SynPlanner
Computer-aided synthesis planning
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Download Latest Version (.zip)- build-docker.yml
- ci.yml
- pypi.yml
- test-pypi.yml
- planning_benchmarking.ipynb
- retrosynthetic_planning.ipynb
- routes_clustering.ipynb
- combined_ranking_filtering_policy.yaml
- extraction_functional_groups.yaml
- mhn_ranking_policy_training.yaml
- planning_combined_policies.yaml
- planning_standard.yaml
- planning_value.yaml
- policy_training.yaml
- reactions_filtration.yaml
- reactions_standardization.yaml
- rules_extraction.yaml
- synthonisation.yaml
- tuning.yaml
- custom.css
- switcher.json
- modules.rst
- synplan.chem.reaction.curation.rst
- synplan.chem.reaction.routes.rst
- synplan.chem.reaction.rules.manual.rst
- synplan.chem.reaction.rules.rst
- synplan.chem.rst
- synplan.chem.synthon.rst
- synplan.interfaces.rst
- synplan.mcts.rst
- synplan.ml.networks.rst
- synplan.ml.rst
- synplan.ml.training.rst
- synplan.rst
- synplan.utils.rst
- configuration.rst
- extraction.rst
- filtration.rst
- planning.rst
- policy.rst
- standardization.rst
- synthonisation.rst
- value.rst
- chemist_review.rst
- index.rst
- package_layout.rst
- pr_review.rst
- release.rst
- setup.rst
- data_download.rst
- docker_images.rst
- index.rst
- installation.rst
- banner.png
- pipeline.png
- extraction.rst
- filtration.rst
- mcts.rst
- methods.rst
- planning.rst
- policy.rst
- priority_rules.rst
- rebalancing.rst
- routes.rst
- standardization.rst
- synthons.rst
- value.rst
- 00_Welcome_to_Chython.ipynb
- 01_Coming_from_RDKit.ipynb
- 02_Data_Curation.ipynb
- 03_Rules_Extraction.ipynb
- 04_Policy_Training.ipynb
- 05_Retrosynthetic_Planning.ipynb
- 06_Tree_Analysis.ipynb
- 07_Clustering.ipynb
- 08_Protection_Scoring.ipynb
- 09_Combined_Ranking_Filtering_Policy.ipynb
- 10_NMCS_Algorithms.ipynb
- 11_Planning_with_RDKit.ipynb
- 12_Rule_Analysis.ipynb
- 13_Priority_Rules.ipynb
- 14_MHN_Ranking_Training.ipynb
- 15_Routes_compare.ipynb
- 16_Building_block_search.ipynb
- 17_Synthon_Based_Design.ipynb
- 18_Retrosynthesis_With_Synthon_Priority_Rules.ipynb
- cli_interface.rst
- data.rst
- index.rst
- migration.rst
- tables.rst
- ten_minutes.rst
- agent_skill.rst
- api.rst
- conf.py
- index.rst
- llms.txt
- release_notes.rst
- tasks.rst
- __init__.py
- config.yaml
- plot_results.py
- run_benchmark.py
- __init__.py
- convert_protection_source_data.py
- rebalance_bench.py
- release.py
- route_cgr_roundtrip.py
- tasks.md
- SKILL.md
- __init__.py
- __init__.py
- config.py
- filtering.py
- mapping.py
- pipeline.py
- reaction_result.py
- rebalancing.py
- standardizing.py
- __init__.py
- core.py
- pseudo_atoms.py
- subclustering.py
- __init__.py
- csv.py
- json.py
- metadata.py
- tree.py
- competing_groups.yaml
- convert_source_data.py
- halogen_groups.yaml
- incompatibility_matrix.tsv
- protection_group_templates.csv
- reactive_function_label_mapping.json
- __init__.py
- config.py
- functional_groups.py
- reaction_classifier.py
- scanner.py
- scorer.py
- strategy.py
- __init__.py
- scorer.py
- __init__.py
- components.py
- container.py
- deconvolution.py
- depiction.py
- hash.py
- route_cgr.py
- sb_cgr.py
- state.py
- __init__.py
- analysis.py
- cli.py
- contracts.py
- notebook_plots.py
- traversal.py
- visualisation.py
- __init__.py
- decompositions.py
- transformations.py
- __init__.py
- config.py
- io.py
- morgan.py
- query_cgr.py
- rdkit_smarts.py
- __init__.py
- analysis.py
- config.py
- extraction.py
- priority.py
- synthon.py
- __init__.py
- config.py
- reactor.py
- __init__.py
- clustering.py
- io.py
- leaving_groups.py
- route_cgr.py
- visualisation.py
- __init__.py
- analysis.py
- extraction.py
- priority.py
- __init__.py
- _convert.py
- _dialect.py
- bb_classes.json
- bb_marks.json
- enamine_naming.json
- ring_rules.json
- rules.json
- validate.py
- validate_retro.py
- __init__.py
- analogues.py
- classify.py
- config.py
- coverage.py
- enumerate.py
- fragment.py
- frames.py
- stock.py
- synthonise.py
- transformer.py
- __init__.py
- precursor.py
- rdkit_compat.py
- rdkit_utils.py
- scaffolds.py
- utils.py
- __init__.py
- cli.py
- gui.py
- synthon_audit.py
- synthon_commands.py
- __init__.py
- base.py
- composite.py
- template_based.py
- template_free.py
- __init__.py
- algorithm.py
- config.py
- evaluation.py
- node.py
- search.py
- tree.py
- __init__.py
- fingerprints.py
- molecules.py
- rules.py
- __init__.py
- molecule.py
- rule.py
- __init__.py
- linear.py
- mhnreact.py
- __init__.py
- base.py
- checkpoint.py
- value.py
- __init__.py
- lightning.py
- preprocessing.py
- reinforcement.py
- supervised.py
- trainers.py
- __init__.py
- config.py
- __init__.py
- __init__.py
- dataset.proto
- dataset_pb2.py
- reaction.proto
- reaction_pb2.py
- reader.py
- __init__.py
- cache.py
- config.py
- files.py
- frames.py
- loading.py
- logging.py
- parallel.py
- visualisation.py
- __init__.py
- _compat.py
- README.md
- routes_mol_complex.json
- routes_mol_medium.json
- routes_mol_simple.json
- tree_1_1.pkl
- suspicious_sample.smi
- BBs.cxsmiles
- final_result.smi
- outSynth_BBmode.smi
- outSynth_Synthmode.smi
- reaction_coverage.smi
- policy_data_small.tsv
- route_cgrs_1_1.pkl
- routes_mol_1.csv
- routes_mol_1.json
- sb_cgrs_1_1.pkl
- test_cli_commands.py
- test_cli_shipped_configs.py
- test_cli_synthon.py
- test_cli_synthon_audit.py
- test_clustering_integration.py
- test_clustering_visualization_e2e.py
- test_data_pipelines.py
- test_mcts_planner_smoke.py
- __init__.py
- conftest.py
- test_apply_rule_cgr_rebuild.py
- test_atom_mapping_validator.py
- test_balance_dataset.py
- test_canonical_query_cgr_key.py
- test_canonical_retro_reactor.py
- test_clustering_robustness.py
- test_error_tsv_format.py
- test_error_tsv_format_static.py
- test_extraction_invariants.py
- test_mcts_invariants.py
- test_ml_logit_vs_prob_metrics.py
- test_pipeline_conservation.py
- test_products_truncation.py
- test_rdf_reader.py
- test_ring_retro_rules.py
- test_route_io_roundtrip.py
- test_route_quality_score.py
- test_rule_loading_contract.py
- test_stereo_handling.py
- test_svg_validity.py
- test_synthon_data_is_current.py
- test_synthon_divergence.py
- test_synthon_enumeration.py
- test_synthon_fixtures.py
- test_synthon_fragment_cli.py
- test_synthon_priority.py
- test_synthon_reaction_coverage.py
- test_synthon_rule_validation.py
- test_synthon_synthonise.py
- test_target_in_stock.py
- test_config_models.py
- test_filtering.py
- test_mapping.py
- test_pipeline.py
- test_rebalancing.py
- test_clustering.py
- test_components_nh.py
- test_exports.py
- test_extract_reactions_fast.py
- test_hash_route.py
- test_leaving_groups.py
- test_make_json_null_node.py
- test_representation_state.py
- test_route_analysis.py
- test_route_cgr.py
- test_route_contracts.py
- test_route_legacy_modules.py
- test_route_tooling_shims.py
- test_traversal.py
- test_analysis.py
- test_extraction.py
- test_manual_rules.py
- test_priority.py
- test_rdkit_smarts_conversion.py
- test_audit.py
- test_audit_config.py
- test_classify.py
- test_stock.py
- test_synthon_frames.py
- test_transformer.py
- test_molecule_cleanup.py
- test_precursor.py
- test_rdkit_compat.py
- test_rdkit_utils.py
- test_stereo_warning.py
- test_validate_and_canonicalize.py
- test_algorithm.py
- test_evaluation.py
- test_forward_direction.py
- test_mhn_ranking_expansion.py
- test_route_export.py
- test_target_reader.py
- test_tree_pickle.py
- test_tree_run.py
- test_tree_stats.py
- __init__.py
- test_checkpoint.py
- test_mhn_ranking.py
- test_ranking_policy.py
- test_supervised_training.py
- __init__.py
- test_functional_groups.py
- test_protection_strategy.py
- test_reaction_classifier.py
- test_scanner.py
- test_scorer.py
- test_cache.py
- test_combined_policy_guard.py
- test_files.py
- test_frames.py
- test_loading.py
- test_ord_reader.py
- test_parallel.py
- test_shipped_configs.py
- test_package_layers.py
- test_release_script.py
- test_route_import_boundaries.py
- test_sascore_bench_script.py
- test_visualisation.py
- conftest.py
- test_skill.py
- 00_Welcome_to_Chython.ipynb
- 01_Coming_from_RDKit.ipynb
- 02_Data_Curation.ipynb
- 03_Rules_Extraction.ipynb
- 04_Policy_Training.ipynb
- 05_Retrosynthetic_Planning.ipynb
- 06_Tree_Analysis.ipynb
- 07_Clustering.ipynb
- 08_Protection_Scoring.ipynb
- 09_Combined_Ranking_Filtering_Policy.ipynb
- 10_NMCS_Algorithms.ipynb
- 11_Planning_with_RDKit.ipynb
- 12_Rule_Analysis.ipynb
- 13_Priority_Rules.ipynb
- 14_MHN_Ranking_Training.ipynb
- 15_Routes_compare.ipynb
- 16_Building_block_search.ipynb
- 17_Synthon_Based_Design.ipynb
- 18_Retrosynthesis_With_Synthon_Priority_Rules.ipynb
- .dockerignore
- .gitignore
- CHANGELOG.md
- cli.Dockerfile
- CODEOWNERS
- Dockerfile
- gui.Dockerfile
- LICENSE
- pyproject.toml
- pytest.ini
- README.md
- readthedocs.yaml
- uv.lock
# Installation Guide
1. Get the code
git clone https://github.com/Laboratoire-de-Chemoinformatique/SynPlanner
Downloads the entire project code from GitHub to your computer.
cd SynPlanner
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Python 3 Python is required to use pip.
pip install SynPlanner
Installs the package published on PyPI directly β no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Docker
EasyPrerequisites
- Git Needed to download the project code from GitHub.
- Docker Desktop Needed to build and run containers. Install it and keep it running in the background.
docker build -t synplanner .
Builds a runnable image based on the Dockerfile.
docker run -p 8080:80 synplanner
Runs the built image as an actual container.
Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.
4. Python
EasyPrerequisites
pip install SynPlanner
Installs the package published on PyPI directly β no need to clone the source.
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
// repository documentation
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