Molecule Studio

Draw a structure the way you would at a whiteboard — bonds, rings, charges — with the formula and the SMILES derived live from what you draw.

A molecule in Quodra is a real structure, not a picture. Atoms carry an element, a position and a charge; bonds carry an order and a wedge or hash. Molecule Studio is the full-screen editor over that graph: a left rail of atoms and rings, a canvas, an inspector that reads out the formula and the SMILES, and a status bar that tells you what the current tool will do next.

Everything is 2-D and nothing is energy-minimised. What you draw is a diagram with real connectivity — which is exactly what a slide needs.

Two ways in#

• From a slide. Insert → Molecule. It arrives as caffeine, so there is something to look at. In the inspector, press Draw in Molecule Studio — or just double-click the structure on the canvas — and the studio opens over your deck. Once a structure has been drawn the button reads Edit structure.
• From the dashboard. In the sidebar, Studio → Molecule Studio opens your library. New molecule offers Blank ("Start from an empty canvas") and six starters: Benzene, Caffeine, Aspirin, Ethanol, Glucose and Pyridine. Each starter shows the SMILES it is built from, and is imported into an editable structure on creation.

The two are not the same document. A molecule opened from a slide edits that object; a molecule in the library is its own stored document with its own name, autosave and sharing.

The workspace#

Across the top bar, left to right:

• A back button — Library when you came from the library, Deck when you opened the studio over a slide.
• The molecule name, editable in place. Enter commits it, Esc puts the old one back, and a blank name is treated as a slip rather than an instruction.
• The save state, on a library molecule only: Saving…, Saved, Save failed, or Reloaded.
• The formula, in Hill order, updating as you draw. An empty canvas reads empty.
• The tools, then Undo and Redo.
• On a shared library molecule: who else is here, Comments, and Share.
• Fit and Done.

The left rail has two sections. Atoms is the element palette — C, N, O, S, P, F, Cl, Br, I, H, B, Si — each button tinted with that element's colour and captioned "click empty to place, an atom to change it". Rings & templates holds the six ring templates, each captioned "drop on empty space, or on a bond to fuse".

The canvas highlights whatever a click would hit, so it is always clear whether you are about to touch an atom or the bond beside it. The zoom control sits bottom-right with Zoom out, a percentage, and Zoom in; the wheel zooms about the pointer, between 25% and 600%. F fits the whole structure in view.

The status bar at the foot always says what the selected tool does, and counts the atoms and bonds you have drawn.

Drawing#

Bonds#

The Bond tool (B) is the workhorse. Its status line reads "Draw bonds — click to start, drag from an atom to extend, click a bond to change its order".

• Click empty space to start a chain. A carbon appears and a bond opens from it.
• Drag from an atom to aim a new bond. A free end snaps to thirty-degree increments at one bond length, so chains come out looking drawn rather than dragged.
• Drop on another atom to bond the two directly. A bond that already exists is left alone, and an atom cannot bond to itself.
• Click an atom to grow a bond into its most open direction — the bisector of the widest gap between the bonds it already has. This is how methyls go on fastest.
• Click a bond to raise its order: single, then double, then triple, then back to single.

Elements#

Pick an element from the left rail, or press C, N, O, P or S for the common ones.

• Click empty space to drop a new atom of that element.
• Click an existing atom to change what it is. Aromatic flags survive the change, so turning one carbon of a benzene ring into nitrogen gives you pyridine.
• Drag from an atom to draw a bond to a new atom of the selected element.

Heteroatoms draw their implied hydrogens — OH, NH₂ — from a small valence table adjusted for charge. Carbon draws no letter at all unless it is charged, isotopically marked, or floating unbonded, which is why a methyl appears simply as a short line.

Elements outside the palette are not offered in the rail. The renderer will still draw any element it is given; it just draws it in ink and implies no hydrogens.

Rings and templates#

Six templates: Benzene, Cyclohexane, Cyclopentane, Cyclobutane, Cyclopropane and Cycloheptane. 6 selects benzene.

• Click empty space to drop a free ring — a regular polygon with side one.
• Click a bond to fuse a ring onto it. The new ring shares that edge and grows on the side away from the rest of the molecule, so a fused system comes out on the correct side without being dragged there.

Benzene is the aromatic template: its bonds are aromatic and its atoms are flagged as such. Fusing benzene onto an existing bond makes that shared bond aromatic too. The other templates are plain saturated rings — raise their bond orders with the Bond tool if you want a Kekulé drawing.

Charges, stereo and erasing#

• Add + charge and Add − charge — click an atom to shift its formal charge by one. Charges show beside the atom label, and are written into the SMILES as bracket atoms.
• Stereo bond (wedge / hash) — click a bond to cycle wedge → hash → plain, for what points at you and what points away. Setting a stereo bond also sets that bond's order to single.
• Erase — click an atom to delete it along with every bond that touched it, or click a bond to delete just the bond.

Moving, selecting, deleting#

Select & move (V) is the pointer.

• Drag an atom to move it; drag a bond to move both of its atoms together.
• Shift-click atoms to add them to, or take them out of, the selection.
• ⌫ or Delete removes the selected atoms and their bonds.
• Clicking empty canvas clears the selection; dragging empty canvas pans the view.
• Esc cancels a drag that is in progress rather than committing a stray edit. Press it again to clear the selection.

A move is previewed while the pointer is down and committed once, on release — so dragging a fragment across the canvas costs one undo step, not fifty.

The inspector#

The right panel shows Structure: the Formula, the Atoms count, the Bonds count, and the SMILES derived from what you have drawn. The SMILES box is a readout — click it and the whole string selects, ready to copy.

Select exactly one atom and a Selected atom section appears: its Element, a Charge stepper, and a Set to row of quick elements — C, N, O, S.

See SMILES and structure data for what the written string does and does not carry.

Undo, saving and the library#

Undo is ⌘Z, redo is ⇧⌘Z or ⌘Y, and the toolbar buttons grey out when there is nothing to undo or redo. Keyboard shortcuts are ignored while you are typing in a text box, so the name field never eats a B.

Where the edit lands depends on how you opened the studio:

• Over a slide, every commit is an object update on the deck. The deck's own history and autosave own the studio — ⌘Z in the studio is the deck's undo, and there is no second save to reconcile.
• From the library, the molecule is its own document with its own history. Edits are saved a moment after you stop drawing, into this browser's storage and — when you are signed in — to your account, so the molecule follows you between devices.

Library cards show the molecule's name, its atom count and when it last changed. The delete button asks first. Done flushes any pending save before it closes.

A molecule drawn on a slide can graduate to the library at any time with Save to library in the slide inspector, which copies the current structure into a new stored document and opens it.

Sharing, presence and comments#

A library molecule shares like any Quodra document. Share, add people by email as Can edit or Can view, and work in it together:

• Everyone present appears in the top bar, with live cursors on the canvas.
• Comments anchor to an atom. Select an atom and the composer offers "Comment on the selected object…"; the thread stays attached to that atom, and it follows if the atom moves. Unresolved threads show as a numbered pin on the atom itself.
• Can view gets a read-only editor — the tools do nothing, the name is fixed, and dragging only pans.

Saves are revision-checked. When two people save at once the studio merges their work rather than letting one overwrite the other; only when merging repeatedly fails does it adopt the server's copy and say Reloaded instead of quietly forking.

A molecule embedded on a slide needs none of this — it is part of the deck, and rides the deck's own collaboration.

On the slide#

The drawn structure uses the same renderer in the editor and previews. Image and PDF exports capture its appearance at the selected resolution; PowerPoint uses an image capture where available, with a placeholder fallback. Shared links show the read-only slide viewer. See Import & export.

The slide inspector styles it:

• SMILES — the string form. See SMILES and structure data for how this field behaves once a structure has been drawn.
• name and Show name — the caption under the structure.
• Atoms — Colour for conventional heteroatom hues, or Ink to match the paper.
• Hydrogens — Implicit or Explicit. This applies to a molecule that is still only a SMILES string; a drawn structure always labels the hydrogens its heteroatoms imply.

If a typed SMILES cannot be read, the object says "Couldn't read that structure" and points at the inspector; fix the string and it redraws.

Keyboard#

Next#

• Tutorial: caffeine, from ring to slide — the whole path, one step at a time.
• SMILES and structure data — what the string carries, honestly.
• Collaboration — sharing, presence and comments across Quodra.