filter problem

Reaction definition:

<?xml version="1.0" ?>

<MDocument>

  <MChemicalStruct>

    <reaction>

      <propertyList>

        <property dictRef="NAME" title="NAME">

          <scalar><![CDATA[C(-) to ketohyde]]></scalar>

        </property>

        <property dictRef="REACTIVITY" title="REACTIVITY">

          <scalar><![CDATA[

dynamicpKb(reactant(0), "1") < 30 

     || min(dynamicpKa(reactant(1), filter(ratom(4), "match('[C:1][H]', 1)"))) > 15

          ]]></scalar>

        </property>

        <property dictRef="EXCLUDE" title="EXCLUDE">

          <scalar><![CDATA[

totalCharge(reactant(1)) < 0

          ]]></scalar>

        </property>

        <property dictRef="STANDARDIZATION" title="STANDARDIZATION">

          <scalar><![CDATA[<?xml version="1.0" encoding="UTF-8"?>

<!-- Standardizer configuration file -->

<!-- This configuration file is created with ChemAxon Config Builder -->



<StandardizerConfiguration Version ="0.1">

	<Actions>

<Transformation ID="O-enolate to C-enolate" Structure="[#8-]C=C>>[#6-]C=O" Type="string" Groups="reactant1"/>

<Transformation ID="nitrile enolate to C-enolate" Structure="[#7-]=C=C>>[#6-]C#N" Type="string" Groups="reactant1"/>

<Transformation ID="imine enolate to C-enolate" Structure="[#7-]C=C>>[#6-]C=N" Type="string" Groups="reactant1"/>

	</Actions>

</StandardizerConfiguration>

]]></scalar>

        </property>

      </propertyList>

      <reactantList>

        <molecule molID="m1">

          <atomArray

              atomID="a1"

              elementType="C"

              formalCharge="-1"

              mrvMap="3"

              x2="-11.348111152648926"

              y2="0.5153747200965881"

              />

          <bondArray>

          </bondArray>

        </molecule>

        <molecule molID="m2">

          <atomArray

              atomID="a1 a2 a3 a4"

              elementType="O C H H"

              mrvMap="2 1 4 0"

              mrvQueryProps="0 0 L,H,C: L,H,C:"

              x2="-7.075778961181641 -7.075778961181641 -8.409458083009676 -5.742099839353605"

              y2="2.1469244956970215 0.6069244956970214 -0.1630755043029789 -0.16307550430297846"

              />

          <bondArray>

            <bond atomRefs2="a1 a2" order="2" />

            <bond atomRefs2="a2 a4" order="1" />

            <bond atomRefs2="a2 a3" order="1" />

          </bondArray>

        </molecule>

      </reactantList>

      <productList>

        <molecule molID="m3">

          <atomArray

              atomID="a1 a2 a3 a4 a5"

              elementType="O C H C H"

              mrvMap="2 1 4 3 0"

              mrvQueryProps="0 0 L,H,C: 0 L,H,C:"

              x2="4.414802551269531 4.414802551269531 3.0811234294414955 5.748481673097567 4.414802551269531"

              y2="2.1145290517807007 0.5745290517807007 -0.19547094821929978 -0.1954709482192989 -0.9654709482192994"

              />

          <bondArray>

            <bond atomRefs2="a1 a2" order="1" />

            <bond atomRefs2="a2 a5" order="1" />

            <bond atomRefs2="a2 a3" order="1" />

            <bond atomRefs2="a2 a4" order="1" />

          </bondArray>

        </molecule>

      </productList>

    </reaction>

  </MChemicalStruct>

</MDocument>

Reactants are [CH3-].CC(=O)CC(C)=O.  

I tried to write a reactivity rule that states that a carbonyl group should react with a carbanion whose pKb is greater than 30 only if all atoms adjacent to the carbonyl that are H-bearing C atoms have a dynamic pKa of 15 or greater.  However, [CH3-].CC(=O)CC(C)=O reacts.  So either there's an error in my reactivity rule (quite possible, because the filter() grammar is incredibly confusing), or there's a bug.  Can you help?

Also, if dynamicpKa returns "NaN" for an atom, the value is ignored by the min() and max() functions, right?

bobgr wrote:

Reactants are [CH3-].CC(=O)CC(C)=O. I tried to write a reactivity rule that states that a carbonyl group should react with a carbanion whose pKb is greater than 30 only if all atoms adjacent to the carbonyl that are H-bearing C atoms have a dynamic pKa of 15 or greater.  However, [CH3-].CC(=O)CC(C)=O reacts.  So either there's an error in my reactivity rule (quite possible, because the filter() grammar is incredibly confusing), or there's a bug.  Can you help?

Your reactivity rule is:

dynamicpKb(reactant(0), "1") < 30 || min(dynamicpKa(reactant(1), filter(ratom(4), "match('[C:1][H]', 1)"))) > 15

1.  min(dynamicpKa(reactant(1), filter(ratom(4), "match('[C:1][H]', 1)"))) > 15

All reactant atoms that can match the query should be listed in filter:

min(dynamicpKa(reactant(1), filter(ratom(4), ratom(5), "match('[C:1][H]', 1)"))) > 15

I mapped ratom(5) in the reaction scheme.

2. "a carbonyl group should react with a carbanion whose pKb is greater than 30 only if ..."

For expressing this you should use expression: dynamicpKb(reactant(0), "1") > 30 && ...

If you use "||" (or), then the subexpression after "||" will not be evaluated if the subexpression before "||" returns "true". In your original rule dynamicpKb(reactant(0), "1") < 30 returned "false" for "[CH3-]", so this part of the or-expression had no effects on the result in this case.

I attached the modified reaction with rules. The rule with "&&" insted of "||" will exclude a lot of reactants that used to react before the modification, but will work on reactants [CH3-].CC(=O)CC(C)=O. I hope you see how filter() function works, and you can extend the rule as you wish.

I attached the modified reaction.

$ react -r c-toketohyde_mod.mrv "[CH3-]" "CC(=O)CC(C)=O"

(no results)

bobgr wrote:

Also, if dynamicpKa returns "NaN" for an atom, the value is ignored by the min() and max() functions, right?

Yes, this is right.

Zsolt

Thanks, that helps a lot.  Although I think I do want,

dynamicpKb(reactant(0), "1") < 30 || ....

For a reaction to take place, either reactant(0) should not be too basic, or the carbonyl compound should not be too acidic.  Also,

[bob@epoch public]$ evaluate -e "dynamicpKb()" "[CH3-]"

50.69

With this definition, [CH3-].CC(=O)CCCC(=O)CC(C)=O gives only CC(=O)CC(=O)CCCC(C)(C)O.  

-- Bob