matching problem in exclude rule

The reaction definition:

Code:

<?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <reaction x1="1.0445367650349073" y1="0.06144778459879451" x2="3.474588352204565" y2="0.0961363041963788">       <propertyList>         <property dictRef="NAME" title="NAME">           <scalar><![CDATA[reductive amination]]></scalar>         </property>         <property dictRef="EXCLUDE" title="EXCLUDE">           <scalar><![CDATA[match(ratom(3), "CC(C)[N:1]C(C)C", 1)]]></scalar>         </property>         <property dictRef="Stop after one reaction" title="Stop after one reaction">           <scalar>true</scalar>         </property>       </propertyList>       <reactantList>         <molecule molID="m1">           <atomArray               atomID="a1 a2 a3 a4"               elementType="C O H H"               mrvMap="1 2 0 0"               mrvQueryProps="0 0 L,H,C: L,H,C:"               x2="-3.6599674224853516 -2.326288300657316 -4.993646544313387 -3.6599674224853516"               y2="0.027313189581036568 0.7973131895810365 0.7973131895810371 -1.5126868104189635"               />           <bondArray>             <bond atomRefs2="a1 a4" order="1" />             <bond atomRefs2="a1 a2" order="2" />             <bond atomRefs2="a1 a3" order="1" />           </bondArray>         </molecule>         <molecule molID="m2">           <atomArray               atomID="a1 a2"               elementType="N H"               mrvMap="3 0"               x2="-0.18053583800792694 -0.18053583800792683"               y2="-0.7920824885368347 0.7479175114631653"               />           <bondArray>             <bond atomRefs2="a1 a2" order="1" />           </bondArray>         </molecule>       </reactantList>       <productList>         <molecule molID="m3">           <atomArray               atomID="a1 a2 a3 a4 a5"               elementType="C H H N H"               mrvMap="1 0 0 3 4"               mrvQueryProps="0 L,H,C: L,H,C: 0 0"               x2="6.012143149971962 4.678464028143926 6.012143149971962 7.437296360731125 4.678464028143926"               y2="0.12458513103425495 0.8945851310342555 -1.4154148689657449 0.9269880278408527 -0.6454148689657456"               />           <bondArray>             <bond atomRefs2="a1 a5" order="1" />             <bond atomRefs2="a1 a4" order="1" />             <bond atomRefs2="a1 a2" order="1" />             <bond atomRefs2="a1 a3" order="1" />           </bondArray>         </molecule>       </productList>     </reaction>   </MChemicalStruct> </MDocument>

With substrates CC(=O)c1ccccc1.[H][C@](C)(N[C@]([H])(C)c2ccccc2)c3ccccc3, the exclude rule should cause no products to be obtained, but I am getting products regardless. Why?

Your query in exclude rule does not match the second reactant, that's why it is not excluded. See the attached image.





Zsolt

Capital C in SMARTS means aliphatic carbon. You might modify the SMARTS in your exclude rule to accept aromatic carbons as well. It is marked with the atomic number: [#6]





For example:


[#6]C(C)[N:1]C(C)[#6]





or if you would like to extend it:


[#6]C([#6])[N:1]C([#6])[#6]

Ah, that makes more sense than Zsolt's response. Thanks.

I could not find out the problem without Zsolt's great explanation image.

Gyuri wrote:

Capital C in SMARTS means aliphatic carbon. You might modify the SMARTS in your exclude rule to accept aromatic carbons as well. It is marked with the atomic number: [#6] For example: [#6]C(C)[N:1]C(C)[#6] or if you would like to extend it: [#6]C([#6])[N:1]C([#6])[#6]

As you redesign Chemical Terms Language, you might want to reconsider that C means aliphatic C only. It is incredibly counterintuitive. I suppose that the people who designed SMARTS made that decision, and you're just maintaining consistency, but good grief!





I've been using SMILES in my exclude rules, not SMARTS. Now I guess I need to go back and rewrite all my rules. Sigh....

SMARTS is a standard for queries, it is not something that Chemical Terms should overdefine. However, I understand your complain, I think, that we should emphasize that anything in the match() function is a query, so the query structures should be specified as SMARTS, not as SMILES.

Gyuri wrote:

SMARTS is a standard for queries, it is not something that Chemical Terms should overdefine. However, I understand your complain, I think, that we should emphasize that anything in the match() function is a query, so the query structures should be specified as SMARTS, not as SMILES.

Yes, and if you want chemists-not-programmers to be able to use Chemical Terms, you ought to note specifically some of the counterintuitive conventions of SMARTS, such as that C means nonaromatic C only. (I repeat: Good grief! what a counterintuitive convention.)