Bondline

Bondline: How to play

Bondline turns a real molecule into a connect-the-pieces puzzle. Every atom in that molecule becomes a draggable "group" you have to wire back together correctly to reform the molecule.

The rules

1. Groups and cells

Each atom becomes a group: a horizontal strip of one or more numbered cells. Each cell is one bond slot that still needs a partner.

2. The number tells you what to look for

A cell's number is the size (chemical valence) of the atom you must connect it to (not the size of its own group).

Element	Size(s)
Hydrogen (H)	1
Fluorine, Chlorine, Bromine (F, Cl, Br)	1
Oxygen (O)	2
Sulfur (S)	2, 4, or 6
Nitrogen (N)	3
Phosphorus (P)	3 or 5
Carbon (C)	4

Sulfur and phosphorus can appear at more than one size, depending on how many bonds that particular atom has in the molecule.

3. Colors tell you which element, not just which size

Since several elements can share the same valence number (e.g. Oxygen and a divalent Sulfur are both "2"), color does the disambiguating:

• A cell's frame/border is colored by the element that cell belongs to.
• A cell's number is colored by the element that cell is looking for.

Color	Element
	Carbon (C)
	Nitrogen (N)
	Oxygen (O)
	Hydrogen (H)
	Sulfur (S)
	Phosphorus (P)
	Fluorine (F)
	Chlorine (Cl)
	Bromine (Br)

4. Double and triple bonds

A double or triple bond shows up as two or three adjacent cells sharing the same number; only the first cell shows the number, the rest show *. To complete it, you need a matching number of * on the partner group. You don't have to wire every cell by hand: connecting one cell of the run automatically completes the rest, as long as it's genuinely the right partner.

5. Making a connection

Drag from the small dot on one cell to a dot on another cell. The connection turns green if it's valid (right size, right element, and, when substitution rules are active, the right substitution match too) or red if it isn't.

7. Winning

You win once every cell in every group is connected and every connection is valid. The game then compares your finished structure to the original molecule:

• "Solved!": you rebuilt the exact same molecule.
• "Valid structure, but different": everything you built is chemically legitimate, but it isn't the molecule you started from. This can happen on puzzles with symmetric or interchangeable groups, where more than one arrangement is technically valid.

Checkpoints (Medium/Hard difficulty only)

On Medium/Hard puzzles, you don't have to risk a full restart every time you're unsure about a move. Set checkpoint saves a snapshot of exactly how your workspace looks right now; you can keep up to 5 at a time. Restore checkpoint shows you a list of your saved snapshots; picking one jumps the workspace straight back to it, undoing anything you did after that point.

A good habit: save a checkpoint before trying a connection you're not fully sure about. If it turns out wrong, restore instead of untangling or redoing everything by hand. Note that Reset puzzle deletes all of your saved checkpoints along with the rest of your progress; you'll get a warning first if you have any saved.

Tutorial: your first puzzle

The app opens with formaldehyde (CH₂O) already loaded: a good first example, since it uses every core mechanic at a small scale.

1. Look at the sidebar. You'll see one Carbon group with four cells: two showing a red "2" (one of them starred) and two showing a gray "1". Read that as: "this Carbon needs a double bond to something size-2-and-red (Oxygen), plus two single bonds to something size-1-and-gray (Hydrogen)." There's also an Oxygen group with two cells showing a gray "4" (again one starred): Oxygen wants a double bond to a size-4, gray (Carbon) partner.
2. Drag the Carbon group into the workspace.
3. Drag the Oxygen group next to it. Connect one of Carbon's red "2" dots to one of Oxygen's gray "4" dots. Since it's a genuine double-bond match, the second connection completes itself automatically.
4. Hydrogens don't appear in the sidebar: they're considered trivial and are handled separately. Once everything else is placed and valid, a "Connect remaining hydrogens" button appears above the workspace; click it and both Hydrogens are placed and wired in automatically.
5. Once every cell is connected and valid, the win banner appears at the bottom: "Solved!"

From here, open New puzzle to select random puzzles from various difficulties or submit a molecule yourself using the trivial name or a SMILES string.

Tools quick reference

Button / control	What it does
New puzzle → 🎲 Random molecule	Immediately picks a random curated molecule, any difficulty
New puzzle → Select difficulty	Reveals a difficulty picker; choosing one searches for and loads a random curated molecule of that difficulty
New puzzle → Submit molecule	Reveals a search box; builds a puzzle from a SMILES string or a common compound name you enter
Connect remaining hydrogens	Appears once everything else is validly connected; auto-places and wires all leftover Hydrogens
Clean up	Automatically re-arranges the groups you've placed into a tidy, untangled layout
Reset puzzle	Sends every group back to the sidebar and clears connections: same molecule, fresh start (also clears any saved checkpoints, with a warning first)
Set checkpoint / Restore checkpoint	(Medium/Hard puzzles only) Save a snapshot of your current progress and jump back to it later (see "Checkpoints" above)
Hint	Gives progressively stronger hints (see below)
"✓ Substitution rules" label	Appears only on Medium/Hard puzzles, where substitution-dot clues are included
Difficulty badge	Auto-computed rating (Easy / Medium / Hard) based on molecule size and how many valid arrangements it has
"Number of solutions" label	How many distinct, valid ways this puzzle's groups could legitimately fit together (using whichever substitution-rules mode is active for its difficulty). A number followed by "+" means there are at least that many; the search stops counting past a certain point rather than running indefinitely
Mouse wheel over the workspace	Zooms in/out, handy on large molecules
Ctrl/Cmd + drag a group	Pulls just that one group out of an already-connected cluster, instead of dragging the whole cluster

The Hint button

Each click gives you one more, stronger hint than the last (earlier hints stay visible):

1. Ring info: how many rings the target molecule has, their sizes, and whether it's aromatic.
2. Start here: highlights the least ambiguous unplaced group in the sidebar in yellow.
3. Free connection: picks a random bond that should exist between two groups you've already placed and makes it for you (shown in yellow). If nothing is placed yet, it'll ask you to place a group first, then try again.

Tips & strategies

• Start with your most distinctive group. A group with an unusual size, or a lot of substitution dots, has fewer possible partners, so there's less guessing. This is exactly what the second-stage hint highlights for you.
• Match by number first, then confirm by color. If two candidates both show "2", the number color tells you which one is actually Oxygen and which is Sulfur.
• Use "Clean up" liberally. A tangled layout with crossing lines is hard to reason about, so clean it up whenever it gets messy.
• On harder puzzles, set a checkpoint before an uncertain move. If it turns out wrong, restore instead of starting over.
• "Valid but different" isn't necessarily a mistake in your logic: it usually means two interchangeable-looking groups got swapped somewhere. Look for two same-size, same-substitution groups and try trading their positions.
• Use the ring hint to picture the shape before you start wiring up a ring-containing molecule: knowing "one 6-ring and one 5-ring, aromatic" tells you roughly what you're building toward.
• Zoom out on sprawling molecules to see the whole layout while you work.

By Alexander Hübner