solvent-guide 0.4.0

Standalone version of the solvent guide as shown in the AI4Green ELN

Solvent Guide

The solvent guide provides a visual interface for the comparison of common laboratory solvents to encourage greener decision-making during reaction design. The data for each solvent was collected from the CHEM21 solvent guide and is provided via a simple visual interface.

This software was first developed as part of AI4Green, a Machine-Learning powered Electronic Lab Notebook (ELN) that aims to facilitate greener choices at the laboratory level. It has been adapted as a standalone tool in the hope that it may be useful outside the ELN.

Installation

First, ensure you have installed the required dependencies:

pip install numpy==1.26.0 pandas==1.4.1 blinker==1.6.2 flask==2.3.2 plotly==5.9.0 colorama==0.4.6 python-dateutil==2.8.2

Then, the package can be installed from pip using the following command:

pip install solvent_guide

Run from command line

Once installed, the Solvent Guide can be launched from the command line with:

python -m solvent_guide.webapp

This should open a web browser and allow you to view the solvent guide.

This process runs on port 5000 by default. If other apps are running on this port then this can cause issues.

The port can be changed by setting the FLASK_RUN_PORT environment variable in the command line before running. For example, to run on port 80:

# Windows
set FLASK_RUN_PORT=80

# Linux/Mac
export FLASK_RUN_PORT=80

The process can be killed by entering:

Ctrl + C

Adding new solvents

New solvents can be added to the Solvent Guide by running:

python -m solvent_guide.add_solvent

and following the prompts therein. If the information is not available, each prompt can be skipped by pressing enter.

Upon rerunning the Solvent Guide, the new solvent will be included.

A summary of the information required is shown below.

---

Enter PubChem ID (if known) (PubChemID to link solvent entry to PubChem)
Enter CAS Number (if known) (CAS number of the solvent if available)
Enter Solvent Family (the class the solvent belongs to (Halogenated, esters etc))
Enter Solvent Name (the solvent name)
Enter Alternative Solvent Name (an alternative name for the solvent if applicable)
Enter Boiling Point (solvent boiling point)
Enter Flash Point: (solvent flash point if applicable)
Enter Worst H3xx statement (the most hazardous H3XX statement)
H3_phrase (the phrase associated with the worst H3XX number. Only needed if H3xx statement was provided.)
Enter Worst H4xx statement (the most hazardous H4XX statement)
H4_phrase (the phrase associated with the worst H4XX number. Only provided if an H4xx statement was provided.)
Enter CHEM21 Safety Score (CHEM21 safety score, can be skipped if not available)
Enter CHEM21 Health Score (CHEM21 health score, can be skipped if not available)
Env (CHEM21 environment score, can be skipped if not available)
Select Ranking (Ranking to determine flashcard colour. Must be chosen from the provided options)
Enter Replacement Issues (justification for replacements)
Enter Possible Replacement 1 (solvent to be used as substitute if applicable)
Enter Replacement 2 (str, solvent to be used as substitute is applicable)

---

Removing solvents

Solvents can be removed from the Solvent Guide by running:

python -m solvent_guide.remove_solvent

and entering the corresponding CAS number.

All solvents can be removed by resetting the Solvent Guide. This can be done via:

python -m solvent_guide.reset_solvents

THIS WILL DELETE ALL ADDED SOLVENTS AND REMOVE ALL CHANGES MADE TO THE DATABASE SINCE INSTALLATION.

You will be prompted to confirm this:

CAUTION! Resetting the database will revert all changes made since installation. Are you sure? (y/n)

Import as python package

It is also possible to run the solvent guide in python by importing the app_run() function.

from solvent_guide.webapp import app_run

app_run()

This will start running the Solvent Guide and should open up a new browser window.

Adding Solvents

Adding individual solvents

Solvents can be added individually using the add_solvent() function and following the prompts.

Running:

from solvent_guide.add_solvent import add_solvent

add_solvent()

gives:

Follow the prompts to add a flashcard for the new solvent. Prompts can be skipped by pressing Enter.
Enter PubChem ID (if known):

Adding multiple solvents

Data for multiple solvents can be added by using add_solvent_from_dataframe(). This function requires the data to be organised in a pandas DataFrame with the following columns:

---

PubChem ID (int, PubChemID to link to entry)
CAS (str, CAS number fo the solvent if available)
Family (str, the class the solvent belongs to (Halogenated, esters etc))
Solvent (str,the solvent name)
Solvent Alternative Name (str,an alternative name for the solvent is applicable)
BP (int, solvent boiling point)
FP (int, solvent flash point if applicable)
Worst H3xx (str,the most hazardous H3XX statement)
Worst H4xx (str,the most hazardous H4XX statement)
Safety (int, CHEM21 safety score)
Health (int, CHEM21 health score)
Env (int, CHEM21 environment core)
Ranking Default (str, CHEM21 default ranking)
Ranking Discussion (str, CHEM21 final ranking)
Replacement Issues (str, justification for replacements)
Replacement 1 (str, solvent to be used as substitute if applicable. Must be an existing solvent in the database.)
Replacement 2 (str, solvent to be used as substitute is applicable. Must be an existing solvent in the database.)
H3_phrase (str, the phrase associated with the worst H3XX number)
H4_phrase (str, the phrase associated with the worst H4XX number)

---

For an example DataFrame containing data for solvents Example1, Example2 and Example3:

import pandas as pd

solvent_df = pd.DataFrame({
                'PubChem ID': [111, 222, 333],
                'CAS': ['1-1-1', '2-2-2', '3-3-3'],
                'Family': ['Ethers', 'Halogenated', 'Alcohols'],
                'Solvent': ['Example1', 'Example2', 'Example3'],
                'Solvent Alternative Name': ['alt1', 'alt2', 'alt3'],
                'BP': [40, 85, 100],
                'FP': [100, 130, 105],
                'Worst H3xx': ['H350', 'H314', 'H314'],
                'Worst H4xx': ['H411', None, None],
                'Safety': [1, 5, 9],
                'Health': [4, 7, 7],
                'Env': [9, 9, 9],
                'Ranking Default': ['Recommended', 'Problematic', 'Highly Hazardous'],
                'Ranking Discussion': ['Recommended', 'Problematic', 'Highly Hazardous'],
                'Replacement Issues': [None, None, 'Carcinogenic'],
                'Replacement 1': ['Acetonitrile', 'Acetone', None],
                'Replacement 2': [None, 'Ethyl Acetate', None],
                'Replacement 1 Number': [7, 6, None],
                'Replacement 2 Number': [None, 23, None],
                'H3_phrase': ['May cause cancer', 'Causes severe skin burns and eye damage', 'Causes severe skin burns and eye damage'],
                'H4_phrase': ['Toxic to aquatic life with long lasting effects', None, None]
              })

The data can be added by:

from solvent_guide.add_solvent import add_solvent_from_dataframe

add_solvent_from_dataframe(solvent_df)

Removing solvents

Solvents can be removed using remove_solvent():

from solvent_guide.remove_solvent import remove_solvent

remove_solvent()

and following the prompt:

Please enter the CAS number for the solvent you wish to remove:

All added solvents can be removed by resetting the Solvent Guide. This can be done via:

from solvent_guide.reset_solvents import reset_solvents

reset_solvents()

THIS WILL DELETE ALL ADDED SOLVENTS AND REMOVE ALL CHANGES MADE TO THE DATABASE SINCE INSTALLATION.

You will be prompted to confirm this:

CAUTION! Resetting the database will revert all changes made since installation. Are you sure? (y/n)

Troubleshooting

In some cases, running the solvent guide via the command line has resulted in permission errors. These can be overcome by running with admin / sudo privileges.