From One Structure to Five Variants in Seconds: Inside the Fragment Editor
The Fragment Editor lets you edit any region of a molecule directly or spin up IUPAC-named variants without redrawing anything. Here is how it works, using serotonin as the example.
Every medicinal chemist and every student who has spent time in a structure editor knows the ritual. You have a molecule. You want to know what happens if one substituent moves, or if the side chain gets one carbon longer, or if you swap a hydroxyl for an amine. So you redraw. Or you go hunting for the SMILES string, paste it into a text editor, make the change by hand, hope the syntax stays valid, and paste it back.
That ritual takes longer than it should. The Fragment Editor removes it.
The Fragment Editor in the creator series — serotonin, two editing modes, and five structural variants in under 45 seconds.
Why serotonin?
Serotonin — 3-(2-aminoethyl)-1H-indol-5-ol — is one of the most recognizable molecules in neuroscience. Almost everyone who has taken an introductory biochemistry or pharmacology course has seen the structure. That familiarity makes it a good teaching molecule: the person looking at it already has an intuition for what matters about it.
Serotonin (3-(2-aminoethyl)-1H-indol-5-ol) — the starting structure for the Fragment Editor demo.
What makes it especially useful for a Fragment Editor walkthrough is that it has three structurally meaningful regions that are easy to reason about independently: the indole ring system, the 2-aminoethyl chain hanging off C-3, and the 5-hydroxy group. Change any one of them and you get a compound with meaningfully different biology. That kind of systematic variation is exactly what the Fragment Editor is designed for.
Two modes, one tool
The Fragment Editor opens alongside the molecule on the canvas and gives you two ways in.
SMILES region editing
In the first mode, the tool breaks the molecule's SMILES string into color-coded segments — each segment corresponds to a region you can click and modify. For serotonin, the three regions light up in amber and blue directly over the SMILES string. Click the aminoethyl segment and you can change it in place. Click the ring-closure tokens and edit the ring. The structure updates as you change the segment; you never have to parse the full string yourself.
This is the mode for people who are comfortable with SMILES and want surgical control. You are not typing a new molecule from scratch — you are operating on a specific piece of one that already exists on your canvas.
IUPAC variant exploration
The second mode is for people who think in names rather than strings, and for anyone exploring structure-activity relationships systematically. You enter the IUPAC name of your molecule and click Resolve. The tool returns the canonical structure, confirms the SMILES, and then generates a set of suggested variants — organized by what changed.
For serotonin, the variant chips the tool generates are:
Chain length — 3-(2-aminopropyl)-1H-indol-5-ol: one extra carbon on the aminoalkyl chain, the same modification that moves you toward tryptamine chemistry.
Chain length — 3-(2-aminobutyl)-1H-indol-5-ol: a two-carbon extension, pushing further into a different lipophilicity and receptor geometry territory.
Functional group — 3-(2-aminoethyl)-1H-indol-5-amine: the 5-hydroxy replaced by a primary amine. Same scaffold, different hydrogen-bond donor character.
Position — 3-(2-aminoethyl)-1H-indol-2-ol: the hydroxyl moved from the 5-position to the 2-position on the indole, a change that substantially alters the electron distribution in the ring system.
Position — 3-(2-aminoethyl)-1H-indol-4-ol: the hydroxyl at the 4-position, adjacent to the nitrogen-containing ring junction.
Each chip is one click. The structure for that variant loads onto the canvas immediately. No new drawing, no SMILES lookup.
What this looks like in practice
Picture a graduate student working through a structure-activity relationship assignment. The question is: how does moving the hydroxyl group on a 5-hydroxyindole scaffold affect the predicted properties? They have serotonin drawn on the canvas from a earlier step in the lesson.
Without the Fragment Editor, answering that question means drawing three new structures — one for each position — or finding the SMILES for each isomer, validating them, and importing them one at a time. That takes ten to fifteen minutes and leaves room for errors.
With the Fragment Editor, the student opens the tool with serotonin already selected, switches to IUPAC mode, hits Resolve, and then clicks the position-variant chips. Three structures are on the canvas in under two minutes. The rest of the session can be spent analyzing the differences, not generating them.
The Fragment Editor in the generator — open it from the left toolbar while any molecule is selected.
For researchers: the same tool, a different workflow
Researchers use the Fragment Editor differently from students. The typical pattern is not exploration from scratch — it is rapid iteration on a lead structure. You have a compound that hits a target. You want to know how the potency profile changes when the chain length shifts, or when a hydrogen-bond acceptor moves. The SMILES region editor is the right mode here: precise, fast, and operating directly on the validated structure already in your canvas.
The key behavior is that the edited structure is placed back onto the canvas as a new molecule object, so your original stays untouched. You build up a canvas of variants side by side, which pairs naturally with the AI generation tools for visual comparison.
How to open it
Draw or create a molecule on the canvas — or open the Generator, which starts with a molecule ready to edit.
Select the molecule by clicking it.
Open the Fragment Editor from the left canvas toolbar — it is the icon below.
Choose SMILES mode for region editing or IUPAC mode for name-based variant generation.
Interactive preview — swap substituents and stereocenters without redrawing the scaffold.
The Fragment Editor icon on the generator canvas toolbar. Available whenever a molecule is selected.
Open the Generator →