{"repo":"a-r-j/graphein","free":true,"listed":false,"github":"https://github.com/a-r-j/graphein","clone":"git clone https://github.com/a-r-j/graphein.git","description":"Protein Graph Library","language":"Jupyter Notebook","stars":1189,"topics":["bioinformatics","computational-biology","deep-learning","dgl","drug-discovery","gene-regulatory-networks","geometric-deep-learning","graph-neural-networks","interactome","interactomics","ppi-networks","protein","protein-data-bank","protein-design","protein-structure","python","pytorch","pytorch-geometric","rna","structural-biology"],"license":"MIT","category":"bioinformatics_tool","readme_excerpt":"[](https://mybinder.org/v2/gh/a-r-j/graphein-binder/master?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252Fa-r-j%252Fgraphein%26urlpath%3Dlab%252Ftree%252Fgraphein%252Fnotebooks%26branch%3Dmaster)\n[](https://badge.fury.io/py/graphein)\n\n[](http://www.graphein.ai)\n[](https://doi.org/10.1101/2020.07.15.204701)\n[](https://www.repostatus.org/#active) [](https://www.repostatus.org/#active)\n[](https://www.codefactor.io/repository/github/a-r-j/graphein)\n[](https://sonarcloud.io/dashboard?id=a-r-j_graphein)\n[](https://sonarcloud.io/dashboard?id=a-r-j_graphein)\n[](https://sonarcloud.io/dashboard?id=a-r-j_graphein)\n[](https://sonarcloud.io/dashboard?id=a-r-j_graphein)\n[](https://gitter.im/graphein)\n[](https://opensource.org/licenses/MIT)\n![\"Code](\"https://img.shields.io/badge/code%20style-black-000000.svg\")
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\n\n[Documentation](http://www.graphein.ai) | [Paper](https://proceedings.neurips.cc/paper_files/paper/2022/hash/ade039c1db0391106a3375bd2feb310a-Abstract-Conference.html) | [Tutorials](http://graphein.ai/notebooks_index.html) | [Installation](#installation)\n\nProtein & Interactomic Graph Library\n\nThis package provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks. We provide compatibility with standard PyData formats, as well as graph objects designed for ease of use with popular deep learning libraries.\n\n## What's New?\n\n| | | |\n|---|---|---|\n| 1.7.0 | [FoldComp Datasets](http://graphein.ai/notebooks/foldcomp.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/foldcomp.ipynb) |\n| 1.7.0 | [Creating Datasets from the PDB](http://graphein.ai/notebooks/creating_datasets_from_the_pdb.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/creating_datasets_from_the_pdb.ipynb) |\n| 1.6.0 | [Protein Tensor Module](http://graphein.ai/notebooks/protein_tensors.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/protein_tensors.ipynb) |\n| 1.5.0 | [Protein Graph Creation from AlphaFold2!](http://graphein.ai/notebooks/alphafold_protein_graph_tutorial.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/residue_graphs.ipynb) |\n| 1.5.0 | [RNA Graph Construction from Dotbracket notation](http://graphein.ai/modules/graphein.rna.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/rna_graph_tutorial.ipynb) |\n| 1.4.0 | [Constructing molecular graphs](http://graphein.ai/notebooks/molecule_tutorial.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/molecule_tutorial.ipynb) |\n| 1.3.0 | [Ready-to-go Dataloaders for PyTorch Geometric](http://graphein.ai/notebooks/dataloader_tutorial.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/dataloader_tutorial.ipynb) |\n| 1.2.0 | [Extracting subgraphs from protein graphs](http://graphein.ai/notebooks/subgraphing_tutorial.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/subgraphing_tutorial.ipynb) |\n| 1.2.0 | [Protein Graph Analytics](http://graphein.ai/notebooks/protein_graph_analytics.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/protein_graph_analytics.ipynb) |\n| 1.2.0 | [Graphein CLI](http://graphein.ai/getting_started/usage.html) | |\n| 1.2.0 |[Protein Graph Visualisation!](http://graphein.ai/notebooks/interactive_plotly_example.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/interactive_plotly_example.ipynb)\n| 1.1.0 | [Protein - Protein Interaction Network Support & Structural Interactomics (Using AlphaFold2!)](http://graphein.ai/notebooks/ppi_tutorial.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/ppi_graph.ipynb) |\n| 1.0.0 | [High and Low-level API for massive flexibility - create your own bespoke workflows!](http://graphein.ai/notebooks/residue_graphs.html) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/residue_graphs.ipynb) |\n\n## Example usage\n\nGraphein provides both a programmatic API and a command-line interface for constructing graphs.\n\n### CLI\n\nGraphein configs can be specified as `.yaml` files to batch process graphs from the commandline.\n\n[Docs](http://graphein.ai/getting_started/usage.html)\n\n```bash\ngraphein -c config.yaml -p path/to/pdbs -o path/to/output\n```\n\n### Creating a Protein Graph\n\n| | | |\n|---|---|---|\n[Tutorial (Residue-level)](http://graphein.ai/notebooks/residue_graphs.html) | [Tutorial (Atomic)](http://graphein.ai/notebooks/atom_graph_tutorial.html) | [Docs](http://graphein.ai/modules/graphein.protein.html#module-graphein.protein.graphs)\n| [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/residue_graphs.ipynb) | [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/atom_graph_tutorial.ipynb) | |\n\n```python\nfrom graphein.protein.config import ProteinGraphConfig\nfrom graphein.protein.graphs import construct_graph\n\nconfig = ProteinGraphConfig()\ng = construct_graph(config=config, pdb_code=\"3eiy\")\n```\n\n### Creating a Protein Graph from the AlphaFold Protein Structure Database\n\n| | |\n|---|---|\n| [Tutorial](http://graphein.ai/notebooks/alphafold_protein_graph_tutorial.html) | [Docs](http://graphein.ai/modules/graphein.protein.html#module-graphein.protein.graphs) |\n| [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/alphafold_protein_graph_tutorial.ipynb)|\n\n```python\nfrom graphein.protein.config import ProteinGraphConfig\nfrom graphein.protein.graphs import construct_graph\nfrom graphein.protein.utils import download_alphafold_structure\n\nconfig = ProteinGraphConfig()\nfp = download_alphafold_structure(\"Q5VSL9\", aligned_score=False)\ng = construct_graph(config=config, path=fp)\n```\n\n### Creating a Protein Mesh\n\n| | |\n|---|---|\n| [Tutorial](http://graphein.ai/notebooks/protein_mesh_tutorial.html) | [Docs](http://graphein.ai/modules/graphein.protein.html#module-graphein.protein.meshes) |\n| [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/protein_mesh_tutorial.ipynb) | |\n\n```python\nfrom graphein.protein.config import ProteinMeshConfig\nfrom graphein.protein.meshes import create_mesh\n\nverts, faces, aux = create_mesh(pdb_code=\"3eiy\", config=config)\n```\n\n### Creating Molecular Graphs\n\nGraphein can create molecular graphs from smiles strings as well as `.sdf`, `.mol2`, and `.pdb` files\n\n| | |\n|---|---|\n| [Tutorial](http://graphein.ai/notebooks/molecule_tutorial.html) | [Docs](http://graphein.ai/modules/graphein.molecule.html) |\n| [](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/molecule_tutorial.ipynb) | |\n\n```python\nfrom graphein.molecule.config import MoleculeGraphConfig\nfrom graphein.molecule.graphs import construct_graph\n\ng = 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