Hi Martin,
The InChI is an identifier and not a structure representation it should
never be used as such. For maximum preservation you should store compounds
as Kekulé SMILES or Molfile. You can store additional data such as
coordinates supplementary to the SMILES.
You might find a recent presentation by Noel (O Babel) and Rajarshi (CDK)
useful:
http://baoilleach.blogspot.co.uk/2015/08/the-whole-of-cheminformatics-best.html
John
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