https://github.com/murrellgroup/dlproteinformats.jl

Proteins, stored nice and flat.
https://github.com/murrellgroup/dlproteinformats.jl

Last synced: 4 months ago
JSON representation

Proteins, stored nice and flat.

• Host: GitHub
• URL: https://github.com/murrellgroup/dlproteinformats.jl
• Owner: MurrellGroup
• License: mit
• Created: 2025-04-26T19:26:26.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2025-08-14T08:46:13.000Z (10 months ago)
• Last Synced: 2025-08-14T10:28:01.576Z (10 months ago)
• Language: Julia
• Homepage:
• Size: 478 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# DLProteinFormats

[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://MurrellGroup.github.io/DLProteinFormats.jl/stable/)

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://MurrellGroup.github.io/DLProteinFormats.jl/dev/)

[![Build Status](https://github.com/MurrellGroup/DLProteinFormats.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/MurrellGroup/DLProteinFormats.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Coverage](https://codecov.io/gh/MurrellGroup/DLProteinFormats.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/MurrellGroup/DLProteinFormats.jl)

## Installation

```julia

using Pkg

pkg"registry add https://github.com/MurrellGroup/MurrellGroupRegistry"

pkg"add DLProteinFormats"

```

## Quickstart

```julia

using DLProteinFormats

data = DLProteinFormats.load(PDBSimpleFlat500);

flat_chains = data[1];

chains = DLProteinFormats.unflatten(

    flat_chains.locs,

    flat_chains.rots,

    flat_chains.AAs,

    flat_chains.chainids,

    flat_chains.resinds)

DLProteinFormats.writepdb("chains-1.pdb", chains) # view in e.g. chimerax or vscode protein viewer extension

```

## Flat atom PDB dataset

Flatom is a dataset that stores biomolecular structures in a minimal flat atom primitive format,

with each atom represented as a 28-byte NamedTuple with the following fields:

- `element::Int8`: element number

- `category::Int8`: structure category

  - 1: protein residue

  - 2: nucleic residue

  - 3: other (e.g. hetero)

- `chainid::Int16`: chain identifier

- `resnum::Int32`: residue number (can be optionally renumbered using the MMCIF file)

- `resname::StaticStrings.StaticString{3}`: 3-character alphanumeric residue name

- `atomname::StaticStrings.StaticString{4}`: 4-character alphanumeric atom name

- `coords::StaticArrays.SVector{3,Float32}`: 3D coordinates

```julia

using DLProteinFormats

# load 169k PDB structures at flat vectors of atoms (~500 million atoms total, 28 bytes per atom)

# once downloaded, takes ~6 seconds to load

structures = DLProteinFormats.load(PDBFlatom169K);

# atoms of the first structure

atoms = structures[1].atoms

# use the `stack(::Function, ...)` method to get a struct of array vibe

elements = stack(atom -> atom.element, atoms)

coords = stack(atom -> atom.coords, atoms)

# etc. etc.

# split by chain

chainids = map(a -> a.chainid, atoms)

chains = [atoms[findall(==(id), chainids)] for id in unique(chainids)]

using DLProteinFormats.Flatom

# write to PDB

write_to_pdb("chains-1.pdb", atoms)

# write to MMCIF

write_to_cif("chains-1.cif", atoms)

```