Software to find similarity of two molecules

  1. I have two files with atomic coordinates for the same generated strucutre (cycle made of eight sulphur atoms), but produced by two different progams (so that output files have different coordinates supposedly connected by translation/rotation). Is there some kind of software to compare the two structures generated.
     
  2. jcsd
  3. mfb

    Staff: Mentor

    If you don't need to do that xxxx times, and if there is no software for that, this still looks manageable with a bit of manual help (identify corresponding atoms, then calculate translation and rotation based on three of them).
     
  4. Unfortunately it doesn't work because one program outputs coordinates in order 1, 2, 3...8 while the other does 1, 3, 5, 7, 2, 4, 6, 8. Isn't there some well-known chemistry program that allows to export atomic positions from the structure drawn, so that I could do sth like insert coordinates from program 1, then standardize and export new positions. Repeat for program 2 and compare?
     
  5. mfb

    Staff: Mentor

    If you know that order already, it is easy to fix that.

    I don't know, that's why I looked for alternative solutions.
     
  6. Borek

    Staff: Mentor

    Basically you are looking for a canonical representation of the molecule. Try to find a tool that will generate IhChI for both molecules, these are guaranteed to be canonical and unique - so if the molecules are identical, InChIs will be identical as well.
     
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