Molecule

1. 01MDL Molfile, SDF, SMILES and MDL reaction files open as their own tab, drawn by RDKit
2. 02An SDF or SMILES file is a container: a Structure picker steps through every record it holds
3. 03Hydrogens drawn as the file wrote them, all of them, or none — three real conversions, not a display trick
4. 04Aromatic rings as a circle or as alternating Kekulé bonds
5. 05R/S and E/Z stereo annotations, atom indices, CoordGen re-layout and free rotation
6. 06SMARTS substructure highlighting, with a stated reason when a pattern cannot be parsed
7. 07Formula, net charge, average and monoisotopic mass, cLogP, TPSA, H-bond counts, rings, stereocentres, canonical SMILES, InChI and InChIKey
8. 08The file’s own data fields shown separately from the computed ones, because the two can legitimately differ
9. 09Reactions drawn whole — reactants, arrow, products — from a real MDL reaction file
10. 10The same viewer draws the file manager preview and the stage tab

Reading, layout and drawing are RDKit’s, through the toolkit’s own WebAssembly build, used as a library rather than reimplemented. Everything runs in your browser; nothing is uploaded. For the bundled molecules, the InChI, InChIKey, formula, net charge, monoisotopic mass, average mass and heavy-atom count computed here reproduce PubChem’s own published values exactly, for every record. The panel runs on @ports/chem, @ports/macromolecule.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Is my structure uploaded anywhere?

No. Everything is parsed and drawn in your browser from the copy stored in your project.

Why does the polar surface area not match the database I got this from?

Because TPSA is not one number. The default here counts nitrogen and oxygen only, following Ertl’s original table; several databases also count sulfur and phosphorus, which adds roughly 25 Ų per divalent sulfur. Both are correct under their own definition, and the readout names the one it is using. The same applies to hydrogen-bond acceptor counts, where no two definitions fully agree.

Why did the rotatable-bond count change when I switched hydrogens?

Because a rotatable bond is defined as a single, non-ring bond between two non-terminal heavy atoms — and a hydroxyl oxygen carrying an explicit hydrogen is no longer terminal. Published values assume hydrogens are implicit, which is the default here for exactly that reason.

Can I open a ChemDraw or Ketcher file?

Not yet. CDXML and KET are not read, and a file in either is refused with that reason rather than opening blank. InChI is also not readable as an input, though an InChI and its key are computed for anything that does open.

Can I edit the molecule?

No — this is a reader. It draws, measures and searches a structure; it does not modify it.

What does the SMARTS box do?

It highlights every match of a substructure query on the drawing. C(=O)N finds amide bonds, [OH] hydroxyls, c1ccccc1 a benzene ring. A pattern that cannot be parsed says so, and a valid pattern matching nothing reports no match rather than failing silently.