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Python API Limitations

Known limitations

  • We only support the following molecule formats currently:
    • smiles
    • cxsmiles
    • cxsmarts
    • smarts
    • MOL V2000
    • MOL V3000
    • mrv
    • cxon
    • name
  • Molecule objects are partly immutable. Only their properties can be changed, but not their structure. This means that you cannot add or remove atoms and bonds from a molecule, but you can change the properties attached to the Molecule object.
  • Because the Chemaxon Python API supports multithreaded usage (i.e., the GIL is not a bottleneck) and is based on a platform-specific native image, the use of the multiprocessing library in client code is not fully supported — specifically, fork() and forkserver() should be avoided, while spawn() works fine. Python threading or similar should be preferred.