valence error failures

CN(C)#C should show a valence error on N, but it does not.

The following structure creates an interesting conundrum:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2"

          elementType="N C"

          radical="divalent1 0"

          x2="1.4361109903123648 -0.10388900968763526"

          y2="-5.2433333678378 -5.2433333678378"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="3" />

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

Note that the N atom has its divalent singlet flag turned on.  This suggests that the N should have an empty orbital, but no valence error for it occurs.  The same is true for C=NC in which the N atom has its divalent singlet flag turned on, as well as C#[C-] in which the anionic C atom has its divalent singlet flag turned on.

I was under the impression that the divalent radical flag indicated an empty valence orbital.  If that is the case, then all the cases above should display valence errors.  If it is not the case, what is your definition of divalent radical?

Hi Bob,

 

Thank you for reporting this problem.

We have noticed this issue earlier and it will be fixed in Marvin 5.7.

We've replaced the full valence checking algorithm, please report if you find any errors in it.

 

Best regards,

Peter

gezapeti wrote:

We have noticed this issue earlier and it will be fixed in Marvin 5.7. We've replaced the full valence checking algorithm, please report if you find any errors in it.

OK.  Is a beta version of Marvin 5.7 available for me to test?  If not, when can we expect Marvin 5.7 to be released?  (Days, weeks, months?)

Hi Bob,

You can download it from here:

https://www.chemaxon.com/download.php?d=/data/download/marvin/5.7.0.0beta

It is in beta testing phase, we have few bugs, found during the testing period, which needs fixing.

I downloaded that package (MarvinBeans), but it doesn't seem to have the MarvinSketch app in it.

Hi Bob,

 

   Which format of the installer you have downloaded? Technically we have no separate MarvinSketch installer. MarvinSketch is included in the MarvinBeans package.

 

Gabor

https://static.chemaxon.com/wp-content/themes/chemaxon/images/header_icons2.png); background-attachment: scroll; background-origin: initial; background-clip: initial; background-color: transparent; background-position: 0px -354px; background-repeat: no-repeat no-repeat;">marvinbeans-5.7.0.148762.zip

The  package downloaded and expanded, but there are no icons for the applications.

marvinbeans-VERSION.zip is the pure Marvin Beans package without installer.

The platform specific installers provides only desktop launchers (with icon).

In the pure package, you can find command line scrips (*.bat for Windows, script without extensions for Linux and Mac OS X).

Got it, thanks.  The abovementioned valence errors seem to be corrected in Marvin 5.7.

Great!

If you find some problems just let us know.