pyproject.toml
src/README.md
src/thermax/__init__.py
src/thermax.egg-info/PKG-INFO
src/thermax.egg-info/SOURCES.txt
src/thermax.egg-info/dependency_links.txt
src/thermax.egg-info/entry_points.txt
src/thermax.egg-info/requires.txt
src/thermax.egg-info/top_level.txt
src/thermax/core/__init__.py
src/thermax/core/constants.py
src/thermax/core/dna/__init__.py
src/thermax/core/dna/energy.py
src/thermax/core/dna/macrostate.py
src/thermax/core/dna/observable.py
src/thermax/core/dna/tokenizer.py
src/thermax/core/peptide/__init__.py
src/thermax/core/peptide/atoms.py
src/thermax/core/peptide/fragments.py
src/thermax/core/peptide/rdkit_io.py
src/thermax/core/peptide/tokenizer.py
src/thermax/core/peptide/visualiser.py
src/thermax/data/__init__.py
src/thermax/data/ensemble.py
src/thermax/data/frame.py
src/thermax/data/graph.py
src/thermax/data/rate_matrix.py
src/thermax/data/sequence.py
src/thermax/data/tau.py
src/thermax/data/trajectory.py
src/thermax/data/truncated.py
src/thermax/data/observable/noe.py
src/thermax/data/observable/pampa.py
src/thermax/data/observable/tm.py
src/thermax/data/transform/__init__.py
src/thermax/data/transform/augment.py
src/thermax/data/transform/discretise.py
src/thermax/data/transform/octree.py
src/thermax/experiments/__init__.py
src/thermax/experiments/solve_vs_observation.py
src/thermax/figures/__init__.py
src/thermax/figures/block.py
src/thermax/figures/bondcount.py
src/thermax/figures/ensemble.py
src/thermax/figures/font.py
src/thermax/figures/langevin.py
src/thermax/figures/marginalcoords.py
src/thermax/figures/solve_vs_observation.py
src/thermax/figures/truncated.py
src/thermax/generate_sequence/10mer.jsonl
src/thermax/generate_sequence/2mer.jsonl
src/thermax/generate_sequence/3mer.jsonl
src/thermax/generate_sequence/4mer.jsonl
src/thermax/generate_sequence/5mer.jsonl
src/thermax/generate_sequence/6mer.jsonl
src/thermax/generate_sequence/7mer.jsonl
src/thermax/generate_sequence/8mer.jsonl
src/thermax/generate_sequence/9mer.jsonl
src/thermax/generate_sequence/__init__.py
src/thermax/generate_sequence/enumerate.py
src/thermax/generate_sequence/load.py
src/thermax/generate_sequence/paint.jsonl
src/thermax/generator/__init__.py
src/thermax/generator/ensemble.py
src/thermax/generator/snis.py
src/thermax/models/__init__.py
src/thermax/models/loss.py
src/thermax/models/optimiser.py
src/thermax/models/sample.py
src/thermax/models/train_arbg.py
src/thermax/models/trainer.py
src/thermax/models/arbg/__init__.py
src/thermax/models/arbg/arbg.py
src/thermax/models/arbg/carbg.py
src/thermax/models/arbg/ddbg.py
src/thermax/models/arbg/sarbg.py
src/thermax/models/backbones/__init__.py
src/thermax/models/backbones/bert.py
src/thermax/models/backbones/cgpt.py
src/thermax/models/backbones/gpt.py
src/thermax/models/backbones/xbert.py
src/thermax/models/backbones/xgpt.py
src/thermax/models/blocks/__init__.py
src/thermax/models/blocks/attention.py
src/thermax/models/blocks/layers.py
src/thermax/models/blocks/mlp.py
src/thermax/models/blocks/position.py
src/thermax/models/otbg/__init__.py
src/thermax/models/otbg/model.py
src/thermax/models/otbg/trainer.py
src/thermax/qc/__init__.py
src/thermax/qc/feature.py
src/thermax/qc/neff.py
src/thermax/qc/tica.py
src/thermax/rates/__init__.py
src/thermax/rates/arrhenius.py
src/thermax/rates/graph.py
src/thermax/rates/mfpt.py
src/thermax/rates/movetype.py
src/thermax/rates/thermo.py
src/thermax/seq/__init__.py
src/thermax/seq/cycle.py
src/thermax/seq/dna.py
src/thermax/seq_to_structure/__init__.py
src/thermax/seq_to_structure/boltz.py
src/thermax/seq_to_structure/cycle.py
src/thermax/seq_to_structure/dna.py
src/thermax/service/__init__.py
src/thermax/service/gillespie.py
src/thermax/service/langevin.py
src/thermax/simulator/__init__.py
src/thermax/simulator/gillespie.py
src/thermax/simulator/truncate.py
src/thermax/simulator/muellerbrown/__init__.py
src/thermax/simulator/muellerbrown/langevin.py
src/thermax/structure_to_sim/__init__.py
src/thermax/structure_to_sim/md.py
src/thermax/tokenizer/__init__.py
src/thermax/tokenizer/peptides.py
src/thermax/transform/__init__.py
src/thermax/transform/prune.py
src/thermax/utils/__init__.py
src/thermax/utils/config.py
src/thermax/utils/env.py
src/thermax/utils/git.py
src/thermax/utils/paths.py
src/thermax/utils/sequence_parser.py
src/thermax/utils/topology_io.py
tests/test_arbg.py
tests/test_arrhenius.py
tests/test_atoms.py
tests/test_augment.py
tests/test_discretise.py
tests/test_fragments.py
tests/test_gillespie_order.py
tests/test_kmer_coverage.py
tests/test_kon_koff.py
tests/test_macrostate.py
tests/test_multistrand_state.py
tests/test_otbg.py
tests/test_position.py
tests/test_profile_dataloader.py
tests/test_prune_trajectory.py
tests/test_rate_comparison.py
tests/test_rdkit_io.py
tests/test_sequence.py