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By chemical database software I mean software with similar functionalities to Instant JChem in that they have a large database of different compounds and have the basic capabilities you, or at least I expect from a chemistry software. Namely:

  • Can approximate the chemical and physical characteristics of the compounds in question.
  • Can approximate products of reactants and their corresponding proportions.
  • Can show the 2d and 3d structure of compounds in the database.
  • Can connect to online chemical databases like PubChem, ChemSpider, NCBI, etc.
  • Has a molecule editor.

I would also prefer it if it is free of charge.

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  • $\begingroup$ 1) Your question is rather vague, what properties and level or approximation you are looking for 2) You are asking for rather unrelated functionalities 3) It is not clear what you don't like with JChem. 4) You may want to check out keywords like "chemoinformatics", and look what you are specifically looking for $\endgroup$
    – Greg
    Jul 12 '16 at 4:04
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A widely used database in academia and industry is ChemACX.The only one of your requirements that I don't believe it does is the product prediction.

http://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemACX/Default.aspx

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Not a database, more a toolset, but there is KNIME in wich you can make workflows that do all kinds of things. With the right plugins you can also work with molecules in various ways, such as reading and writing, descriptors, manipulation, reactions, etc.

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