incorrect number of implicit H atoms added

This MRV:

<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_8_4.xsd" version="ChemAxon file format v14.8.4, generated by v14.9.8.0">

<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4" elementType="H C O C" formalCharge="-1 0 2 0" mrvValence="- - 2 -" x2="0.0 4.18 5.513679121828035 6.847358243656071" y2="0.0 0.2566666666666666 -0.5133333333333334 0.25666666666666704"></atomArray><bondArray><bond id="b1" atomRefs2="a2 a3" order="1"></bond><bond id="b2" atomRefs2="a3 a4" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument>

</cml>

when loaded into MarvinSketch correctly shows no implicit H atoms on the O atom, but when loaded into MarvinJS incorrectly shows two implicit H atoms, despite MarvinJS's evident recognition of the valence 2 flag.

Also, can you implement an option to turn off the visibility of the valence flag? It will be meaningless to students.

Dear Bob,

Thank you for reporting this issue. 

The problem was that in Marvin JS the "Bond orders" atom query property is not connected with the valence calculations, currently.

We have added this issue to our backlog, and we will notify you, when it's done.

 

The development of the visibility of the valence flag is out of our scope.

 

Best Regards,

Eszter Szabo

 

Here's another example:

<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="P" x2="-2.3333333333333335" y2="1.3333333333333333" mrvValence="3" formalCharge="1" radical="monovalent"/><atom id="a2" elementType="C" x2="-2.3333333333333335" y2="2.873333333333333"/><atom id="a3" elementType="C" x2="-0.7933333333333334" y2="1.3333333333333333"/><atom id="a4" elementType="C" x2="-2.3333333333333335" y2="-0.20666666666666678"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"/><bond atomRefs2="a1 a3" order="1"/><bond atomRefs2="a1 a4" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>

I'd really, really like it if you added return characters to the exported MRV, BTW.

We are checking how we can prettify the text  in the import dialog, hopefully we will find a solution.

Regards,

Efi

I've just been replacing > with >[carriage return].

I would also like to ask you again to provide an option to toggle the visibility of the valence flag. I understand that it is not very high priority for you, but it really will be very confusing to students if it is displayed. It shouldn't be any harder to program than the option to toggle visibility of atom numbers and atom mapping. Please add it to my Hanukkah list.

Hi Bob,

ok, it has been added to the backlog.

 

regards, 

 

Janos

Any idea when this valence calculation bug will be fixed?

Unfortunately, we have know estimation when we can add this improvment to Marvin JS yet.

Regards,

Efi

This request is not for an improvement. It is for a bug fix. As you said,

The problem was that in Marvin JS the "Bond orders" atom query property is not connected with the valence calculations, currently.

Again, this is a bug, and a fairly serious one for us. Let me explain why. See the two screen captures below. Both show our mechanism calculator program, one using MarvinSketch, and the other using MarvinJS. In both, I drew protonated tert-butyl methyl ether with an electron-flow arrow pointing from the O⁺–H bond to H (incorrectly) — see the left side of the equation at the top of each picture — and I calculated the products. The calculated products are:

<?xml version="1.0" encoding="UTF-8"?>

<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_12_01.xsd" version="ChemAxon file format v14.12.01, generated by v14.12.15.0">

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3 a4 a5 a6 a7" elementType="C C C C O C H" formalCharge="0 0 0 0 2 0 -1" radical="0 0 0 0 divalent1 0 0" x2="-4.693064898698925 -4.693064898698925 -6.233064898698925 -4.693064898698925 -3.153064898698925 -2.2478756101685162 -0.7784124794373328" y2="4.094604576302018 2.5546045763020175 2.554604576302018 1.0146045763020175 2.5546045763020175 3.8004907476394365 -0.7138240809727696"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="1"/>

        <bond id="b2" atomRefs2="a2 a3" order="1"/>

        <bond id="b3" atomRefs2="a2 a4" order="1"/>

        <bond id="b4" atomRefs2="a2 a5" order="1"/>

        <bond id="b5" atomRefs2="a5 a6" order="1"/>

      </bondArray>

    </molecule>

  </MChemicalStruct>

  <MElectronContainer id="o2" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a5" difLoc="-0.09813011722893039 -0.4264349147204487 0.0"/>

    <MElectron atomRefs="m1.a5" difLoc="0.1282342829636245 -0.4183685278230258 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o3" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a7" difLoc="-0.3789553961879948 -0.21878999999999937 0.0"/>

    <MElectron atomRefs="m1.a7" difLoc="-0.21879000000000293 -0.3789553961879948 0.0"/>

  </MElectronContainer>

</MDocument>

</cml>

The program then both drew the calculated products at the top and loaded the calculated products into the sketcher window. You can see that in the MarvinJS case, the sketcher shows incorrect products. (The pictures of the products on the top are displayed correctly in both cases because we use JChem, not the sketchers, to generate those pictures.) The reason it draws incorrect products is that it doesn't recognize the divalent radical. I understand that you might not have planned to implement divalent radicals anytime soon, but, as you can see, we rely on them quite heavily to show students the results of a very common mistake that they make.