I want to be able to quickly generate an organic compound and export it to SVG format. In particular I need to be able to draw polymer units with brackets. Is there an online tool for this?


My recently favorited online editor draw.io does sadly not support drawing organic or chemical compounds, but I looked at the list of Online Molecule editors and searched for one provided SVG export.

Maybe more than one support it, but I found one which does support SVG export (although it calls "SVG Image"), and that is the PubChem online molecule editor, which supports SMILES, SMARTS and InChI as well as all common chemical file formats.

The interface is a little dated, but it seems like it is possible to draw stuff rather quickly, and it does indeed export to SVG (Select "SVG Image" and hit the "Export" button"). Go try it out, and see if it suits you! If not, try out some of the alternatives from the list from Wikipedia linked at the top.

  • That's a very good editor, but a major feature is missing: polymer notation.
    – Sparkler
    Sep 1 '15 at 23:17
  • @Sparkler, HeHe... And I don't have a clue what you are talking about. :-) Do however please add that requirement to your question, so that other (more into organic compounds than me) might guide you.
    – holroy
    Sep 1 '15 at 23:19
  • @Sparkler, Have you tried any of the other in the list? The list is extensive, and does offer various options with regards to how to draw the compounds. As I don't entirely get your request, you might want to try them out for your self.
    – holroy
    Sep 12 '15 at 19:29

Currently I am working on a C#/.NET project where you you can give the name of an organic compound and the image of the compound will be generated.

The code of the console and WPF app can be found here https://github.com/thieupepijn/OrganicCompoundVisualizerWinApps

The library behind these apps can be found here https://github.com/thieupepijn/OrganicCompoundVisualizerLibraries

Export to SVG isn't supported yet, but mayby I will put it on my todo-list.

However if you are willing to do some coding, you could easily add this feature yourself.


I think you are looking for python + python-indigo, (documentation can be found here - at the time of writing the links with the github sources are broken).

  • Free & GPL
  • Input formats support: Molfiles/Rxnfiles v2000 and v3000, SDF, RDF, CML, SMILES, SMARTS.
  • Portability: Pre-built binary packages are provided for Linux and Windows (both 32-bit and 64-bit), and also for Mac OS X systems (both 10.5 and 10.6).
  • Molecule and reaction rendering. Best picture quality among all available products. Easy SVG support.
  • Automatic layout for SMILES-represented molecules and reactions.
  • Canonical (isomeric) SMILES computation.
  • Exact matching, substructure matching, SMARTS matching.
  • Matching of tautomers and resonance structures.
  • Molecule fingerprinting, molecule similarity computation.
  • Fast enumeration of SSSR rings, subtrees, and edge subgraphs.
  • Molecular weight, molecular formula computation.
  • R-Group deconvolution and scaffold detection. Pioneer work in computing the exact maximum common substructure for an arbitrary amount of input structures.
  • Combinatorial chemistry
  • Plugins support in the API. As a reference, see the Renderer plugin distributed together with the Indigo API.

Some examples can be found in the manual, actual files not uploaded because they are SVG which is not supported here: enter image description here

  • Is this an online tool like the OP is asking for?
    – holroy
    Sep 2 '15 at 6:33
  • Is there any public server that offers this as a service?
    – Sparkler
    Sep 2 '15 at 16:52

If you wish to draw such molecules yourself, rather than automatically, then you could use InkScape.

  • Free
  • SVG support - definitely
  • You can draw whatever you would like but it will not generate the drawing from the formula.
  • maybe if there was an inkscape extension that generates something initial from formula...
    – Sparkler
    Sep 2 '15 at 16:50

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