LICENSE
README.md
pyproject.toml
proto_language/__init__.py
proto_language/__main__.py
proto_language/cli.py
proto_language/py.typed
proto_language.egg-info/PKG-INFO
proto_language.egg-info/SOURCES.txt
proto_language.egg-info/dependency_links.txt
proto_language.egg-info/entry_points.txt
proto_language.egg-info/requires.txt
proto_language.egg-info/top_level.txt
proto_language/constraint/__init__.py
proto_language/constraint/constraint_registry.py
proto_language/constraint/protein_quality/__init__.py
proto_language/constraint/protein_quality/balanced_aa_constraint.py
proto_language/constraint/protein_quality/overall_protein_quality_constraint.py
proto_language/constraint/protein_quality/protein_complexity_constraint.py
proto_language/constraint/protein_quality/protein_diversity_constraint.py
proto_language/constraint/protein_quality/protein_domain_constraint.py
proto_language/constraint/protein_quality/protein_length_constraint.py
proto_language/constraint/protein_quality/protein_max_identity_constraint.py
proto_language/constraint/protein_quality/protein_nearest_neighbor_gap_gini_constraint.py
proto_language/constraint/protein_quality/protein_profile_hmm_constraint.py
proto_language/constraint/protein_quality/protein_repetitiveness_constraint.py
proto_language/constraint/protein_structure/__init__.py
proto_language/constraint/protein_structure/af3_chain_pair_prot_dna_iptm_constraint.py
proto_language/constraint/protein_structure/af3_offtarget_iptm_specificity_constraint.py
proto_language/constraint/protein_structure/boltz_binding_strength_constraint.py
proto_language/constraint/protein_structure/consensus_specificity_constraint.py
proto_language/constraint/protein_structure/dbp_design_metrics_constraint.py
proto_language/constraint/protein_structure/dna_base_contact_quality_constraint.py
proto_language/constraint/protein_structure/dna_binding_structure_helper.py
proto_language/constraint/protein_structure/dna_motif_contact_constraint.py
proto_language/constraint/protein_structure/dna_motif_specificity_constraint.py
proto_language/constraint/protein_structure/dna_phosphate_contact_constraint.py
proto_language/constraint/protein_structure/gyration_radius_constraint.py
proto_language/constraint/protein_structure/ipsae_constraint.py
proto_language/constraint/protein_structure/protein_globularity_constraint.py
proto_language/constraint/protein_structure/protein_symmetry_ring_constraint.py
proto_language/constraint/protein_structure/pyrosetta_interface_constraint.py
proto_language/constraint/protein_structure/structure_confidence_constraint.py
proto_language/constraint/protein_structure/structure_constraint_config.py
proto_language/constraint/protein_structure/structure_ensemble_similarity_constraint.py
proto_language/constraint/protein_structure/structure_geometry_constraint.py
proto_language/constraint/protein_structure/structure_similarity_constraint.py
proto_language/constraint/rna_secondary_structure/__init__.py
proto_language/constraint/rna_secondary_structure/structure_similarity_constraint.py
proto_language/constraint/rna_splicing/__init__.py
proto_language/constraint/rna_splicing/alphagenome_splice_junction.py
proto_language/constraint/rna_splicing/alphagenome_splice_site_usage.py
proto_language/constraint/rna_splicing/splice_transformer_intron_boundary.py
proto_language/constraint/rna_splicing/splice_transformer_specificity.py
proto_language/constraint/rna_splicing/splice_transformer_target.py
proto_language/constraint/sequence_alignment/__init__.py
proto_language/constraint/sequence_alignment/gap_gini_constraint.py
proto_language/constraint/sequence_annotation/__init__.py
proto_language/constraint/sequence_annotation/alphagenome_interval_track_constraint.py
proto_language/constraint/sequence_annotation/borzoi_chromatin_accessibility_morse_constraint.py
proto_language/constraint/sequence_annotation/borzoi_track_activity_constraint.py
proto_language/constraint/sequence_annotation/chromatin_accessibility_morse_utils.py
proto_language/constraint/sequence_annotation/crispr_array_constraint.py
proto_language/constraint/sequence_annotation/enformer_chromatin_accessibility_morse_constraint.py
proto_language/constraint/sequence_annotation/malinois_activity_constraint.py
proto_language/constraint/sequence_annotation/mirna_specificity_constraint.py
proto_language/constraint/sequence_annotation/mmseqs_similarity_constraint.py
proto_language/constraint/sequence_annotation/operator_site_constraint.py
proto_language/constraint/sequence_annotation/orf_length_constraint.py
proto_language/constraint/sequence_annotation/promoter_strength_constraint.py
proto_language/constraint/sequence_annotation/puffin_promoter_activity_constraint.py
proto_language/constraint/sequence_annotation/seq_motif_constraint.py
proto_language/constraint/sequence_annotation/sigma70_promoter_constraint.py
proto_language/constraint/sequence_annotation/targetscan_site_constraint.py
proto_language/constraint/sequence_annotation/tracr_rna_constraint.py
proto_language/constraint/sequence_composition/__init__.py
proto_language/constraint/sequence_composition/dinucleotide_composition_constraint.py
proto_language/constraint/sequence_composition/gc_content_constraint.py
proto_language/constraint/sequence_composition/kmer_frequency_constraint.py
proto_language/constraint/sequence_composition/max_homopolymer_constraint.py
proto_language/constraint/sequence_composition/sequence_length_constraint.py
proto_language/constraint/sequence_composition/specific_kmer_constraint.py
proto_language/constraint/sequence_scoring/__init__.py
proto_language/constraint/sequence_scoring/ablang_perplexity_constraint.py
proto_language/constraint/sequence_scoring/esm2_perplexity_constraint.py
proto_language/constraint/sequence_scoring/mpnn_perplexity_constraint.py
proto_language/core/__init__.py
proto_language/core/constraint.py
proto_language/core/construct.py
proto_language/core/generator.py
proto_language/core/optimizer.py
proto_language/core/program.py
proto_language/core/segment.py
proto_language/core/sequence.py
proto_language/generator/__init__.py
proto_language/generator/esm2_generator.py
proto_language/generator/esm3_generator.py
proto_language/generator/evo1_generator.py
proto_language/generator/evo2_generator.py
proto_language/generator/freebindcraft_generator.py
proto_language/generator/generator_registry.py
proto_language/generator/ligandmpnn_generator.py
proto_language/generator/msa_generator.py
proto_language/generator/position_weight_generator.py
proto_language/generator/progen2_generator.py
proto_language/generator/proteinmpnn_generator.py
proto_language/generator/random_nucleotide_generator.py
proto_language/generator/random_protein_generator.py
proto_language/generator/rfdiffusion_mpnn_binder_generator.py
proto_language/generator/semigreedy_mutation_generator.py
proto_language/optimizer/__init__.py
proto_language/optimizer/beam_search_optimizer.py
proto_language/optimizer/cycling_optimizer.py
proto_language/optimizer/gradient_optimizer.py
proto_language/optimizer/mcmc_optimizer.py
proto_language/optimizer/optimizer_registry.py
proto_language/optimizer/rejection_sampling_optimizer.py
proto_language/optimizer/constraint_compiler/__init__.py
proto_language/optimizer/constraint_compiler/alphafold2_binder_provider.py
proto_language/optimizer/constraint_compiler/base.py
proto_language/optimizer/constraint_compiler/compiler.py
proto_language/optimizer/constraint_compiler/esmfold_provider.py
proto_language/optimizer/constraint_compiler/malinois_provider.py
proto_language/optimizer/constraint_compiler/protenix_provider.py
proto_language/utils/__init__.py
proto_language/utils/alphafold2_binder.py
proto_language/utils/base.py
proto_language/utils/docs_api.py
proto_language/utils/field_docs.py
proto_language/utils/gradients.py
proto_language/utils/io.py
proto_language/utils/logging_config.py
proto_language/utils/ml_optimizers.py
proto_language/utils/orf_selection.py
proto_language/utils/scheduling.py
proto_language/utils/scoring.py
proto_language/utils/sequence_matrices.py
proto_language/utils/serialization.py
proto_language/utils/spinner.py
tests/test_codebase_consistency.py
tests/test_docstring_consistency.py
tests/test_schema_metadata.py