├── .gitignore ├── LICENSE ├── README.md ├── accelerator_single_machine.json ├── assets ├── Intellifold-Model-Arc.png ├── intellifold-cover.png ├── intellifold-server-screenshot.png └── intellifold_metrics.png ├── docs ├── input_yaml_format.md ├── installation.md ├── kernels.md └── usage.md ├── environment.yaml ├── examples ├── 5S8I_A.yaml ├── 7WCF_A.yaml ├── 7yds.yaml ├── examples_wo_msa │ └── example_without_msa.yaml └── msas │ ├── 5s8i_A.a3m │ ├── 7wcf_A.a3m │ ├── 7yds_0.csv │ ├── 7yds_1.csv │ └── 7yds_2.csv ├── intellifold ├── __init__.py ├── data │ ├── __init__.py │ ├── augmentation │ │ ├── __init__.py │ │ └── utils.py │ ├── const.py │ ├── crop │ │ ├── __init__.py │ │ ├── boltz.py │ │ └── cropper.py │ ├── feature │ │ ├── __init__.py │ │ ├── featurizer.py │ │ ├── pad.py │ │ └── symmetry.py │ ├── filter │ │ ├── __init__.py │ │ ├── dynamic │ │ │ ├── __init__.py │ │ │ ├── date.py │ │ │ ├── filter.py │ │ │ ├── max_residues.py │ │ │ ├── resolution.py │ │ │ ├── size.py │ │ │ └── subset.py │ │ └── static │ │ │ ├── __init__.py │ │ │ ├── filter.py │ │ │ ├── ligand.py │ │ │ └── polymer.py │ ├── inference │ │ ├── __init__.py │ │ ├── data_tools.py │ │ ├── params.py │ │ └── utils.py │ ├── module │ │ ├── __init__.py │ │ ├── inference.py │ │ └── training.py │ ├── msa │ │ ├── __init__.py │ │ └── mmseqs2.py │ ├── parse │ │ ├── __init__.py │ │ ├── a3m.py │ │ ├── csv.py │ │ ├── fasta.py │ │ ├── schema.py │ │ └── yaml.py │ ├── sample │ │ ├── __init__.py │ │ ├── cluster.py │ │ ├── distillation.py │ │ ├── random.py │ │ └── sampler.py │ ├── tokenize │ │ ├── __init__.py │ │ ├── boltz.py │ │ └── tokenizer.py │ ├── types.py │ └── write │ │ ├── __init__.py │ │ ├── mmcif.py │ │ ├── pdb.py │ │ ├── utils.py │ │ └── writer.py └── openfold │ ├── __init__.py │ ├── config.py │ ├── inference_config.py │ ├── model │ ├── __init__.py │ ├── backbone.py │ ├── confidences.py │ ├── diffusion.py │ ├── dropout.py │ ├── embedders.py │ ├── heads.py │ ├── model.py │ ├── outer_product_mean.py │ ├── pairformer.py │ ├── primitives.py │ ├── triangular_attention.py │ └── triangular_multiplicative_update.py │ └── utils │ ├── __init__.py │ ├── atom_token_conversion.py │ ├── chunk_utils.py │ ├── kernel │ ├── __init__.py │ └── traceable_evoformer_attn.py │ ├── layer_norm │ ├── __init__.py │ ├── kernel │ │ ├── compat.h │ │ ├── layer_norm_cuda.cpp │ │ ├── layer_norm_cuda_kernel.cu │ │ └── type_shim.h │ ├── layer_norm.py │ └── torch_ext_compile.py │ ├── precision_utils.py │ └── tensor_utils.py ├── predict.sh ├── pypi └── intellifold-0.1.0-py3-none-any.whl ├── run_intellifold.py ├── runner ├── __init__.py └── intellifold_inference.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IntelliGen-AI/IntelliFold/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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