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Doubts about the pharma-frag.xml example
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Alexandre

Joined: 03 Sep 2014
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Link to postPosted: Tue May 31, 2016 8:53 pmPost subject: Doubts about the pharma-frag.xml example Reply with quote

Hello,

I was trying to understand the rules defined at the pharma-frag.xml file, but I have two questions:

1) In the below rule, you've defined which atoms would be hydrogen bond donors.

<AtomSet ID="HydrogenBondDonor" Symbol="d">

            <![CDATA[ qh:1 || tertamine:1 && !{Anionic}]]>

</AtomSet> 

According to the precedence of Logical Operators, the AND has a higher precedence than the OR. So, by this rule, the Nitrogen of a tertiary amine will be classified as a donor atom only if it isn't an Anion. And, whatever the atom classified as qh (heteroatom) will be a donor. Did you just wanted to mean it?

In fact, a tertiary amine that has a Hydrogen (quaternary amine) is a Cation. Thus, shouldn't the rule be defined as (tertamine:1 && {Cationic})? I'm asking it because I didn't understand which cases this rule should comprise.

2) In the below rule, you've defined which atoms are an Anion.

<AtomSet ID="Anionic" Symbol="-">

<![CDATA[ !pos && ((neg && !nitro:2,3) || carbox:2,3 || carboxylate:2,3 || sulfonyl:2,3,4 || sulfonate || phosphonyl:2,3,4 || phosphonate) ]]>

</AtomSet>

Why did you exclude the Oxygens of the nitro group from being classified as an Anion? Due to the resonance I think that these two atoms should be anions. I'm aware that I can edit these rules in order to keep them the way I want, but as I said before, I would like to understand what led you to define it.

Thank you a lot.

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