ChemicalCalculator

A chemical calculator designed to determine if a product meets the definition of an Organic Peroxide under CFR 173.128(a)(4)

• Which of the provided formulated products meet the definition Organic Peroxide under CFR 173.128(a)(4)?

  • Product 2 and 3 meet the definition of organic peroxide

• Which of the provided formulated products do not meet the definition?

  • Product 1 and 4 do not meet the definition of organic peroxide

• Which subsection under CFR 173.128(a)(4) was used to determine whether the product meets or does not meet the definition of an Organic Peroxide?

  • Product 2 and 3 are determined as organic peroxide as they contain peroxide but doesn't meet conditions described under CFR 173.128(a)(4). Product 1 and 4 are not determined as organic peroxide as they meet conditions described under CFR 173.128(a)(4). See table below.

    Product ID	Is organic peroxide?	Reason
    Product 1	No	Meets CFR 173.128(a)(4)(i)
    Product 2	Yes	Contains peroxide and doesn't meet CFR 173.128(a)(4)
    Product 3	Yes	Contains peroxide and doesn't meet CFR 173.128(a)(4)
    Product 4	No	Meets CFR 173.128(a)(4)(i)

• Are any of the products eligible for an exemption?

  • Based on the compositions and ingredients, product 1 seems to be an acne product, while product 2 to 4 seem to be cleaning products. Product 1 may be eligible for an exemption if they fall into a different category of products, e.g. cosmetic products.

Incremental commits

• Designed a class ChemicalSpecies to hold and process information associated with a chemical species

  • Takes CAS number and chemical name as inputs
  • Uses CAS number to search for smiles string of the chemical species from cactus.nci.nih.gov
    • Throws warning if smiles string cannot be found
  • Uses smiles string to construct a RDKit molecule
  • Uses RDKit's substructure match function to obtain
    • Number of peroxide group structure (-O-O-) in the chemical species
    • Number of hydrogen peroxide structure (H-O-O-H) in the chemical species
  • Uses RDKit's Descriptors to obtain molecular weight of the chemical species

• Designed a class ChemicalComposition to hold and process information associated with a chemical composition

  • Takes a ChemicalSpecies, min conc, and max conc as inputs
  • Uses max conc and information contained in chemical species to calculate max conc of hydrogen peroxide

• Designed a class FormulatedProduct to hold and process information associated with a formulated product

  • Takes a list of ChemicalComposition and product ID as inputs
  • Check if the formulated product meets the definition of organic peroxide based on CFR 173.128(a)(4)
    • Check if the formulated product contains chemical species that has non-zero number of peroxide group structure
      • If the formulated product doesn't contain peroxides, then the formulated product doesn't meet the definition of organic peroxide
    • CFR 173.128(a)(4): If the formulated product contains peroxides, check the conc of hydrogen peroxide and the Oa
      • If the hydrogen peroxide conc and the Oa falls into either CFR 173.128(a)(4)(i) or CFR 173.128(a)(4)(ii), then the formulated product doesn't meet the definition of organic peroxide
      • Otherwise, the formulated product meets the definition of organic peroxide

• Designed a function to help easy usage of the chemical calculator

  • Takes the path to the product list csv file
  • Returns the modified csv file containing chemical calculator results

• Other miscellaneous tasks

  • Listed out required packages in environment.yml file to create conda env
  • Created setup.py file to use pip install
  • Created .gitignore file to ignore files generated by pip install
  • Created jupyter notebook example to run test suite
  • Created main.py for example
  • Created DockerFile and updated instructions to create docker image and build docker container to run test suite

Instructions for installing the package and running the test suite

• Clone the repo by git clone https://github.com/hwpang/ChemicalCalculator.git

• There are three options to use this package:

  • Use docker
    • Install Docker (https://www.docker.com/get-started/)
    • Use docker build -t chem_calc . in the package folder ChemicalCalculator to build image chem_calc
    • Use docker run -p 8888:8888 chem_calc to create a container
    • On the terminal, a URL similar to http://127.0.0.1:8888/lab?token=<token> can be found
    • Copy the URL and paste in a browser
  • Use pip install
    • Run pip install jupyter numpy pandas rdkit to install necessary packages
    • Install the package by pip install -e . in the package folder ChemicalCalculator
  • Use conda environment
    • Install Anaconda 3 (https://www.anaconda.com/products/individual#Downloads)
    • Use conda env create -f environment.yml to create a conda environment chem_calc
    • Activate the conda environment by conda activate chem_calc
    • Install the package by pip install -e . in the package folder ChemicalCalculator

• After installing the necessary packages, navigate to the ipython folder to run the test suite in the Running_test_suite.ipynb jupyter notebook

  • cd to the ipython folder
  • jupyter notebook to open up the jupyter notebook