graphein
Protein Graph Library
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Download Latest Version (.zip)- devcontainer.json
- docker-compose.yml
- bug_report.md
- feature_request.md
- autopublish.yaml
- build.yaml
- changelog.yaml
- code-style.yaml
- code-tests-docker.yaml
- minimal__install.yaml
- dependabot.yml
- FUNDING.yml
- PULL_REQUEST_TEMPLATE.md
- base.in
- dev.in
- docs.in
- extras.in
- torch_cpu.in
- torch_gpu.in
- download_pcddb.py
- all_dset_list.pkl
- deepPISP.py
- deepppisp_clean.csv
- dset164_dssp_data.pkl
- dset164_label.pkl
- dset164_pssm_data.pkl
- dset164_sequence_data.pkl
- dset186_dssp_data.pkl
- dset186_label.pkl
- dset186_pssm_data.pkl
- dset186_sequence_data.pkl
- dset72_dssp_data.pkl
- dset72_label.pkl
- dset72_pssm_data.pkl
- dset72_sequence_data.pkl
- ppisp_example.ipynb
- testing_list.pkl
- training_list.pkl
- BME.csv
- EDO.csv
- HEM.csv
- NAG.csv
- parse_dataset.ipynb
- PLP.csv
- PO4.csv
- PROTEINS_LIGANDS.csv
- SO4.csv
- CA.csv
- CO.csv
- FE.csv
- MG.csv
- MN.csv
- NI.csv
- parse_dataset.ipynb
- PROTEINS_METAL.csv
- ZN.csv
- dna.csv
- parse_dataset.ipynb
- PROTEINS_NUCLEIC.csv
- rna.csv
- ADP.csv
- ATP.csv
- FAD.csv
- FMN.csv
- GDP.csv
- GTP.csv
- NAD.csv
- parse_dataset.ipynb
- PROTEINS_NUCLEOTIDES.csv
- UDP.csv
- example_model_nb.ipynb
- make_rearrangement_data.py
- process_data.ipynb
- structural_rearrangement_data.csv
- structural_rearrangement_data.feather
- README.md
- graphein.png
- CODE_OF_CONDUCT.md
- code_of_conduct.rst
- contributing.md
- contributing.rst
- CONTRIBUTORS.md
- contributors.rst
- ppisp.rst
- pscdb.rst
- installation.rst
- introduction.rst
- usage.rst
- graphein.grn.rst
- graphein.ml.rst
- graphein.molecule.rst
- graphein.ppi.rst
- graphein.protein.rst
- graphein.protein.tensor.rst
- graphein.rna.rst
- graphein.utils.rst
- 3eiy.cif
- alphafold_protein_graph_tutorial.nblink
- atom_graph_tutorial.nblink
- creating_datasets_from_the_pdb.nblink
- dataloader_tutorial.nblink
- datasets_and_dataloaders.nblink
- foldcomp.nblink
- grn_tutorial.nblink
- higher_order_graphs.nblink
- interactive_plotly_example.nblink
- molecule_model_tutorial_tox.nblink
- molecule_tutorial.nblink
- molecules_from_zinc_and_chembl.nblink
- ppi_tutorial.nblink
- protein_graph_analytics.nblink
- protein_mesh_tutorial.nblink
- protein_tensors.nblink
- pscdb_baselines.nblink
- pscdb_processing.nblink
- residue_graphs.nblink
- rna_graph_tutorial.nblink
- splitting_a_dataset.nblink
- subgraphing_tutorial.nblink
- tdc_developability.nblink
- conf.py
- dataset_readme.rst
- datasets.rst
- grn_notebooks.rst
- index.rst
- license.rst
- ml_examples.rst
- ml_protein_tensors.rst
- molecule_notebooks.rst
- ppi_notebooks.rst
- problematic_pdbs.rst
- protein_notebooks.rst
- readme.rst
- rna_notebooks.rst
- make.bat
- Makefile
- 3eiy_contacts.tsv
- 4hhb_contacts.tsv
- 3eiy.pdb
- 4hhb.pdb
- __init__.py
- node_features.py
- __init__.py
- config.py
- edges.py
- graphs.py
- parse_regnetwork.py
- parse_trrust.py
- __init__.py
- foldcomp_dataset.py
- pdb_data.py
- torch_geometric_dataset.py
- __init__.py
- gdt.py
- tm_score.py
- __init__.py
- clustering.py
- conversion.py
- diffusion.py
- utils.py
- visualisation.py
- __init__.py
- atomic.py
- distance.py
- __init__.py
- bonds.py
- __init__.py
- molecule.py
- __init__.py
- atom_type.py
- __init__.py
- __init__.py
- atoms.py
- chembl.py
- config.py
- graphs.py
- utils.py
- visualisation.py
- zinc.py
- __init__.py
- node_features.py
- __init__.py
- config.py
- edges.py
- graph_metadata.py
- graphs.py
- parse_biogrid.py
- parse_stringdb.py
- visualisation.py
- __init__.py
- atomic.py
- distance.py
- intramolecular.py
- __init__.py
- __init__.py
- dynamics.py
- structure.py
- __init__.py
- aaindex.py
- amino_acid.py
- amino_acid_properties.csv
- dssp.py
- geometry.py
- meiler_embeddings.csv
- __init__.py
- swissprot-reviewed-protvec.model
- __init__.py
- embeddings.py
- propy.py
- sequence.py
- utils.py
- __init__.py
- utils.py
- __init__.py
- angles.py
- data.py
- dataloader.py
- dataset.py
- edges.py
- geometry.py
- io.py
- plot.py
- pnerf.py
- reconstruction.py
- representation.py
- sequence.py
- testing.py
- types.py
- __init__.py
- analysis.py
- config.py
- folding_utils.py
- graphs.py
- meshes.py
- resi_atoms.py
- subgraphs.py
- utils.py
- visualisation.py
- __init__.py
- atomic.py
- base_pairing.py
- distance.py
- __init__.py
- atom.py
- __init__.py
- config.py
- constants.py
- graphs.py
- nussinov.py
- subgraphs.py
- utils.py
- visualisation.py
- __init__.py
- utils.py
- __init__.py
- compat.py
- core.py
- IPYMOL_LICENSE
- __init__.py
- config.py
- config_parser.py
- dependencies.py
- utils.py
- __init__.py
- cli.py
- graph_construction_overview.png
- graphein.png
- graphein_dark.png
- alphafold_protein_graph_tutorial.ipynb
- atom_graph_tutorial.ipynb
- baseline.ipynb
- creating_datasets_from_the_pdb.ipynb
- dataloader_tutorial.ipynb
- datasets_and_dataloaders.ipynb
- foldcomp.ipynb
- grn_tutorial.ipynb
- higher_order_graphs.ipynb
- interactive_plotly_example.ipynb
- molecule_model_tutorial_tox.ipynb
- molecule_tutorial.ipynb
- molecule_utils.ipynb
- molecules_from_zinc_and_chembl.ipynb
- ppi_graph.ipynb
- protein_graph_analytics.ipynb
- protein_mesh_tutorial.ipynb
- protein_tensors.ipynb
- residue_graphs.ipynb
- rna_graph_tutorial.ipynb
- splitting_a_dataset.ipynb
- subgraphing_tutorial.ipynb
- tdc_developability.ipynb
- code_format.sh
- download_expasy_protein_scales.py
- __init__.py
- pdb_data.py
- __init__.py
- test_graphs.py
- __init__.py
- test_conversion.py
- test_torch_geometric_dataset.py
- long_test.mol2
- long_test.pdb
- long_test.sdf
- short_test.mol2
- short_test.pdb
- short_test.sdf
- short_test.smi
- test_graphs.py
- test_rdkit_utils.py
- test_zinc.py
- __init__.py
- test_graphs.py
- __init__.py
- test_distance.py
- __init__.py
- test_amino_acid.py
- test_dssp.py
- test_geometry.py
- __init__.py
- __init__.py
- test_angles.py
- test_data.py
- test_geometry.py
- test_io.py
- test_reconstruction.py
- test_representation.py
- test_sequence.py
- 1lds.pdb
- 4hhb.cif
- 4hhb.pdb
- alphafold_structure.pdb
- input_pdb_cryst1.pdb
- P04629.pdb
- __init__.py
- test_graphs.py
- test_subgraphs.py
- test_utils.py
- 2jyf.pdb
- __init__.py
- test_graphs.py
- test_nussinov.py
- test_subgraphs.py
- __init__.py
- utils.py
- __init__.py
- test_cli.py
- test_protein_graph_config.yml
- test_yml_parser.py
- __init__.py
- conftest.py
- test_graphein.py
- .gitattributes
- .gitignore
- .pre-commit-config.yaml
- CHANGELOG.md
- citation.bib
- docker-compose.cpu.yml
- docker-compose.yml
- Dockerfile
- environment-dev.yml
- environment.yml
- LICENSE
- Makefile
- MANIFEST.in
- pyproject.toml
- README.md
- setup.py
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