formalCharge()?

I want to exclude any atom with a formal charge > 0 from participating in a reaction. I found your charge() function, which calculates partial charges. I don't want anything so sophisticated; I just want the formal charge to be 0. Do you have such a function? I can't find it.





I tried defining formal charge = 0 in the configuration file, but when the file was loaded into the Reactor jsp page, the line was simply deleted. The same thing happened when I tried to include the requirement in a SMARTS string.





The only workaround I can find is to use the match() function to exclude atoms with formal charge +1, +2, etc.

Yes, this would be a simple, but useful function. We will implement it. Till that, the match function can work as a workaround. Use it with this SMARTS query expression:


[+0]

Thanks, that works well.





Another useful function would be Hcount(). It should include implicit H atoms in the count.

It is a similar case. Can be achieved by using the hydrogen count query, but a separate function might be helpful. Thanks for the idea.

Gyuri wrote:

Can be achieved by using the hydrogen count query.

Yes for match(), but I think not if I want to compare the number of H atoms attached to various query atoms, e.g. in the selectivity rule:





-HCount(ratom(2))





where, if there are different choices for ratom(2), the one with the fewest H atoms is chosen.

I was misinformed, I realized both formalCharge and hCount functions already exist in Chemical Terms:


http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#atompropex

Oh, yes, there they are, clustered together. My bad.





Does hCount include implicit and explicit H atoms? The documentation doesn't say.

A hydrogen is a hydrogen.

That isn't always your philosophy, but I'm glad it is in this case.

We are usually referring properties of molecules in Chemical Terms. The implicit and explicit hydrogens are interpreted differently in case of queries only.