COordinates of Small MOleculeS (COSMOS) is a high-throughput method to predict the 3D structure of small molecules from their 1D/2D representations.

You can download COSMOS and the open crystallography structure library here (requires python 2.7.1, OEChem TK, and Szybki TK).

An older version of COSMOS that uses data from the CSD can be found at

  1. Select an input format.
  2. Enter up to 1000 molecules by clicking "browse" and select the corresponding formatted file that you wish to upload. Alternatively you can paste the corresponding formatted molecule[s] straight into the text area.
  3. Select a format you wish as output.
  4. Type in how many isomers you would like to have for each molecule, valid options are integers 1-64, and then click the submit button.
  5. Access your predicted models using the link in your results email.

Just paste here: