.gitignore
CHANGELOG.md
CITATION.cff
LICENSE
README.md
THIRD_PARTY_NOTICES.md
cliff.toml
mkdocs.yml
pyproject.toml
uv.lock
.github/workflows/docs.yml
.github/workflows/publish.yaml
.github/workflows/test.yml
docs/api.md
docs/index.md
docs/limitations.md
docs/visualization.md
docs/assets/banner.png
docs/assets/logo.png
examples/01_dna_thermodynamics.py
examples/02_hairpin_folding.py
examples/03_tmsd_kinetics.py
examples/04_sequence_design.py
examples/05_leakage_and_screening.py
examples/06_parameter_sweep.py
examples/07_cha_to_mantis.py
examples/08_tube_analysis.py
examples/09_dynamical_design.py
examples/10_domain_enumeration.py
examples/11_gradient_design.py
examples/11_quadruplex_aptamer.py
examples/12_shot_noise_lod.py
examples/13_complex_and_cascade.py
examples/14_gallery_hairpin.py
examples/15_gallery_multiloop.py
examples/16_gallery_toehold.py
examples/17_gallery_captured.py
examples/18_gallery_bulge.py
examples/19_gallery_fourway.py
examples/20_gallery_fiveway.py
examples/21_gallery_dendrimer.py
examples/cha_cascade.png
examples/cha_pipeline.png
examples/complex_and_cascade.png
examples/dynamical_design.png
examples/gallery_14_hairpin.png
examples/gallery_15_multiloop.png
examples/gallery_16_toehold.png
examples/gallery_17_captured.png
examples/gallery_18_bulge.png
examples/gallery_19_fourway.png
examples/gallery_20_complex_fiveway.png
examples/gallery_21_dendrimer_network.png
examples/h1h2cp_complex.png
examples/hairpin_folding.png
examples/hairpin_structure2d.png
examples/leakage_screening.png
examples/parameter_sweep.png
examples/sequence_design.png
examples/tmsd_kinetics.png
scripts/bench_accuracy.py
scripts/bench_design.py
scripts/bench_mfe.py
scripts/bench_vs_nupack.py
scripts/bench_vs_primer3.py
scripts/download_datasets.py
scripts/export_paramset.py
scripts/generate_dna_enthalpy_tables.py
scripts/generate_dna_stack_tables.py
scripts/generate_rna_enthalpy_tables.py
scripts/release.sh
scripts/validate_loop_decomposition.py
strider/__init__.py
strider/cli.py
strider/dsd.py
strider/equilibrium.py
strider/tube.py
strider/benchmarks/__init__.py
strider/benchmarks/accuracy.py
strider/benchmarks/runners.py
strider/benchmarks/structure_refs.py
strider/bridge/__init__.py
strider/bridge/mantis_bridge.py
strider/circuits/__init__.py
strider/circuits/base.py
strider/circuits/cha.py
strider/circuits/cha_architecture.py
strider/circuits/checks.py
strider/circuits/hcr.py
strider/circuits/seesaw.py
strider/circuits/translator.py
strider/design/__init__.py
strider/design/assay.py
strider/design/benchmarks.py
strider/design/constraints.py
strider/design/decomposition.py
strider/design/diff_designer.py
strider/design/mutation.py
strider/design/objective.py
strider/design/optimizer.py
strider/design/policies.py
strider/design/rerank.py
strider/export/__init__.py
strider/export/formats.py
strider/kinetics/__init__.py
strider/kinetics/arrhenius.py
strider/kinetics/enumerator.py
strider/kinetics/leakage.py
strider/kinetics/tmsd.py
strider/screen/__init__.py
strider/screen/offtarget.py
strider/structure/__init__.py
strider/structure/cotranscriptional.py
strider/structure/dot_bracket.py
strider/structure/mfe.py
strider/structure/mountain.py
strider/structure/pseudoknot.py
strider/structure/quadruplex.py
strider/structure/sampling.py
strider/surface/__init__.py
strider/surface/labels.py
strider/surface/stochastic.py
strider/surface/thermo.py
strider/surface/transducer.py
strider/sweep/__init__.py
strider/sweep/batch.py
strider/sweep/cache.py
strider/thermo/__init__.py
strider/thermo/_dna_enthalpy_generated.py
strider/thermo/_param_context.py
strider/thermo/_rna_enthalpy_generated.py
strider/thermo/diff_design.py
strider/thermo/differentiable.py
strider/thermo/dimer_thermo.py
strider/thermo/engine.py
strider/thermo/ensemble.py
strider/thermo/hairpin.py
strider/thermo/modified.py
strider/thermo/nn_dna.py
strider/thermo/nn_dna_rna.py
strider/thermo/nn_rna.py
strider/thermo/parameters.py
strider/thermo/parameters_dna.py
strider/thermo/parameters_native.py
strider/thermo/parameters_rna.py
strider/thermo/salt.py
strider/thermo/structure_thermo.py
strider/thermo/temperature.py
strider/thermo/train.py
strider/thermo/vienna_backend.py
strider/thermo/parameters/dna-low-salt-50mM-Na.json
strider/viz/__init__.py
strider/viz/annotate.py
strider/viz/arc.py
strider/viz/circuit_diagram.py
strider/viz/geometry.py
strider/viz/layout.py
strider/viz/mountain_plot.py
strider/viz/reaction.py
strider/viz/structure2d.py
strider/viz/style.py
strider_dna.egg-info/PKG-INFO
strider_dna.egg-info/SOURCES.txt
strider_dna.egg-info/dependency_links.txt
strider_dna.egg-info/entry_points.txt
strider_dna.egg-info/requires.txt
strider_dna.egg-info/top_level.txt
tests/conftest.py
tests/test_assay.py
tests/test_benchmarks.py
tests/test_bridge.py
tests/test_circuits.py
tests/test_cli.py
tests/test_cotranscriptional.py
tests/test_design.py
tests/test_design_convergence.py
tests/test_design_dynamical.py
tests/test_design_rerank.py
tests/test_diff_design.py
tests/test_differentiable.py
tests/test_dimer_thermo.py
tests/test_dsd.py
tests/test_enumerator.py
tests/test_equilibrium.py
tests/test_formats.py
tests/test_hairpin_tm.py
tests/test_leakage.py
tests/test_mfe.py
tests/test_mfe_dimers.py
tests/test_pair_probs.py
tests/test_parameter_sets.py
tests/test_quadruplex.py
tests/test_salt_temperature.py
tests/test_sampling.py
tests/test_screener.py
tests/test_stochastic_surface.py
tests/test_structure_thermo.py
tests/test_surface.py
tests/test_thermo_dna.py
tests/test_tmsd.py
tests/test_tube.py
tests/test_viz_artists.py
tests/test_viz_baseline.py
tests/test_viz_cli.py
tests/test_viz_geometry.py
tests/test_viz_layout.py
tests/test_viz_reaction.py
tests/baseline/test_duplex_complex_baseline.png
tests/baseline/test_hairpin_structure_baseline.png