Chem-Reporter (MVP)

Windows-ready chemistry utility for resolving SMILES via PubChem and extracting melting points (°C). with a feature to visualize molecules

2D

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3D interactive

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Quick start (one click)

Recommended for new users (even without Python/Conda installed):

1. Download/clone this folder from GitHub.

2. Double-click: bootstrap_chem_reporter.bat

What the bootstrap does:

Detects (or installs) Miniforge in your user profile (no admin needed).

Creates/updates the chem-reporter conda environment from environment.yml.

Ensures the launcher works and creates a Desktop shortcut (supports OneDrive Desktop).

Starts the Unified Launcher GUI.

If Windows warns about execution policy, right-click the .bat → Run anyway.
The Desktop link will appear under your real Desktop path (often C:\Users\<you>\OneDrive\Desktop).

⚙️ Setup

Requires:

• Miniforge / Conda
• Windows 10 or 11
• Internet connection (for live PubChem)

Create the environment:

conda env create -f environment.yml
conda activate chem-reporter
copy .env.example .env

🚀 Usage

single compound (paste in the window and example molecule:CC(=O)OC1=CC=CC=C1C(=O)O)

scripts\run_app.bat

Batch (CSV list), example inside input folder

scripts\run_batch.bat input\test_molecules.csv

Unified launcher GUI

scripts\run_launcher.bat

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GUI launcher

• choose option manually or fetch CSV

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Manual

• paste a SMILES structure in the box and press search
• example SMILES: aspirin: CC(=O)OC1=CC=CC=C1C(=O)O

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Fetch a CSV

• in the folder: input you can find an example csv

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🧩 Output structure

Each compound folder includes:

results/<compound>/
  metadata.json
  melting_point.csv
  structure.sdf
  IUPAC.txt

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Using structure.sdf from the output visualize your molecules

• open visualize_molecule.ipynb and run the cells

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2D molecule

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3D molecule

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A global summary.csv aggregates all results.

🧪 Offline tests

Offline unit tests use cached PubChem JSONs (aspirin/caffeine) to verify parsing.

pytest

Project structure

chem-reporter/
  assets/
    icon.ico
  input/
    test_molecules.csv
  results/                   # auto-created by runs
  scripts/
    run_app.bat
    run_batch.bat
    run_launcher.bat
    run_batch.py
  src/
    app_gui.py               # GUI for single compound
    launcher_gui.py          # Unified launcher (Tkinter)
    pubchem.py               # network + parsing
    io_utils.py, rdkit_utils.py, models.py, config.py
  tests/
    data/                    # cached JSON (aspirin/caffeine)
    test_offline_parsing.py
  tools/
    make_shortcut.ps1
  environment.yml
  bootstrap_chem_reporter.bat
  README.md

Configuration

edit src/config.py

• TIMEOUT_SECONDS – HTTP timeout for PubChem requests
• USER_AGENT – sent with every request (keep it informative) logging is enabled in entrypoints>

import logging
logging.basicConfig(level=logging.INFO, format='[%(levelname)s] %(message)s')

Troubleshooting

• No Desktop shortcut appears: Your Desktop may be under OneDrive. The bootstrap targets the real path from
• PowerShell: [Environment]::GetFolderPath('Desktop'). Check that folder.
• “No module named src” running tests: Ensure tests/conftest.py exists and src/init.py is present.
• Icon not showing in taskbar: Tkinter sets the window icon; the taskbar may still show python.exe until packaging (post-MVP).

Conda not found: The bootstrap auto-installs Miniforge. If you prefer manual install, install Miniforge and re-run.

📦 Packaging

To make a portable version:

1. Zip the project folder with /scripts/*.bat and /assets/icon.ico

2. Optionally create a desktop shortcut via PowerShell script in tools/make_shortcut.ps1