Checks structures and tries to normalize them, if necessary. Structures that are normalized already will appear in the first output table. Structures, which need to be normalized will be corrected and also put in the first output table. Information about the normalization is made available as bit mask (flags) as well as warning messages. Structures, which cannot be normalized or have been normalized causing a certain warning flag that the user wants to treat as error are put in the second table ("Failed Molecules").
The following flags and messages are currently used:
- 1 - BAD_MOLECULE, Unable to recognize a molecule (ERROR)
- 2 - ALIAS_CONVERSION_FAILED, The atom alias conversion failed (ERROR)
- 4 - TRANSFORMED, Structure has been transformed
- 8 - FRAGMENTS_FOUND, Multiple fragments have been found
- 16 - EITHER_WARNING, A wiggly bond has been removed
- 32 - STEREO_ERROR, Stereo chemistry is ambiguously defined (ERROR)
- 64 - DUBIOUS_STEREO_REMOVED, A stereo bond has been removed
- 128 - ATOM_CLASH, There are two atoms or bonds are too close to each other (ERROR)
- 256 - ATOM_CHECK_FAILED, The atom environment is not correct(ERROR)
- 512 - SIZE_CHECK_FAILED, The molecule is too big (ERROR)
- 1024 - RECHARGED, Structure has been recharged
- 2048 - STEREO_FORCED_BAD, Structure has failed: Bad stereo chemistry (ERROR)
- 4096 - STEREO_TRANSFORMED, Stereo chemistry has been modified
- 8192 - TEMPLATE_TRANSFORMED, Structure has been modified using a template