🧪 ForMileS — Formation of Mass SMILES

ForMileS (Formation of Mass SMILES) is a molecular graph generation engine built for systematic SMILES enumeration, mass-based filtering, and charge modeling.
It allows researchers to explore chemical space consistent with a given molecular formula, exact mass, and bonding rules using RDKit, while respecting valence and structural constraints.

Article for Details. Please consider citing it when using ForMileS: https://doi.org/10.1021/acsomega.5c08184

---

🔬 Key Features

• Automated Molecular Graph Expansion
  Expands molecular scaffolds recursively following valence rules, bond orders, and formula constraints.

• Charge Enumeration
  Assigns formal charges to symmetry-unique atoms according to allowed elements.

• Mass Filtering
  Retains only molecules within a specified tolerance of the target mass.

• Structure Visualization and Export

  • PNG and optional SVG 2D structure images with formula/mass annotation.
  • 3D coordinate generation (.xyz and .mol) using RDKit + UFF optimization.

• Parameter File (parameters.json)

  • Defines bond orders, max valence per element, and allowed chargeable atoms.
  • Easy to customize for different chemical systems.

• Optional GUI (gui.py)

  • Simple cross-platform Tkinter interface for defining formula, scaffold, charge, and export options.
  • Allows structure generation without command-line usage.

---

⚙️ Installation

Requirements

Library	Purpose
rdkit	Molecule construction, SMILES, and 3D optimization
pillow	Image annotation and export
tqdm	Progress visualization
psutil (optional)	Memory usage monitoring
tkinter	GUI interface (usually included with Python)

Install dependencies:

pip install rdkit-pypi pillow tqdm psutil