Getting started with Visual SmallMol

What we offer

You can compute molecular weight, logP (octanol–water partition coefficient), TPSA (topological polar surface area), and a Lipinski rule of five check from a SMILES string or by loading a structure. Results are deterministic and citable. You can also generate a 3D structure from SMILES, view it in-browser, and export SDF, PDB, or PNG. For many molecules at once, use Batch SMILES to get a table and optional CSV or a ZIP of PDF reports.

Typical workflow

1. Single molecule: Go to Molecular Properties, enter a SMILES (e.g. CCO for ethanol), and get MW, logP, TPSA, Lipinski, and a downloadable PDF report.
2. 3D view: Use SMILES to 3D to generate and view the structure; rotate, zoom, and export PDB or PNG. Or upload your own SDF/PDB in SDF Upload.
3. Many molecules: Use Batch SMILES to paste multiple SMILES and download a table (CSV) or a ZIP of PDF reports.
4. Validate SMILES: The SMILES Validator checks syntax and shows the structure; the same page offers unit conversions (mcg ↔ mg, etc.).

Tools at a glance

• Molecular Properties (MW/logP/Lipinski) — SMILES or structure → molecular weight, logP, TPSA, Lipinski rule of five, rotatable bonds. Export PDF.
• Batch SMILES — Multiple SMILES → table + optional CSV or ZIP of PDFs.
• SMILES Validator — Validate SMILES and common unit conversions.
• SMILES to 3D — Generate 3D from SMILES; view, measure, export PDB/PNG.
• SDF Upload — Load SDF or PDB; view and export.
• Conformer Preview — Multi-frame 3D demo.

Export options: Export (overview), Export formats (SDF, PDB, PNG, PDF), Batch export.

Docs and reference

• Descriptors explained — MW, logP, TPSA, Lipinski, rotatable bonds.
• Data sources — PubChem, ChEMBL, and standards we use.
• Tutorials — Step-by-step for Molecular Properties, Batch SMILES, 3D Viewer.
• API — Programmatic access for properties and 3D.

More questions? FAQ. About this site: About.