├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── Makefile ├── README.md ├── cover.png ├── examples ├── 01_toy_minimization │ └── toy_minimization.py ├── 02_xTB_property_optimization │ └── optimize_solvation_energy_QM9.py ├── 03_distributed_random_walk │ ├── parallelized_optimize_solvation_energy_EGP.py │ └── parallelized_toy_minimization.py ├── 04_blind_optimization_protocol │ ├── solvation_energy_minimization_beta_optimization.py │ └── toy_minimization_beta_optimization.py └── 05_chemspacesampler │ ├── README.md │ ├── app │ ├── Dockerfile │ ├── app.py │ ├── chemspace.yml │ └── radar.png │ ├── app_shot.png │ ├── run_representations │ ├── run_BoB.py │ ├── run_CM.py │ ├── run_ECFP.py │ ├── run_MBDF.py │ ├── run_MolDescriptors.py │ ├── run_SOAP.py │ ├── run_atomic_energies.py │ ├── run_cliffs.py │ └── run_inv_ECFP.py │ └── tutorial │ └── tutorial.ipynb ├── mosaics ├── __init__.py ├── beta_choice.py ├── chem_graph │ ├── __init__.py │ ├── base_chem_graph.py │ ├── chem_graph.py │ ├── heavy_atom.py │ └── resonance_structures.py ├── crossover.py ├── data.py ├── distributed_random_walk.py ├── elementary_mutations.py ├── ext_graph_compound.py ├── minimized_functions │ ├── __init__.py │ ├── chemspace_potentials.py │ ├── chemspace_sampler_default_params.py │ ├── inversion_potentials.py │ ├── morfeus_quantity_estimates.py │ ├── representations.py │ └── toy_problems.py ├── misc_procedures.py ├── modify.py ├── optimization_protocol.py ├── periodic.py ├── random_walk.py ├── rdkit_draw_utils.py ├── rdkit_utils.py ├── test_utils.py ├── trajectory_analysis.py ├── utils.py └── xyz2graph.py ├── pyproject.toml └── tests ├── 01_toy_minimization ├── toy_minimization.py └── toy_minimization_benchmark.log ├── 03_distributed_random_walk ├── parallelized_toy_minimization.py ├── parallelized_toy_minimization_benchmark.log ├── parallelized_toy_minimization_other_seed.py └── parallelized_toy_minimization_other_seed_benchmark.log ├── 04_blind_optimization_protocol ├── toy_minimization_beta_optimization.py └── toy_opt_benchmark.log ├── benchmark_env.yml └── old_0.2.0_benchmarks ├── 01_toy_minimization ├── toy_minimization.py └── toy_minimization_benchmark.log ├── 03_distributed_random_walk ├── parallelized_toy_minimization.py ├── parallelized_toy_minimization_benchmark.log ├── parallelized_toy_minimization_other_seed.py └── parallelized_toy_minimization_other_seed_benchmark.log └── 04_blind_optimization_protocol ├── toy_minimization_beta_optimization.py └── toy_opt_benchmark.log /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chemspacelab/mosaics/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chemspacelab/mosaics/HEAD/.pre-commit-config.yaml 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