README.md
pyproject.toml
requirements.txt
requirements_pyvista.txt
crisscross/README.md
crisscross/__init__.py
crisscross/assembly_handle_optimization/__init__.py
crisscross/assembly_handle_optimization/hamming_compute.py
crisscross/assembly_handle_optimization/handle_evolution.py
crisscross/assembly_handle_optimization/handle_evolve_with_optuna.py
crisscross/assembly_handle_optimization/handle_mutation.py
crisscross/assembly_handle_optimization/random_hamming_optimizer.py
crisscross/assembly_handle_optimization/katzi_genetic_algorithm_prototyping/Katzi_Hamming.py
crisscross/assembly_handle_optimization/katzi_genetic_algorithm_prototyping/hamming_functions_multiprocessing.py
crisscross/assembly_handle_optimization/torch_dqn_prototyping/__init__.py
crisscross/assembly_handle_optimization/torch_dqn_prototyping/dqn_eval.py
crisscross/assembly_handle_optimization/torch_dqn_prototyping/dqn_optimization.py
crisscross/assembly_handle_optimization/torch_dqn_prototyping/dqn_optimization_v2.py
crisscross/assembly_handle_optimization/torch_dqn_prototyping/handle_array_dataloader.py
crisscross/assembly_handle_optimization/torch_dqn_prototyping/neural_optimization.py
crisscross/assembly_handle_optimization/torch_dqn_prototyping/scikit_tests.py
crisscross/assembly_handle_optimization/torch_dqn_prototyping/torch_hamming_compute.py
crisscross/cli_functions/__init__.py
crisscross/cli_functions/handle_evolution.py
crisscross/cli_functions/plate_resuspension.py
crisscross/core_functions/__init__.py
crisscross/core_functions/megastructure_composition.py
crisscross/core_functions/megastructures.py
crisscross/core_functions/plate_handling.py
crisscross/core_functions/slat_design.py
crisscross/core_functions/slats.py
crisscross/core_functions/stepwise_plots.py
crisscross/graphics/__init__.py
crisscross/graphics/blender_3d.py
crisscross/graphics/pyvista_3d.py
crisscross/graphics/static_plots.py
crisscross/helper_functions/__init__.py
crisscross/helper_functions/lab_helper_sheet_generation.py
crisscross/helper_functions/simple_plate_visuals.py
crisscross/helper_functions/slat_salient_quantities.py
crisscross/helper_functions/slurm_process_and_run.py
crisscross/helper_functions/standard_sequences.py
crisscross/plate_mapping/__init__.py
crisscross/plate_mapping/hash_cad_plates.py
crisscross/plate_mapping/plate_constants.py
crisscross/plate_mapping/non_standard_plates/__init__.py
crisscross/plate_mapping/non_standard_plates/cargo_plates.py
crisscross/plate_mapping/non_standard_plates/core_plates.py
crisscross/plate_mapping/non_standard_plates/crisscross_plates.py
crisscross/plate_mapping/non_standard_plates/hash_cad_plate_converter.py
crisscross/plate_mapping/non_standard_plates/hybrid_plates.py
crisscross/plate_mapping/non_standard_plates/old_cargo_plates.py
crisscross/plate_mapping/non_standard_plates/plate_concentrations.py
crisscross/plate_mapping/non_standard_plates/seed_plates.py
crisscross/scripts/3D_stacking/version_1_2024/3D_stairs_handle_evolution.py
crisscross/scripts/3D_stacking/version_1_2024/7_layer_viz.py
crisscross/scripts/3D_stacking/version_1_2024/design_setup_and_visualisation.py
crisscross/scripts/3D_stacking/version_2_march_2025/design_setup_and_echo_export.py
crisscross/scripts/3D_stacking/version_2_march_2025/echo_combining_script.py
crisscross/scripts/3D_stacking/version_2_march_2025/evolution_version_2.py
crisscross/scripts/3D_stacking/version_3_april_2025/evolution.py
crisscross/scripts/PAINT/hexagon_cargo_carpet_design_and_echo.py
crisscross/scripts/PAINT/singleslatPAINT.py
crisscross/scripts/PAINT/singleslatPAINT2.py
crisscross/scripts/PAINT/singleslatPAINT_combined.py
crisscross/scripts/SM01_hexagon_battleship_v1/square_example_script.py
crisscross/scripts/SM01_hexagon_battleship_v1/test.txt
crisscross/scripts/SW099_kineticsweep_script/kineticsweep_slathandleselection.py
crisscross/scripts/SW101_handleaggregation/ handleaggregation_echoprotocol.py
crisscross/scripts/SW102_finiteassembly_repeatingunits/SW102_echoprotocol.py
crisscross/scripts/SW102_finiteassembly_repeatingunits/SW102_handleselection.py
crisscross/scripts/SW102_finiteassembly_repeatingunits/combine_magnonics_and_repeating_unit.py
crisscross/scripts/SW105_psoralenslatduplex/psoralen6hbduplex_make_echo.py
crisscross/scripts/SW110_UFribourg_Design1-4xCNT_Design2/SW110_combine_echoprotocols.py
crisscross/scripts/SW110_UFribourg_Design1-4xCNT_Design2/SW110_echoprotocol.py
crisscross/scripts/SW111_largefiniteassembly_repeatingunits/20241030_testpartialareahamming.py
crisscross/scripts/SW111_largefiniteassembly_repeatingunits/SW111_combine_echoprotocols.py
crisscross/scripts/SW111_largefiniteassembly_repeatingunits/SW111_echoprotocol copy.py
crisscross/scripts/SW111_largefiniteassembly_repeatingunits/SW111_echoprotocol.py
crisscross/scripts/SW111_largefiniteassembly_repeatingunits/h29_handlearray.xlsx
crisscross/scripts/SW111_largefiniteassembly_repeatingunits/true_mighty_29_square.npy
crisscross/scripts/SW113_psoralen3primeTT/SW113_echoprotocol.py
crisscross/scripts/SW114_psoralenunitsq/20241216_limitedhandlearraysquare_echoprotocol.py
crisscross/scripts/SW119_newlibkinetics/SW119_echoprotocol.py
crisscross/scripts/SW121_spuriousassembly/SW121_newlib_spuriousassembly.py
crisscross/scripts/SW121_spuriousassembly/h29_handlearray.xlsx
crisscross/scripts/SW126_bionwire_wide_trench/20250324_square-handle-test_echoprotocol.py
crisscross/scripts/SW127_UFribourg_Design3_8xCNT_4handletypes/SW127_echoprotocol.py
crisscross/scripts/SW128_UFribourg_Design1_aggregationtest/SW128_echoprotocol_design1.py
crisscross/scripts/SW129_hexstar/design_setup.py
crisscross/scripts/SW129_hexstar/handle_evolution_server_prep.py
crisscross/scripts/SW131_bionwire_square_trenches/SW131_echoprotocol_separatetrenchslats.py
crisscross/scripts/SW132_repeatingunitassembly_epmotion_smallscale/SW132_echoprotocol_script.py
crisscross/scripts/TMSD/basic_designs.py
crisscross/scripts/TMSD/basic_designs_v2_incomplete.py
crisscross/scripts/TMSD/basic_designs_v3_no_knock_in.py
crisscross/scripts/TMSD/basic_designs_v4_extended_trench.py
crisscross/scripts/TMSD/basic_designs_v5_mixed_gnps_nelson.py
crisscross/scripts/TMSD/basic_designs_v6_multiple_reactions.py
crisscross/scripts/TMSD/split_design.py
crisscross/scripts/antigen_presenting_cells/CAPC_v1.py
crisscross/scripts/antigen_presenting_cells/capc_pattern_generator.py
crisscross/scripts/antigen_presenting_cells/handle_evolution.py
crisscross/scripts/antigen_presenting_cells/preliminary_work/CAPC_v1.py
crisscross/scripts/antigen_presenting_cells/preliminary_work/H5_bart_edna_handle_library_generation.py
crisscross/scripts/antigen_presenting_cells/preliminary_work/K99_designs_v2.py
crisscross/scripts/antigen_presenting_cells/preliminary_work/creating_designs_for_fellowships.py
crisscross/scripts/antigen_presenting_cells/preliminary_work/design_display.py
crisscross/scripts/assembly_handle_optimization/64_seq_square_test.py
crisscross/scripts/assembly_handle_optimization/batch_file_generation_round_1.py
crisscross/scripts/assembly_handle_optimization/debugging_evolution.py
crisscross/scripts/assembly_handle_optimization/debugging_multi_split_evolution.py
crisscross/scripts/assembly_handle_optimization/heatmap_experiment_analysis.py
crisscross/scripts/assembly_handle_optimization/hyperparam_sweep_1.py
crisscross/scripts/assembly_handle_optimization/library_sweep_optuna_optimized.py
crisscross/scripts/assembly_handle_optimization/multi_run_quick_comparison.py
crisscross/scripts/assembly_handle_optimization/optimization_with_optuna.py
crisscross/scripts/assembly_handle_optimization/optuna_sweep_quick_graph.py
crisscross/scripts/assembly_handle_optimization/optuna_viz.py
crisscross/scripts/assembly_handle_optimization/unfinished_scripts/hyperparam_sweep_2.py
crisscross/scripts/assembly_handle_optimization/unfinished_scripts/results_interp_2d.py
crisscross/scripts/assembly_handle_optimization/unfinished_scripts/results_interpretation.py
crisscross/scripts/battleships/design_prep_and_echo.py
crisscross/scripts/battleships/server_evolve_generator.py
crisscross/scripts/bionwire_collab/design_v1_visualization.py
crisscross/scripts/bionwire_collab/design_v2_wider_trench.py
crisscross/scripts/bionwire_collab/unfinished_designs/crossbar_example.py
crisscross/scripts/bionwire_collab/unfinished_designs/deep_trench.py
crisscross/scripts/design_debugging/gliders_stellatest/glider_megastructure_creation_stellatest.py
crisscross/scripts/generic/attach_handles_to_slats.py
crisscross/scripts/generic/combining_seeds_into_one_plate.py
crisscross/scripts/generic/convert_idt_email_plate_into_2d_format.py
crisscross/scripts/generic/convert_src002_into_src009.py
crisscross/scripts/generic/creating_combined_p8064_seed_plate.py
crisscross/scripts/generic/creating_new_assembly_handle_plates.py
crisscross/scripts/generic/generate_dna_paint_plate.py
crisscross/scripts/generic/gnp_concentration_tester_designs.py
crisscross/scripts/generic/prepare_plate_for_resuspension_with_liquid_handler.py
crisscross/scripts/generic/regenerate_handle_array_from_echo_commands.py
crisscross/scripts/generic/src_007_refill_script.py
crisscross/scripts/generic/sw_src007_plate_generation.py
crisscross/scripts/generic/testing_crisscross_animation.py
crisscross/scripts/generic/testing_triple_layer_designs.py
crisscross/scripts/generic/update_old_seed_to_hashcad_seed.py
crisscross/scripts/glass conjugation/design1.py
crisscross/scripts/glass conjugation/design2.py
crisscross/scripts/gliders/glider_design.py
crisscross/scripts/gliders/glider_megastructure_creation.py
crisscross/scripts/gliders/glider_v2_design_and_assembly.py
crisscross/scripts/hash_cad_validation/cost_calculations.py
crisscross/scripts/hash_cad_validation/design_evolution.py
crisscross/scripts/hash_cad_validation/design_prep_and_echo.py
crisscross/scripts/hash_cad_validation/echo_combining_script.py
crisscross/scripts/hash_cad_validation/experiment_1_quick_check_hammings.py
crisscross/scripts/hash_cad_validation/experiment_2_sunflower_design_prep_and_echo.py
crisscross/scripts/magnonics/basic_squares.py
crisscross/scripts/magnonics/basic_squares_with_new_library.py
crisscross/scripts/new_handle_library_generation/TT_no_crosscheck96to104_64_sequence_pairs_flipped.txt
crisscross/scripts/new_handle_library_generation/analyze_idt_plate_cost.py
crisscross/scripts/new_handle_library_generation/create_working_stocks_from_master_stocks.py
crisscross/scripts/new_handle_library_generation/handle_library_resuspension.py
crisscross/scripts/new_handle_library_generation/hist_check.png
crisscross/scripts/new_handle_library_generation/new_handle_library_plateify.py
crisscross/scripts/new_handle_library_generation/new_handle_library_quick_checks.py
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/256_set.txt
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/chris_handle_distribution.pkl
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/core_32_sequences.pkl
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/distribution_generation.py
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/gc_3_4_full_sweep_energies.pkl
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/generate_all_binding_energies.py
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/handle_antihandle_binding_energies.pkl
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/handlenotebook_katzi.ipynb
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/nupack_testing.py
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/seq_sampler.py
crisscross/scripts/new_handle_library_generation/matthew_handle_energy_prototyping/test_2.py
crisscross/scripts/optical_computing_collab/calculating_crossbar_placement.py
crisscross/scripts/optical_computing_collab/generating_crossbar_handle_pattern.py
crisscross/scripts/optical_computing_collab/new_designs_june_2025.py
crisscross/scripts/optical_computing_collab/new_square_w_double purification.py
crisscross/scripts/optical_computing_collab/preparing_more_y_slats_with_h29.py
crisscross/scripts/optical_computing_collab/square_design_for_optical_computers.py
crisscross/scripts/optical_computing_collab/standard_design_with_2_step_purification.py
crisscross/scripts/optical_computing_collab/testing_octa_pattern.py
crisscross/scripts/plate_resuspension_scripts/general_2_vol_plate_resuspension.py
crisscross/scripts/plate_resuspension_scripts/prepare_plate_for_biodot_resuspension.py
crisscross/scripts/two_point_bead_purification/design_iteration_1.py
crisscross/scripts/two_point_bead_purification/design_iteration_2.py
crisscross/scripts/two_point_bead_purification/plate_generation.py
crisscross_kit.egg-info/PKG-INFO
crisscross_kit.egg-info/SOURCES.txt
crisscross_kit.egg-info/dependency_links.txt
crisscross_kit.egg-info/entry_points.txt
crisscross_kit.egg-info/requires.txt
crisscross_kit.egg-info/top_level.txt
docs/mkdocs.yml
docs/requirements.txt
docs/docs/index.md
docs/docs/api/complete.md
docs/docs/crisscross/assembly-optimization.md
docs/docs/crisscross/core-functions.md
docs/docs/crisscross/echo-export.md
docs/docs/crisscross/graphics.md
docs/docs/crisscross/helper-functions.md
docs/docs/crisscross/lab-helpers.md
docs/docs/crisscross/plate-handling.md
docs/docs/crisscross/quick_start.md
docs/docs/orthoseq/library_reference.md
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orthoseq_generator/.gitignore
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orthoseq_generator/__init__.py
orthoseq_generator/helper_functions.py
orthoseq_generator/sequence_computations.py
orthoseq_generator/vertex_cover_algorithms.py
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orthoseq_generator/scripts/run_sequence_search.py
orthoseq_generator/scripts/legacy/legacy_sequence_search.py
orthoseq_generator/scripts/legacy/precompute_energies.py