.gitignore
LICENSE
MANIFEST.in
README.md
environment.yml
pyproject.toml
setup_mood.ipynb
.github/workflows/publish.yml
.github/workflows/release.yml
.vscode/launch.json
.vscode/settings.json
configs/fad_retention_example.json
configs/mood-dev-minimal.yml
configs/mood-dev.yml
configs/mood-esmc.yml
configs/mood-esmfold2.lock.txt
configs/mood-esmfold2.yml
configs/runner.sh
configs/runner_preamble.sh
configs/test.json
configs/toy_example.json
configs/wcn_example.json
docs/METRICS.md
docs/STRUCTURE_GENERATION.md
docs/algorithm_flow.dio
docs/algorithm_flow.png
docs/algorithm_flow_simple.dio
docs/mutation_handler.dio
docs/new_relation.dio
docs/old_relation.dio
external/README.md
external/EpHod/.gitignore
external/EpHod/LICENSE
external/EpHod/README.rst
external/EpHod/env.yml
external/EpHod/ephod/__init__.py
external/EpHod/ephod/run.py
external/EpHod/ephod/data/ESM1v-SVR.pkl
external/EpHod/ephod/training/__init__.py
external/EpHod/ephod/training/nn_models.py
external/EpHod/ephod/training/train_ml_models.py
external/EpHod/ephod/training/train_nnmodels.py
external/EpHod/ephod/training/trainutils.py
external/EpHod/example/test_sequences.fasta
mood/__init__.py
mood/_version.py
mood/cli.py
mood/generate_version.py
mood/main.py
mood/multiObjectiveOptimization.py
mood/base/__init__.py
mood/base/aminoacids.py
mood/base/data.py
mood/base/log.py
mood/base/sequence.py
mood/base/silent_file.py
mood/base/state.py
mood/metrics/__init__.py
mood/metrics/alphabetic.py
mood/metrics/colabfold_Metrics.py
mood/metrics/ephod_Metrics.py
mood/metrics/esm2_Metrics.py
mood/metrics/esmc_Metrics.py
mood/metrics/esmfold_Metrics.py
mood/metrics/frustraR_Metrics.py
mood/metrics/hmmer_Metrics.py
mood/metrics/ligandmpnn_Metrics.py
mood/metrics/metric.py
mood/metrics/nmutations_Metrics.py
mood/metrics/potts_Metrics.py
mood/metrics/proteinMPNN_Metrics.py
mood/metrics/pyrosetta_Metrics.py
mood/metrics/toy_metrics.py
mood/metrics/utils.py
mood/metrics/wcn_Metrics.py
mood/metrics/ProteinMPNN/__init__.py
mood/metrics/ProteinMPNN/make_fixed_positions_dict.py
mood/metrics/ProteinMPNN/parse_multiple_chains.py
mood/metrics/ProteinMPNN/protein_mpnn_run.py
mood/metrics/ProteinMPNN/protein_mpnn_utils.py
mood/metrics/scripts/thread_rosetta_metrics.py
mood/optimizers/__init__.py
mood/optimizers/benchmarks.py
mood/optimizers/genetic_algorithm.py
mood/optimizers/holder.py
mood/optimizers/mutation_handler.py
mood/optimizers/optimizer.py
mood/optimizers/selection_strategies.py
mood/structures/__init__.py
mood/structures/colabfold.py
mood/structures/esmfold.py
mood/structures/esmfold2.py
mood/structures/predictor.py
mood/structures/rosetta.py
mood/utils/__init__.py
mood/utils/colabfold.py
mood/utils/device.py
mood/utils/esmfold.py
mood/utils/esmfold2.py
mood/utils/generate_pdbs.py
mood/utils/iteration.py
mood/utils/msfa.py
mood/utils/plotting.py
mood/utils/proteinmpnn_weights.py
mood/utils/structure_confidence.py
mood/utils/utils.py
mood/utils/utils_proteinMPNN.py
protein_mood.egg-info/PKG-INFO
protein_mood.egg-info/SOURCES.txt
protein_mood.egg-info/dependency_links.txt
protein_mood.egg-info/entry_points.txt
protein_mood.egg-info/requires.txt
protein_mood.egg-info/scm_file_list.json
protein_mood.egg-info/scm_version.json
protein_mood.egg-info/top_level.txt
recipe/meta.yaml
tests/eval_basic.ipynb
tests/eval_start.ipynb
tests/sequences_test_mutational_profile.pkl
tests/test_Felip9.py
tests/test_hmfo.py
tests/test_moo.py
tests/test_mood.py
tests/test_selection_strategies.py
tests/test_top7.py
tests/test_top7_cli.py
tests/test_upo.py
tests/test_zdt1_selection.py
tests/test_zdt23_selection.py
tests/base/sequence_test.py
tests/base/silent_test.py
tests/base/test_data.py
tests/metrics/conftest.py
tests/metrics/mn_fold_tests.sh
tests/metrics/mn_fold_tests_esmfold2.sh
tests/metrics/mn_pyrosetta.sh
tests/metrics/test_colabfold_metric.py
tests/metrics/test_colabfold_metric_fold.py
tests/metrics/test_esm2.py
tests/metrics/test_esmc.py
tests/metrics/test_esmfold2_fold.py
tests/metrics/test_esmfold_metric.py
tests/metrics/test_esmfold_metric_fold.py
tests/metrics/test_frustar.py
tests/metrics/test_hmmer.py
tests/metrics/test_ligandmpnn.py
tests/metrics/test_metric_contract.py
tests/metrics/test_potts.py
tests/metrics/test_proteinmpnn.py
tests/metrics/test_thread_rosetta_argparse.py
tests/optimizers/optimizers.py
tests/optimizers/test_crossover.py
tests/optimizers/test_ga.py
tests/runners/mn_smoke_esmfold2.sh
tests/runners/mn_smoke_esmfold_rosetta.sh
tests/runners/mn_smoke_rosetta_predictor.sh
tests/runners/mn_smoke_shared_predictor.sh
tests/runners/plot_iteration_front.py
tests/runners/run_proteinmpnn_rosetta_moo.py
tests/runners/run_toy_moo.py
tests/runners/run_toy_selection_only.py
tests/runners/run_zdt1.py
tests/runners/runner.sh
tests/runners/select_pareto_sequences.py
tests/runners/setUp_mood_Singmax_noRoss.py
tests/runners/setUp_smoke_esmfold2.py
tests/runners/setUp_smoke_esmfold_rosetta.py
tests/runners/setUp_smoke_rosetta_predictor.py
tests/runners/setUp_smoke_shared_predictor.py
tests/structures/test_esmfold2_predictor.py
tests/structures/test_predictor.py
tests/utils/test_general.py
tests/utils/test_iteration.py
tests/utils/test_renum_pdb.py