negative number of lone pairs?

Sometimes the number of lone pairs recorded in a MRV file will have a negative number (usually "-3" as far as I can tell) instead of the expected value of "0" (zero).

I'm not sure how to reproduce it consistently. It sometimes shows up on C atoms, sometimes on H. I haven't seen it yet on other atom types.

I'm wondering if there is any special significance to the program assigning the value "-3" instead of "0". Is this a bug or a feature? If a feature, what does it mean? I couldn't find any documentation on it.

 

Dear Michiel,

I'm wondering if there is any special significance to the program assigning the value "-3" instead of "0".

The API documentation at http://chemaxon.com/marvin/help/developer/beans/api/chemaxon/struc/MolAtom.html#getElectronProp() says:

The number of lone pairs is not set when the returned value is less then 0.

Regards,

Gabor

gimre wrote:

Dear Michiel, I'm wondering if there is any special significance to the program assigning the value "-3" instead of "0". The API documentation at http://chemaxon.com/marvin/help/developer/beans/api/chemaxon/struc/MolAtom.html#getElectronProp() says: The number of lone pairs is not set when the returned value is less then 0. Regards, Gabor

Dear Gabor,

The documentation also says:

Returns:

the number of lone pairs

• a value between 0 and 4

which distinctly does not include a value of "-3" ... as is the case I'm reporting.

So why does it return "-3" in some instances and "0" in other instances?

When I'm grading student-answers I'm looking for consistency. What causes Marvin to return "-3" instead of "0", and which should be regarded as the "correct" return value?

That's all I need to know.

Thanks,

  Michiel

 

Dear Michiel,

I think the original question is related to the mrv file where you detected the value -3. Where and why does it cause problem? Do you use the mrv file format for comparison?

More explanation about setElectronProp()/getElectronProp() see:
http://www.chemaxon.com/forum/viewpost18330.html&highlight=getelectronprop#18330 />So "the less then 0" value is not a bug. "the less then 0" value is equal with 0 from your point of view.

I wasn't able to reproduce the above described behavior and get the above mentioned negative value in the mrv file. Please try to reproduce it, and describe how you created the C or H atoms.

Best Regards,
Erika

Erika wrote:

Dear Michiel, I think the original question is related to the mrv file where you detected the value -3. Where and why does it cause problem? Do you use the mrv file format for comparison? More explanation about setElectronProp()/getElectronProp() see: http://www.chemaxon.com/forum/viewpost18330.html&highlight=getelectronprop#18330 />So "the less then 0" value is not a bug. "the less then 0" value is equal with 0 from your point of view. I wasn't able to reproduce the above described behavior and get the above mentioned negative value in the mrv file. Please try to reproduce it, and describe how you created the C or H atoms. Best Regards, Erika

 

Hi Erica,

I'm using an XML parser to see if a student answer is "essentially" the same as my MRV file, so the "-3" threw an error. I can rewrite it on-the-fly now that I know it's the same as "0". I'd rather have the "0" there in the first place, but this is workable.

The difference between the two MRV files I attached is that I drew the first one free-style (I generally use the single bond/line tool to draw up the scaffold, then change the element types; next I assign electrons (pairs/radical) and finally add the required electron flow) only assigning electrons where I thought they should be, and the second specifically setting the value to "0 Lone Pair" where I knew there shouldn't be any. I think the error came to light when lone pairs were accidentally set on the C, then reset to zero when discovered. I'm having a hard time reproducing it myself. I scanned (grep) through my MRV files and found a couple others that have the same "-3" value set, this time on "N". I don't think I did anything out of the ordinary when I drew the structures.

If there is a way to always write "0" that would be preferable, but as I said, this is workable now that I know.

 

Thanks,

   Michiel

 

Hi Michiel,

I agree with you that "0" would be preferable. We will try to change this.

Best regards,
Erika.