From 6e44416edecbfe3eef7efe223d1c7ee1eac148f0 Mon Sep 17 00:00:00 2001 From: Anton Oresten Date: Fri, 19 Jul 2024 15:03:03 +0200 Subject: [PATCH] Update README.md --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b794c16..e05408b 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ AssigningSecondaryStructure provides a way to assign loops, helices, and strands to protein backbones using a simplified version of the [DSSP](https://swift.cmbi.umcn.nl/gv/dssp/) algorithm. -Both the [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl) and [ProteinSecondaryStructures.jl](https://github.com/m3g/ProteinSecondaryStructures.jl) packages provide interfaces for more sophisticated secondary structure assignment, but they both call the [DSSP_jll.jl](https://docs.juliahub.com/General/DSSP_jll/stable/) binary under the hood, which requires writing structures to a file, leading to significant overhead. +Both the [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl) and [ProteinSecondaryStructures.jl](https://github.com/m3g/ProteinSecondaryStructures.jl) packages provide interfaces for more sophisticated secondary structure assignment, but they both call the [DSSP_jll.jl](https://docs.juliahub.com/General/DSSP_jll/stable/) binary under the hood, which requires writing structures to a file with significant overhead. ## Installation @@ -18,6 +18,8 @@ The package is registered in the General registry, and can be installed from the ```julia julia> using AssigningSecondaryStructure +julia> using Backboner # package with an extension that adds support for PDB files + julia> assign_secondary_structure("test/data/1ASS.pdb") # 1 chain 1-element Vector{Vector{Int64}}: [1, 1, 1, 3, 3, 3, 1, 1, 1, 1 … 3, 3, 3, 3, 3, 3, 3, 1, 1, 1] @@ -28,7 +30,7 @@ julia> assign_secondary_structure("test/data/1ZAK.pdb") # 2 chains [1, 1, 1, 1, 3, 3, 3, 3, 3, 3 … 2, 2, 2, 2, 2, 2, 2, 1, 1, 1] ``` -The `assign_secondary_structure` function can also take a vector of atom coordinate arrays of size (3, 3, L), in cases where the atom coordinates are already loaded. The first axis is for the x, y, and z coordinates, the second axis is for the atom types (N, CA, C), and the third axis is for the residues. +Without Backboner, `assign_secondary_structure` takes a vector of atom coordinate arrays of size (3, 3, L), in cases the atom coordinates are already loaded. The first axis is for the x, y, and z coordinates, the second axis is for the atom types (N, CA, C), and the third axis is for the residues. ## Acknowledgements