ttc-nccrp 0.1.1__tar.gz

ttc_nccrp-0.1.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# DotEnv configuration
+.env
+
+# Database
+*.db
+*.rdb
+
+# Pycharm
+.idea
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+# VS Code
+.vscode/
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+# Spyder
+.spyproject/
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+# Jupyter NB Checkpoints
+.ipynb_checkpoints/
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+# exclude data from source control by default
+/data/
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+# vim
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+
+# Mypy cache
+.mypy_cache/
+site/

ttc_nccrp-0.1.1/.python-version

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+3.13

ttc_nccrp-0.1.1/LICENSE

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+
+The MIT License (MIT)
+Copyright (c) 2025, patlewig
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

ttc_nccrp-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: ttc-nccrp
+Version: 0.1.1
+Summary: A simple python implementation of the Kroes TTC workflow
+Author-email: Grace Patlewicz <grace@comptoxscience.com>
+License: MIT
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.3.1
+Requires-Dist: pandas>=2.3.1
+Requires-Dist: rdkit>=2025.3.3
+Provides-Extra: dev
+Requires-Dist: ipykernel>=6.29.5; extra == "dev"
+Requires-Dist: jupyter>=1.1.1; extra == "dev"
+Requires-Dist: matplotlib>=3.10.3; extra == "dev"
+Requires-Dist: seaborn>=0.13.2; extra == "dev"
+Requires-Dist: scikit-learn>=1.7.0; extra == "dev"
+Requires-Dist: openpyxl>=3.1.5; extra == "dev"
+Requires-Dist: pyarrow>=20.0.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.6.1; extra == "docs"
+Dynamic: license-file
+
+# Python Kroes workflow implementation (ttc_nccrp) 
+==============================
+
+[![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
+
+
+The foundation is taken from `https://github.com/g-patlewicz/ttc_exclusions` but relying on alerts described in Benigni et al (2008) `https://publications.jrc.ec.europa.eu/repository/bitstream/JRC43157/eur%20report%20benigni%20130208%20final.pdf` 
+
+An updated workflow to facilitate assigning of substances through the Kroes et al workflow. Substances are assigned as inorganics, out of scope of TTC due to their TCDD like features, steroid moiety, high potency genotoxic carcinogens, presenting a genotoxicity alert and organophosphates/carbamates. A new optional offramp exists for PFAS substances. 
+
+Specific Updates:
+
+17-May-2026
+- Adjusted simple aldehyde to cover formaldehyde
+- Added new vinyl halides from Bailey et al Regul. Toxicol. Pharmacol. 2005; 42 (2) 225-35 
+- Adjusted hydrazine and nitroso patterns
+- Added additional patterns for a number of other alerts
+- Re-figured the logic for inorganics to capture alerting fragments for organic fragments when using SaltRemover.SaltRemover()
+
+19-May-2026
+
+- Added offramp for PFAS
+- Created validation set to evaluate initial performance and refine all alerts that were resulting in discrepancies
+
+## Installation
+
+This package requires RDKit. Dependencies are captured in the pyproject.toml file.
+
+`uv add ttc_nccrp`
+
+## Licensing
+
+This implementation is licensed under **MIT**.
+
+## Citation
+
+Please cite Patlewicz and Mihalchik (2026) Revisiting the Threshold of Toxicological Concern: a computational framework for structural classification, cross-scheme comparison and opportunities for refinement. *Computational Toxicology* *under review* 
+
+## Acknowledgements
+
+A handful of SMARTS patterns and ring detection logic were developed with assistance from Claude Haiku (Anthropic), with subsequent code review to verify correctness.
+

ttc_nccrp-0.1.1/README.md

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+# Python Kroes workflow implementation (ttc_nccrp) 
+==============================
+
+[![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
+
+
+The foundation is taken from `https://github.com/g-patlewicz/ttc_exclusions` but relying on alerts described in Benigni et al (2008) `https://publications.jrc.ec.europa.eu/repository/bitstream/JRC43157/eur%20report%20benigni%20130208%20final.pdf` 
+
+An updated workflow to facilitate assigning of substances through the Kroes et al workflow. Substances are assigned as inorganics, out of scope of TTC due to their TCDD like features, steroid moiety, high potency genotoxic carcinogens, presenting a genotoxicity alert and organophosphates/carbamates. A new optional offramp exists for PFAS substances. 
+
+Specific Updates:
+
+17-May-2026
+- Adjusted simple aldehyde to cover formaldehyde
+- Added new vinyl halides from Bailey et al Regul. Toxicol. Pharmacol. 2005; 42 (2) 225-35 
+- Adjusted hydrazine and nitroso patterns
+- Added additional patterns for a number of other alerts
+- Re-figured the logic for inorganics to capture alerting fragments for organic fragments when using SaltRemover.SaltRemover()
+
+19-May-2026
+
+- Added offramp for PFAS
+- Created validation set to evaluate initial performance and refine all alerts that were resulting in discrepancies
+
+## Installation
+
+This package requires RDKit. Dependencies are captured in the pyproject.toml file.
+
+`uv add ttc_nccrp`
+
+## Licensing
+
+This implementation is licensed under **MIT**.
+
+## Citation
+
+Please cite Patlewicz and Mihalchik (2026) Revisiting the Threshold of Toxicological Concern: a computational framework for structural classification, cross-scheme comparison and opportunities for refinement. *Computational Toxicology* *under review* 
+
+## Acknowledgements
+
+A handful of SMARTS patterns and ring detection logic were developed with assistance from Claude Haiku (Anthropic), with subsequent code review to verify correctness.
+

ttc_nccrp-0.1.1/docs/index.md

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+# Description
+
+ttc_nccrp is a python package aimed at profiling substances through the Kroes et al (2004) Threshold of Toxicological Concern (TTC) workflow. 
+
+## Installation
+
+UV install
+
+```uv add ttc_nccrp```
+
+or clone the repository
+
+```git clone https:github.com/patlewig/ttc_nccrp.git```
+
+then sync the dependencies using ```uv sync``
+

ttc_nccrp-0.1.1/docs/kroes.md

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+# Quickstart
+
+## To get started
+
+Import the main functions
+
+```from ttc_nccrp.chm.chm import MoleculeProcessor```
+
+## Single chemical
+Instantiate the MolecularProcessor()
+
+```mol = MolecularProcessor()```
+
+Then add a chemical providing a identifier using the parameter `dtxsid` and a smiles with `smiles`
+
+```mol.add_chemical(dtxsid = 'dtx123', smiles = 'CCCCC(=O)')```
+
+To invoke the Kroes decision tree use:
+
+```mol.decision_tree()```
+
+## Batch processing
+
+Assuming that the list of substances of interest are in a tabular form such as within a CSV or Excel file.
+Import the ```csv``` or ```excel``` into a pandas dataframe `df`. Ensure that there is an identifier column called ```dtxsid``` and a smiles column called ```smiles```.
+
+Instantiate MoleculeProcessor as an instance as before:
+
+```mol = MolecularProcessor()
+res = mol.process_batch(df)
+```   
+
+```mol.process_batch(df)``` returns the original dataframe but with a new column called `final_TTC_category`
+
+The outcome returns the TTC category triggered e.g. `DLC - TTC not applicable` or `GeneTox - TTC of 0.15 ug/day` or `Like Cramer class applicable`.
+
+
+

ttc_nccrp-0.1.1/mkdocs.yml

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+site_name: ttc_nccrp
+
+nav:
+  - home: index.md
+  - quickstart: kroes.md
+  
+
+site_author: patlewig
+
+theme: readthedocs
+