Molfile-Smiles conversion

An example of a client class of the above Molfile-Smiles conversion API is as follows ... 

Figure 12.10 The sequence diagram that illustrates how objects work together in the Molfile-Smiles conversion framework.

The same approach can be used for property calculations, because you may have multiple choices and each one has different APIs. It is possible that today you choose one vendor solution to do the work. Some time in the future you may switch to a different vendor for the purpose of cost savings, better algorithm, performance, or reliability. Or you may face a harder choice—the vendor you chose in the past is going out of business. The solution we described above for Molfile-Smiles conversion keeps your system closed for... 

It defines two simple methods. The molfileToSmiles() method converts a Molfile string to a Smiles string. The smilesToMolfile() method does the opposite—converting a Smiles string to a Molfile string. They both throw MolstructureConversionException to flag conversion failures. The failure can be caused by exceptions from the vendor implementation or from the CRS code. 

The vendor tools that you end up using may have completely different APIs. But you should not care when you design the interfaces of your system. Remember, the vendor API may not be the best design, or at least it may not be ideal for your system. All you need to care about is what makes the most sense to the clients that use the structure conversion API in your system. To do the conversion between Molfile and Smiles, the above API is the simplest. 

The external representation of molecular structure is a less rigorous definition. For example, there are many programs available that can convert to and from SMILES and molfiles. These can be used when a molfile (the external representation) needs to be imported as a SMILES (the internal representation) into the database. Similarly, a SMILES can be easily exported as a SMILES or converted to a molfile or other file format. It is useful to have these conversion functions as SQL extensions. 

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