git a/README.md b/README.md index 7bea776..16fe9ef 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![Build Status](https://github.com/MurrellGroup/Backboner.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/MurrellGroup/Backboner.jl/actions/workflows/CI.yml?query=branch%3Amain) [![Coverage](https://codecov.io/gh/MurrellGroup/Backboner.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/MurrellGroup/Backboner.jl) -Backboner is a Julia package that offers a suite of tools for storing protein backbone atom positions, estimating oxygen atom positions, assigning secondary structure, and more. +Backboner is a Julia package that offers a set of types and functions for working with molecular backbones. It also includes functions for working with protein chains, reading/writing PDB files and assigning secondary structure. ## Installation @@ -18,13 +18,11 @@ using Pkg Pkg.add("Backboner") ``` -## Types and functions +## Overview -Proteins are represented as vectors of `Chain`s, which wrap the `Backbone` type to store the coordinates of N, Ca, and C atoms. +The `Backbone` type is a wrapper for a 3xN matrix of coordinates representing absolute positions of atoms of a continuous molecular backbone. For working with the geometry of a backbone, the `ChainedBonds` type exists to store bond lengths, bond angles, and dihedral angles of a continuous chain of bonds. -The secondary structures of a chain are 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. - -Proteins can be loaded from a PDB file using the `readpdb` function, which returns a `Vector{Chain}` instance. Inversely, a `Vector{Chain}` instance can be written to a PDB file using the `writepdb` function. +Proteins can be loaded from a PDB file using the `readpdb` function, which returns a `Vector{Protein.Chain}`. Inversely, a `Vector{Protein.Chain}` instance can be written to a PDB file using the `writepdb` function. ## Example @@ -52,4 +50,4 @@ julia> chain.backbone 21.808 22.263 21.085 13.861 13.862 14.233 2.734 1.355 0.446 -``` \ No newline at end of file +```