chemfig and MolDraw: Paste chemfig, Edit It Visually, Export LaTeX

Who this is for

chemfig is the standard way to draw molecules inside LaTeX. The output is beautiful and it lives in the same file as your text, but writing it is slow. You type -[:30] and =[::-60], compile, look, and adjust an angle. Fixing someone else's chemfig is harder still, and a curly arrow in \chemmove can take many attempts.

MolDraw now reads and writes chemfig. You keep chemfig as your format and use a canvas for the drawing:

• See what a chemfig snippet draws without compiling.
• Fix it with the mouse: move an atom, flip a double bond, add a charge or a curly arrow.
• Get chemfig back that compiles with pdflatex, with the same angles you see on screen.
• Start from other formats (SMILES, MOL, ChemDraw files, a compound name) and get chemfig out.

Everything runs in your browser. Your code is not sent to a server to be converted.

Paste chemfig onto the canvas

1. Copy the code from your editor or Overleaf. A single \chemfig{…}, several of them, a \schemestart … \schemestop block or a complete document all work.
2. Open the MolDraw editor, click an empty part of the canvas and press Ctrl+V (Cmd+V on a Mac). You can also use the Paste button or right-click → Paste.
3. The drawing appears selected, beside anything already on the canvas. Drag it where you want it.

Try it with this scheme:

\schemestart
  \chemname{\chemfig{*6(=-=-=-)}}{benzene}
  \+
  \chemfig{Br-Br}
  \arrow{->[FeBr$_3$][CH$_2$Cl$_2$]}
  \chemname{\chemfig{*6(=-=(-Br)-=-)}}{bromobenzene}
\schemestop

MolDraw keeps the bond angles and lengths you wrote, so the drawing has the same shape as your PDF. Labels such as H_3C, NH_2 or {CO_2Me}, charges, lone pairs from \lewis or \charge, and @{name} nodes all carry over.

Edit it like any drawing

The pasted drawing is a normal MolDraw structure, so every tool works on it:

• drag atoms, or select a group and rotate it;
• hover a bond and press 1, 2 or 3 to make it single, double or triple, and click a double bond with the double-bond tool to move its second line to the other side;
• add charges, lone pairs and radicals from the toolbar or the right-click menu;
• draw curly arrows and fish-hooks with the arrow tool. They attach to lone pairs, bonds and charges and stay attached when you move atoms;
• edit the text above and below a reaction arrow by double-clicking it.

You also get the chemistry checks that chemfig cannot give you: valence warnings, the formula and mass, SMILES, and a 3D view of each structure.

Export chemfig back to LaTeX

There are two ways out:

• Download → chemfig (.tex) saves a complete, standalone LaTeX file. Compile it on its own to get a PDF of the drawing, or include that PDF in your document with \includegraphics.
• Copy as chemfig (LaTeX) (in the Copy menu and in the right-click Copy as menu) copies only the drawing code, with no \documentclass. Paste it straight into your thesis or paper.

For copied code, add these two lines to your preamble once:

\usepackage{chemfig}
\usetikzlibrary{arrows.meta,decorations.pathmorphing}

If a drawing has curly arrows or polymer brackets, compile twice. chemfig draws those from positions it saves in the first run. If you select part of the canvas first, only the selection is exported.

What the exported code looks like

This is the file MolDraw writes for the SN2 scheme in the first screenshot:

% Exported from MolDraw — compile with pdflatex / lualatex (twice: arrows and brackets use positions from the first run)
\documentclass[border=22pt,varwidth=60cm]{standalone}
\usepackage{chemfig}
\usetikzlibrary{arrows.meta,decorations.pathmorphing}
\begin{document}
\setchemfig{+ sep left=2em, + sep right=2em, arrow offset=6pt}
{\centering \textbf{SN2 of bromomethane}\par}
\par\bigskip
\schemestart
  \chemname[2em]{\chemfig{@{a1}HO^{-}}}{hydroxide}
  \+
  \chemname[2em]{\chemfig{@{a2}-[@{b1}:90]@{a3}Br}}{bromomethane}
  \arrow{->[SN2][acetone]}
  \chemname[2em]{\chemfig{-[:90,,,1]OH}}{methanol}
  \+
  \chemfig{Br^{-}}
\schemestop
\chemmove{
  \draw[-{Stealth[length=4pt,inset=1.5pt]}]([shift={(1.07em,0.77em)}]a1) to[bend right=47] ([shift={(-0.39em,-0.23em)}]a2);
  \draw[-{Stealth[length=4pt,inset=1.5pt]}]([shift={(0.21em,-0.36em)}]b1) to[bend right=77] ([shift={(0.64em,-0.23em)}]a3);
}
\end{document}

A few things to notice:

• Bonds use absolute angles (-[:90]), so each bond points the same way as on the canvas. A bond that is not the standard length gets a length factor such as -[:30,1.2].
• Atoms and bonds that a curly arrow touches get node names (@{a1}, @{b1}). \chemmove draws each arrow between them, with a bend angle that matches the curve on the canvas.
• Compound names sit under the structures, with room left for curly arrows that bow underneath.
• Ring bonds are closed with hooks (?[a]), and each double bond gets =^ or =_ so its second line is on the same side as in MolDraw, inside the ring for rings.

Get chemfig from SMILES, MOL or ChemDraw files

Because MolDraw reads many formats, it also works as a converter to chemfig:

1. Bring the structure in: paste SMILES or InChI, search a compound name in the PubChem box, or open a MOL, SDF, RXN, CDXML or CDX (ChemDraw) file.
2. Tidy it if needed. Clean-up and rotation are in the toolbar.
3. Choose Download → chemfig (.tex).

This is the quickest way to move a set of ChemDraw figures into a LaTeX thesis: open each file and download it as chemfig.

Reaction mechanisms and curly arrows

Curly arrows are the hardest part of chemfig to write by hand. In MolDraw you draw them with the mouse, or ask the AI assistant to draw a mechanism, and the export writes the @{…} names and the \chemmove block for you.

When you paste chemfig that already has \chemmove arrows, MolDraw reads which atoms or bonds each arrow joins. It then places the arrow by its own drawing rules: the tail starts on the lone pair, charge or bond, and the head stops just short of its target. You do not have to copy the exact TikZ curve.

For complete worked examples, see the chemfig mechanism samples: radical chain reactions with fish-hooks and multi-step polar mechanisms, each as a .tex file you can download.

Ask the AI assistant

The chat assistant in the editor knows chemfig. For example, you can ask:

• “Export this as chemfig.” It returns the code for what is on the canvas.
• “Draw this: \chemfig{H_3C-C(=[:60]O)-[:-60]OH}.” It puts the structure on the canvas.
• “Draw the mechanism of acid-catalysed ester hydrolysis, then give me the chemfig.”

What carries over in both directions

Each item below is exported, compiled with pdflatex, read back into MolDraw and checked against the original drawing.

When you paste, MolDraw also understands \definesubmol with !{name}, a starting angle such as \chemfig{[:30]…}, invisible bonds (draw=none), arrows at an angle such as \arrow{->}[-90] (the next compound goes below), \subscheme, and colour names such as red and blue.

What chemfig cannot hold

Some things on a MolDraw canvas have no chemfig form: pasted images, shapes and lab glassware, freehand strokes, orbitals, ring fills and highlights. They are left out of the export, and the hint bar tells you what was left out after each download or copy, so nothing disappears without notice.

Curved or S-shaped scheme arrows become straight chemfig arrows. Text placed beside the drawing (not above or below it) is kept as a % comment in the file.

chemfig quick reference

The pieces of chemfig syntax you will meet most often, and what MolDraw draws for each:

Troubleshooting

• Nothing happens when I paste. The text must contain \chemfig or \schemestart. Click the canvas first, so the paste goes to the drawing and not to a text box.
• Curly arrows are in the wrong place in the PDF. Compile a second time.
• “I do not know the key /tikz/Stealth”. Add \usetikzlibrary{arrows.meta,decorations.pathmorphing} to your preamble.
• A structure looks squashed after pasting. If the chemfig puts two atoms on the same spot, MolDraw lays the structure out again and says so in the hint bar. Use the clean-up button to tidy it.
• “B” or “D” turned into boron or deuterium. MolDraw reads atom labels as chemistry. Placeholder letters from the chemfig manual are read as elements where one exists.

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