I. Overview

This website/software integrates JSME and RDKit into one workflow:

• Draw molecular bond-line structures in the JSME editor.
• Enter SMILES manually in the input box.
• Query known compounds (for example, from PubChem) and display compound name and basic properties.
• Generate RDKit 2D depiction and 3D ball-and-stick model.
• Enumerate multiple 3D conformers (if available) for the same molecule.
• Visualize stereocenters (chiral carbon atoms) for easier stereochemistry interpretation.

II. JSME Molecular Editor Introduction

JSME (JavaScript Molecule Editor) is a lightweight web-based molecular structure editor used for drawing atoms, bonds, rings, and common functional fragments. In this project, JSME is used as the molecular input front end.

III. Interface and Toolbar Guide (Figure 1)

Figure 1 labels the JSME drawing area and toolbar items. The numbered annotations (1-25) correspond to buttons commonly used in structure drawing.

A. Frequently used core tools

• 4: Delete mode (click atoms/bonds to remove).
• 6 / 7: Undo / Redo.
• 11: Stereo bond tools (solid wedge / hashed wedge / wavy bond).
• 12 / 13 / 14: Single / Double / Triple bond.
• 15: Fast continuous bond drawing.
• 16-22: Ring shortcuts (3-membered to 8-membered, including benzene).
• 24 / 25: Common atom list and custom bracket atom input.

B. Less frequently used controls

• 1: Show current SMILES in the drawing panel.
• 2 / 3: Clear drawing / start a new disconnected component.
• 5: Toggle allowed charge state on selected atom.
• 8: Spiro ring option for next ring placement.
• 9: Move selected atoms for layout adjustment.
• 10: Version/help information.
• 23: Functional group menu (also available by right-click).

IV. Conversion Area and Main Workflow (Figure 2)

Figure 2 shows the lower operation area where drawing input, manual SMILES input, and RDKit analysis are connected.

Recommended workflow

1. Input molecule by either drawing in JSME or typing a SMILES string manually.
2. If you draw first, click Show SMILES to get the generated SMILES text.
3. Click Analyze (RDKit) (or the Analyze button next to Manual SMILES input) to process the molecule.
4. Review returned compound information (name/status/formula/exact mass when available).
5. Compare the RDKit 2D depiction with the 3D ball-and-stick model.
6. Use conformer navigation (for molecules with multiple conformers) to compare 3D geometries.
7. Click Add Label to show atom indices and inspect stereocenters more clearly.

V. Notes on Stereochemistry and Conformers

• Configuration (chirality) and conformation are different: chirality concerns stereocenter assignment; conformers are different 3D shapes mainly caused by bond rotation.
• For chiral molecules, check consistency across SMILES stereo marks, 2D wedge/hash depiction, and 3D labeled model.
• The tool is intended to make this cross-check straightforward for learning and for practical structure validation.

VI. Quick Reference

Input (JSME draw / Manual SMILES) -> Analyze -> Name & properties -> 2D depiction -> 3D model -> Conformer check -> Stereocenter labeling