Chemical Editor

Open the editor and keep your work

• File > New opens an empty Chemical Drawing Editor. Draw directly or use Add Structure…. Save to Managed Repository… stores the drawing as a managed chemistry entry.
• Add Structure… is also available while editing an existing molecule or reaction and in the query editor. Choose a structure from the Molecule Browser, select a structure file, or enter a supported chemical name or structure text. Click or tap the canvas to place the addition alongside the existing drawing. Undo removes the addition; cancelling leaves the drawing unchanged. Browser and file selections copy their content into the draft. Whole reactions retain their roles and layout, but cannot be used as molecule-search queries.
• From an existing document, Draw Structure or Draw Reaction opens a staged edit in its own movable, resizable Mac window. Drag the title bar to reposition it. The top and bottom tool strips wrap into additional rows between button groups at narrow widths, keeping all toolbar controls visible at their normal size; the inspector scrolls vertically, and Cancel and Use Structure (or Use Reaction) remain at the bottom. Use Structure or Use Reaction updates the source document; Cancel or closing the editor leaves it unchanged. Reopening the editor brings the existing draft forward. Closing the source document also closes its editor. Save or export the updated document when you want to keep a copy.
• Search by Query Structure opens the same editor for a repository molecule search. Choose Similarity or Substructure and Search. Searching does not save the query as a repository entry.
• On iPad, choose New > Draw Structure in Library or Add > Draw New Structure in a document. Cancel discards the draft; Use Structure opens the new document. Tap and drag replace Mac mouse interaction; source and drawing editors remain separate from the document canvas.

Editor layout

The editor has three main areas:

• Toolbar: choose what the mouse or trackpad does next, such as select, draw an atom, draw a bond, place a ring, or erase.
• Canvas: the large drawing area. Click or drag here to place atoms, bonds, templates, and reaction marks.
• Inspector: the panel on the right. It shows atom and bond counts, formula, mass, valence checks, selection actions, cleanup tools, and detailed properties for the selected atom or bond.

Basic drawing workflow

1. Start with carbon. Carbon is the usual starting atom for organic structures, and the editor uses carbon by default.
2. Choose an element when needed. Use the element menu to switch from carbon to oxygen, nitrogen, sulfur, chlorine, or another common element before placing an atom.
3. Draw bonds between atoms. Choose the bond tool and click or drag from one atom to another. Use the bond order menu for single, double, triple, or aromatic bonds.
4. Use templates for common shapes. Ring and chain tools quickly place structures such as a carbon chain, cyclohexane, or benzene.
5. Clean up the layout. If the drawing looks crowded or uneven, use Clean Up in the inspector to improve the 2D layout without changing the chemical connections.
6. Run the search or continue editing. In query search, choose Substructure or Similarity, then click Search.

Tool groups

Atom and bond properties

Select one atom or bond to edit its details in the inspector.

• Atom label and element: change a carbon atom to another element, or type a label such as Cl, N, or O.
• Charge: add or remove formal charge with the charge tools or the atom inspector. For example, ammonium nitrogen is often positive.
• Isotope, radical, valence, and explicit hydrogens: use these only when you know the structure needs them. For most simple drawings, automatic hydrogen and valence handling is enough.
• Bond order: choose single, double, triple, or aromatic. A double bond means two shared electron pairs; an aromatic bond is used for aromatic rings such as benzene.
• Stereo bonds: wedge and hash bonds show a bond pointing out of or behind the page. Use them when stereochemistry matters.

Query tools for searching

Query tools describe what is allowed in a search, rather than drawing one exact atom or bond. They are useful when you know the pattern you want but not every detail of the result.

• Query Atom can mean "any atom", "any hetero atom", a generic group, or a list of allowed or excluded elements.
• Query Bond can allow more than one bond type, or require that a bond is in a ring or in a chain.
• Aromaticity and Topology options can say whether an atom or bond should be aromatic, aliphatic, in a ring, or in a chain.
• Use exact atoms and bonds when you need precise matches. Use query atoms and query bonds when you want broader search results.

Reaction tools

Reaction drawings combine structures with reaction marks.

• Reaction arrow: shows the direction from reactants to products.
• Reaction plus: separates multiple reactants or products.
• Reaction minus: marks subtraction-like reaction notation when needed.
• Atom Map: adds map numbers so the same atom can be followed from reactant to product. This is useful for reaction analysis, but it is optional for simple drawings.
• Reaction role: when a selection can be assigned a role, the inspector can mark it as reactant, product, agent, catalyst, condition, or solvent.

Checking your drawing

The inspector helps you catch common mistakes before using the drawing for search or export.

• Atoms and Bonds show the size of the drawing.
• Formula and Mass update when AtomLens can calculate them.
• Implicit H counts hydrogens AtomLens adds automatically. In line drawings, carbon hydrogens are often implied rather than drawn explicitly.
• Valence and Validation warn when an atom has too many or too few bonds for normal chemistry.
• Aromatize and Dearomatize switch suitable ring systems between aromatic and alternating-bond forms.
• Save Template stores a selected fragment so you can reuse it from the template menu later.

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