LICENSE
README.md
pyproject.toml
setup.py
benchmarks/__init__.py
benchmarks/benchmark_runner.py
benchmarks/mutation_benchmark.py
benchmarks/web_backend_test.py
docs/source/conf.py
examples/ligand_aware_folding_demo.py
examples/mutation_prediction_demo.py
examples/mutation_scanning_demo.py
experiments/test_templates_openfold.py
odinfold.egg-info/PKG-INFO
odinfold.egg-info/SOURCES.txt
odinfold.egg-info/dependency_links.txt
odinfold.egg-info/not-zip-safe
odinfold.egg-info/top_level.txt
openfold/__init__.py
openfold/config.py
openfold/benchmarks/comprehensive_benchmark.py
openfold/cuda_kernels/setup.py
openfold/model/__init__.py
openfold/model/cuda_kernels_interface.py
openfold/model/cuda_triangle_ops.py
openfold/model/delta_predictor.py
openfold/model/dropout.py
openfold/model/embedders.py
openfold/model/evoformer.py
openfold/model/heads.py
openfold/model/ligand_integration.py
openfold/model/model.py
openfold/model/msa.py
openfold/model/outer_product_mean.py
openfold/model/pair_transition.py
openfold/model/primitives.py
openfold/model/structure_module.py
openfold/model/template.py
openfold/model/torchscript.py
openfold/model/triangular_attention.py
openfold/model/triangular_multiplicative_update.py
openfold/np/__init__.py
openfold/np/protein.py
openfold/np/residue_constants.py
openfold/np/relax/__init__.py
openfold/np/relax/amber_minimize.py
openfold/np/relax/cleanup.py
openfold/np/relax/relax.py
openfold/np/relax/utils.py
openfold/services/mutation_with_refinement.py
openfold/services/optimized_mutation_server.py
openfold/services/websocket_server.py
openfold/training/delta_trainer.py
openfold/utils/__init__.py
openfold/utils/all_atom_multimer.py
openfold/utils/argparse_utils.py
openfold/utils/callbacks.py
openfold/utils/checkpointing.py
openfold/utils/chunk_utils.py
openfold/utils/exponential_moving_average.py
openfold/utils/feats.py
openfold/utils/gpu_memory_optimization.py
openfold/utils/import_weights.py
openfold/utils/logger.py
openfold/utils/loss.py
openfold/utils/lr_schedulers.py
openfold/utils/md_refinement.py
openfold/utils/mmseqs2_integration.py
openfold/utils/multi_chain_permutation.py
openfold/utils/precision_utils.py
openfold/utils/quantization.py
openfold/utils/rigid_utils.py
openfold/utils/script_utils.py
openfold/utils/superimposition.py
openfold/utils/tensor_utils.py
openfold/utils/trace_utils.py
openfold/utils/validation_metrics.py
openfold/utils/geometry/__init__.py
openfold/utils/geometry/quat_rigid.py
openfold/utils/geometry/rigid_matrix_vector.py
openfold/utils/geometry/rotation_matrix.py
openfold/utils/geometry/test_utils.py
openfold/utils/geometry/utils.py
openfold/utils/geometry/vector.py
openfold/utils/kernel/__init__.py
openfold/utils/kernel/attention_core.py
openfoldpp/setup.py
openfoldpp/test_migration.py
openfoldpp/confidence/__init__.py
openfoldpp/confidence/confidence_estimator.py
openfoldpp/confidence/early_exit.py
openfoldpp/confidence/tm_score_predictor.py
openfoldpp/docking/__init__.py
openfoldpp/docking/docking_utils.py
openfoldpp/docking/gnina_docking.py
openfoldpp/docking/pose_analysis.py
openfoldpp/docking/vina_docking.py
openfoldpp/ligand/__init__.py
openfoldpp/ligand/ligand_cross_attention.py
openfoldpp/ligand/ligand_encoder.py
openfoldpp/ligand/ligand_utils.py
openfoldpp/modules/flash_triangle_attention.py
openfoldpp/modules/fused_triangle_multiplication.py
openfoldpp/modules/ligand/__init__.py
openfoldpp/modules/ligand/ligand_attention.py
openfoldpp/modules/ligand/ligand_encoder.py
openfoldpp/modules/ligand/ligand_utils.py
openfoldpp/modules/mutation/__init__.py
openfoldpp/modules/mutation/ddg_predictor.py
openfoldpp/modules/mutation/mutation_scanner.py
openfoldpp/modules/mutation/stability_predictor.py
openfoldpp/modules/structure/fast_ipa.py
openfoldpp/multimer/__init__.py
openfoldpp/multimer/attention_utils.py
openfoldpp/multimer/chain_processing.py
openfoldpp/multimer/multimer_runner.py
openfoldpp/scripts/evaluation/casp_benchmark.py
openfoldpp/scripts/evaluation/confidence_benchmark.py
openfoldpp/scripts/evaluation/esm_3b_benchmark.py
openfoldpp/scripts/evaluation/evaluate_full_infrastructure.py
openfoldpp/scripts/evaluation/evaluate_realistic_predictions.py
openfoldpp/scripts/evaluation/evaluate_trained_openfold.py
openfoldpp/scripts/evaluation/evaluate_working_openfold.py
openfoldpp/scripts/evaluation/final_comprehensive_comparison.py
openfoldpp/scripts/evaluation/gpu_ci_benchmark.py
openfoldpp/scripts/evaluation/hard_target_benchmark.py
openfoldpp/scripts/evaluation/production_benchmark.py
openfoldpp/scripts/evaluation/relaxation_benchmark.py
openfoldpp/scripts/evaluation/simple_casp_benchmark.py
openfoldpp/scripts/evaluation/simple_sparse_benchmark.py
openfoldpp/scripts/evaluation/sparse_attention_benchmark.py
openfoldpp/scripts/legacy/add_metrics_simple.py
openfoldpp/scripts/legacy/add_structural_metrics.py
openfoldpp/scripts/legacy/benchmark_script.py
openfoldpp/scripts/legacy/calculate_metrics_final.py
openfoldpp/scripts/legacy/complete_openfold_pipeline.py
openfoldpp/scripts/legacy/comprehensive_comparison.py
openfoldpp/scripts/legacy/download_openfold_weights.py
openfoldpp/scripts/legacy/download_real_weights.py
openfoldpp/scripts/legacy/enhanced_benchmark_script.py
openfoldpp/scripts/legacy/fix_structural_metrics.py
openfoldpp/scripts/legacy/full_infrastructure_pipeline.py
openfoldpp/scripts/legacy/mock_openfold_server.py
openfoldpp/scripts/legacy/openfold_plus_plus_completion_report.py
openfoldpp/scripts/legacy/quick_metrics_fix.py
openfoldpp/scripts/legacy/quick_realistic_eval.py
openfoldpp/scripts/legacy/real_openfold_server.py
openfoldpp/scripts/legacy/run_casp_benchmark.py
openfoldpp/scripts/legacy/run_pretrained_openfold.py
openfoldpp/scripts/legacy/run_real_predictions.py
openfoldpp/scripts/legacy/setup.py
openfoldpp/scripts/legacy/start_openfold_server.py
openfoldpp/scripts/legacy/thread_sequence.py
openfoldpp/scripts/legacy/train_openfold.py
openfoldpp/scripts/legacy/trained_openfold_pipeline.py
openfoldpp/scripts/legacy/working_openfold_pipeline.py
openfoldpp/src/openfoldpp/__init__.py
openfoldpp/src/openfoldpp/models/__init__.py
openfoldpp/src/openfoldpp/modules/__init__.py
openfoldpp/src/openfoldpp/pipelines/__init__.py
openfoldpp/src/openfoldpp/pipelines/basic_pipeline.py
openfoldpp/src/openfoldpp/pipelines/complete_pipeline.py
openfoldpp/src/openfoldpp/pipelines/trained_pipeline.py
openfoldpp/src/openfoldpp/utils/__init__.py
openfoldpp/tests/benchmarks/ultimate_comprehensive_benchmark.py
openfoldpp/tests/integration/test_cuda_triangle_kernels.py
openfoldpp/tests/integration/test_delta_prediction.py
openfoldpp/tests/integration/test_enhanced_benchmark.py
openfoldpp/tests/integration/test_flash_attention_integration.py
openfoldpp/tests/integration/test_gpu_memory_optimization.py
openfoldpp/tests/integration/test_language_model_embeddings.py
openfoldpp/tests/integration/test_ligand_aware_folding.py
openfoldpp/tests/integration/test_ligand_parsing.py
openfoldpp/tests/integration/test_md_refinement.py
openfoldpp/tests/integration/test_mmseqs2_integration.py
openfoldpp/tests/integration/test_multimer_attention_contact_loss.py
openfoldpp/tests/integration/test_multimer_support.py
openfoldpp/tests/integration/test_mutation_refinement.py
openfoldpp/tests/integration/test_optimized_mutation_server.py
openfoldpp/tests/integration/test_pybind11_interface.py
openfoldpp/tests/integration/test_quantization_checkpointing.py
openfoldpp/tests/integration/test_websocket_server.py
runpod/execute_runpod_benchmark.py
runpod/runpod_benchmark_client.py
runpod/runpod_production_benchmark.py
runpod/runpod_server.py
runpod/runpod_setup.py
runpod/test_runpod_connection.py
scripts/__init__.py
scripts/alignment_data_to_fasta.py
scripts/build_deepspeed_config.py
scripts/convert_of_weights_to_jax.py
scripts/convert_v1_to_v2_weights.py
scripts/data_dir_to_fasta.py
scripts/deepspeed_inference_test.py
scripts/download_cameo.py
scripts/expand_alignment_duplicates.py
scripts/fasta_to_clusterfile.py
scripts/generate_alphafold_feature_dict.py
scripts/generate_chain_data_cache.py
scripts/generate_mmcif_cache.py
scripts/precompute_alignments.py
scripts/precompute_alignments_mmseqs.py
scripts/precompute_embeddings.py
scripts/prep_proteinnet_msas.py
scripts/unpack_proteinnet.py
scripts/utils.py
scripts/alignment_db_scripts/add_non_unique_to_alignment_db.py
scripts/alignment_db_scripts/create_alignment_db.py
scripts/alignment_db_scripts/create_alignment_db_sharded.py
scripts/alignment_db_scripts/unify_alignment_db_indices.py
scripts/docker/test_api.py
scripts/evaluation/casp_validation.py
scripts/evaluation/distillation_report.py
scripts/evaluation/gpu_ci_benchmark.py
scripts/evaluation/phase_d_benchmark.py
scripts/evaluation/quick_phase_b_benchmark.py
scripts/evaluation/quick_phase_d_benchmark.py
scripts/evaluation/run_phase_b_benchmark.py
scripts/evaluation/run_plm_benchmark.py
scripts/local/validate_optimizations.py
scripts/training/train_distill.py
src/openfoldpp/cli/confidence_command.py
src/openfoldpp/cli/relax_command.py
src/openfoldpp/configs/slim_evoformer_config.py
src/openfoldpp/losses/distillation_loss.py
src/openfoldpp/models/esm_3b_quantized.py
src/openfoldpp/models/esm_quantization.py
src/openfoldpp/models/esm_wrapper.py
src/openfoldpp/modules/confidence_head.py
src/openfoldpp/modules/diffusion_refiner.py
src/openfoldpp/modules/enhanced_plm_projection.py
src/openfoldpp/modules/lora_adapters.py
src/openfoldpp/modules/plm_projection.py
src/openfoldpp/modules/slim_evoformer.py
src/openfoldpp/modules/sparse_attention.py
src/openfoldpp/modules/sparse_evoformer.py
src/openfoldpp/pipelines/complete_pipeline.py
src/openfoldpp/relaxation/fast_relaxation.py
src/openfoldpp/training/hard_target_finetuning.py
src/openfoldpp/utils/quantization.py
src/openfoldpp/utils/teacher_transfer.py
tests/__init__.py
tests/compare_utils.py
tests/config.py
tests/data_utils.py
tests/test_confidence.py
tests/test_cpp_engine.py
tests/test_data_pipeline.py
tests/test_data_transforms.py
tests/test_deepspeed_evo_attention.py
tests/test_docking.py
tests/test_embedders.py
tests/test_evoformer.py
tests/test_fast_ipa.py
tests/test_feats.py
tests/test_flash_triangle_attention.py
tests/test_fused_triangle_multiplication.py
tests/test_import_weights.py
tests/test_kernels.py
tests/test_ligand.py
tests/test_ligand_aware_folding.py
tests/test_loss.py
tests/test_model.py
tests/test_msa.py
tests/test_multimer.py
tests/test_multimer_datamodule.py
tests/test_mutation_prediction.py
tests/test_mutation_scanning.py
tests/test_mutation_scanning_simple.py
tests/test_outer_product_mean.py
tests/test_pair_transition.py
tests/test_permutation.py
tests/test_primitives.py
tests/test_structure_module.py
tests/test_template.py
tests/test_triangular_attention.py
tests/test_triangular_multiplicative_update.py
tests/test_utils.py
tests/test_wasm_build.py
tests/benchmarks/test_plm_accuracy.py
wasm_build/serve_demo.py
wasm_build/scripts/quantize_for_wasm.py
web_backend/mutation_server.py