Identify the salt stripped

#1

Hi,

I am using Standardizer node to strip my salts and it works perfectly in removing the salts from the molecule. But i need to know which salt has been removed from the molecule. Can you please suggest a way to work out that?

Thanks,
Shiva

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#2

Hi Shiva,

After stripping off salts, you can use the salt-stripped molecule as a query to run a full-fragment search against the input structures. The Mol Search node has an option to add the hit atom indexes to the output; these atom indexes can be used in the Set Atom Selection node. You can then use the Invert Atom Selection node to change the selection to everything that was removed, followed by the Extract Atom Selection node, which will move the selected atoms (the removed salts) to a new field.

I will attach a short workflow to demonstrate.

Tim


Identify Stripped Salts.knwf (42.7 KB)

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#3

Hi Tim,

Thanks. This really helps. The output produced by the workflow has given us the ability to reach half way line. But we would like to know how many salts were present in the compound. For instance, if we have HCl as salt in compound with 2 equivalents, we would like to say HCl is present in the compound with 2 in numbers.

Thanks,
Shiva

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#4

Hi Shiva,

One thing that might help would be adding an Elemental Analysis node, where you can get the Grouped dot-disconnected formula of the Salts Removed column. If your input structure was an amine dihydrochloride monohydrate, the Salts Removed column would show H20 H20 HCl, and the Grouped dot-disconnected formula would be (H2O)1.(HCl)2. Maybe this will be good enough for your purposes?
We are looking at some other options, but this is the best I can offer now.

Tim

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