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Transformations with atom lists
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Joined: 15 Jun 2004
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Link to postPosted: Thu Jan 08, 2009 12:47 amPost subject: Transformations with atom lists Reply with quote

Consider this transformation:


For atom 2, I want the heavier atoms to take precedent over the lighter ones. So, for example, I want CN=N(C)=O to be converted to CN=[N+](C)[O-], but it is being converted to C[N-][N+](C)=O. Is there a way to enforce an order of operations in the atom list short of listing the transformation multiple times, each with a different atom 2?

And another question. If I list multiple transformations such as the one above in a single Standardizer file, how many transformations would I have to have before Standardizer became less efficient than simply going through the molecule bond by bond and looking for the pattern manually?
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Link to postPosted: Thu Jan 08, 2009 3:52 pmPost subject: Reply with quote

The simplest solution currently is to create a queue of separate specific transforms. I do not expect any serious slowdown even if you have some dozens of transforms.

Regarding related future plans, we will add a new Chemical Terms function with a parameter list of functional groups, that will match those functional groups in their listed order.
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