Database search functions

[akokai]

For each chemical group: We should have already formulated the logic of the query to define the group -- i.e. simply "has substructure X" or maybe there are multiple logical conditions "... and not Y". We should also have formulated as precisely as possible a SMARTS query for each search operation.

The function should read these logical components from some data interchange format, like JSON or a spreadsheet. Then, the function should:

• From the SMARTS string create an RDKit Mol object corresponding to the query molecule.
  • Use Chem.AdjustQueryProperties(), where appropriate, as described here and in the official docs.
  • Need to better understand how this works!
• Save an image of the query molecule using Draw.MolToFile().
• Construct an SQL query that expresses the proper logic and also refers to the proper table and fields.
• Execute the SQL query and retrieve the results.

[akokai]

Running into unexpected behavior from SQL queries of the form ...WHERE mol @> :patt1 ::qmol AND NOT mol @> :patt2 ::qmol... They end up returning molecules that do have a substructure match with :patt2, i.e., mol.HasSubstructMatch(MolFromSmarts(patt2)) == True. See notebook on inorganic compounds and issue #41.