.gitignore
.readthedocs.yml
LICENSE
README.md
logo.svg
pyproject.toml
.github/workflows/ci.yml
docs/Makefile
docs/README.md
docs/make.bat
docs/source/cli-reference.md
docs/source/concepts.md
docs/source/conf.py
docs/source/index.md
docs/source/installation.md
docs/source/quickstart.md
docs/source/_static/custom.css
docs/source/_static/logo-dark.svg
docs/source/_static/logo-light.svg
docs/source/_static/logo-without-name.svg
docs/source/_static/logo.svg
docs/source/api/index.md
docs/source/guides/admet-data.md
docs/source/guides/index.md
notebooks/activity_comment_analysis.ipynb
notebooks/caco2_assay_discovery.sh
notebooks/capricho-marimo-example.py
notebooks/case-1-transparent_quality_control_cross-assay_aggr.ipynb
notebooks/case-2-cyp-inhibition-mt-dataset.ipynb
notebooks/case-3-caco2-permeability-w-unit-standardization.ipynb
notebooks/performance-profiling/.gitignore
notebooks/performance-profiling/README.md
notebooks/performance-profiling/benchmark_case_studies.sh
notebooks/performance-profiling/measure_command.py
notebooks/permeability_ids/ChEMBL-all-caco2-a2b-assays.txt
notebooks/permeability_ids/ChEMBL-all-caco2-assays.txt
notebooks/permeability_ids/ChEMBL-all-caco2-b2a-assays.txt
notebooks/permeability_ids/ChEMBL-all-mdck-mdr1-a2b-assays.txt
notebooks/permeability_ids/ChEMBL-all-mdck-mdr1-assays.txt
notebooks/permeability_ids/ChEMBL-all-mdck-mdr1-b2a-assays.txt
src/Capricho/__init__.py
src/Capricho/_version.py
src/Capricho/_version_helper.py
src/Capricho/analysis.py
src/Capricho/logger.py
src/Capricho/unichem.py
src/Capricho/chembl/atp_extraction.py
src/Capricho/chembl/data_flag_functions.py
src/Capricho/chembl/exceptions.py
src/Capricho/chembl/parsing.py
src/Capricho/chembl/processing.py
src/Capricho/chembl/similarity.py
src/Capricho/chembl/unit_conversions.py
src/Capricho/chembl/api/downloader.py
src/Capricho/chembl/api/sql_explorer.py
src/Capricho/chembl/api/webresource.py
src/Capricho/cli/chembl_data_pipeline.py
src/Capricho/cli/main.py
src/Capricho/cli/prepare.py
src/Capricho/core/binarization.py
src/Capricho/core/default_fields.py
src/Capricho/core/fp_utils.py
src/Capricho/core/pandas_helper.py
src/Capricho/core/rate_limit.py
src/Capricho/core/smiles_utils.py
src/Capricho/core/stats_make.py
src/Capricho/core/stereo.py
src/Capricho/core/table_format.py
src/Capricho/pubchem/api.py
src/Capricho/pubchem/core.py
src/CompoundMapper/_version.py
src/capricho.egg-info/PKG-INFO
src/capricho.egg-info/SOURCES.txt
src/capricho.egg-info/dependency_links.txt
src/capricho.egg-info/entry_points.txt
src/capricho.egg-info/requires.txt
src/capricho.egg-info/top_level.txt
tests/conftest.py
tests/test_activity_curation.py
tests/test_analysis.py
tests/test_assay_overlap.py
tests/test_atp_extraction.py
tests/test_binarization.py
tests/test_chembl_processing.py
tests/test_core.py
tests/test_data_flag_functions.py
tests/test_fp_utils.py
tests/test_logging.py
tests/test_rate_limit.py
tests/test_stereocenter.py
tests/test_table_format.py
tests/test_unit_conversions.py
tests/test_workflow.py
tests/resources/ADORA3_data.csv
tests/resources/ADORA3_data_not_aggregated.csv
tests/resources/ADORA3_data_recipe.json