radicals autocalc off???

I'm trying to work with Lewis structures.





I can have:





msketch_param("lonePairsVisible", "true");


msketch_param("lonePairsAutoCalc", "false");





to turn automatic determination of lone pairs off, yet still show them when entered through the GUI.





Is there an option to turn automatic determination of radicals off, yet still show them when entered through the GUI? (I didn't find it in the parameter list at http://www.chemaxon.com/marvin/help/developer/sketchman.html)





If I feed TeF5 (smi: F[Te](F)(F)(F)F ) into JMSketch it automatically determines and displays a lone electron/radical symbol. I need students to determine whether this is required, so I want to suppress the automatic determination.

Along those lines: is there a way to turn automatic charge calculation off?

Hello,





We're sorry for the late answer.


We are investigating what can cause the lone electron appearing on TeF5 and we will get back with an answer soon.


Unfortunately, there is no way to switch off the automatic charge calculation at the moment. The automatic calculation and display of valence errors can be switched off with the valenceErrorVisible parameter.





Best regards,


Erika.

Switching autocalculation and autodisplay off for charges is important.





I also ran into an error on your system: the resonance structures of borazine are automatically calculated and display the charges for nitrogen, but the corresponding charge for boron is not calculated/displayed.





Apart from giving students a clue as to what is going on, it would also throw them off that they would have to set/suppress explicit charges for some atoms but not for others.





The resonance SMILES are:   B([H])1N([H])B([H])N([H])B([H])N([H])1.B([H])1=N([H])B([H])=N([H])B([H])=N([H])1.B([H])1=N([H])B([H])=N([H])B([H])=N([H])1

Thank you for reporting the problem with Boron, this is indeed a bug.





We recognized that switching autocalculation and autodisplay off for charges is really important.





Automatic charge calculation is done in valence check, so we will introduce a new applet parameter to allow switching off the valence check.


We will notify you as soon as the implementation is out.





The extra lone electron appearing on TeF5 is calculated in SMILES import. This problem could be solved by using SMARTS or Mrv format of the structure. Please give us feedback if this is suitable for you.











Best regards,





Erika.

Quote:

The extra lone electron appearing on TeF5 is calculated in SMILES import. This problem could be solved by using SMARTS or Mrv format of the structure. Please give us feedback if this is suitable for you.

As a temporary work-around I can provide the mrv file format, but this is not a sustainable solution for the long-term. As we open up the application to other faculty we want to be able to provide SMILES for all our input structures. The problem appears to be a bug in the SMILES processor so that is what needs to be fixed.





Even if the SMILES processor generates the wrong structure, I should still be able to suppress the display of the radical by another/independent means...

Quote:

Best regards, Erika.

Quote:

As a temporary work-around I can provide the mrv file format, but this is not a sustainable solution for the long-term. As we open up the application to other faculty we want to be able to provide SMILES for all our input structures. The problem appears to be a bug in the SMILES processor so that is what needs to be fixed.

I think the suggestion to use the SMARTS or the MRV format was given to avoid the automatic calculation of lone electrons in the SMILES import, which is not a bug. E.g. try to import [OH]; do you expect a lone electron here or not?





Best regards,





Akos

Quote:

I think the suggestion to use the SMARTS or the MRV format was given to avoid the automatic calculation of lone electrons in the SMILES import, which is not a bug. E.g. try to import [OH]; do you expect a lone electron here or not?

 


As a teacher, I would not expect to see a single dot there under most circumstances. Most students would expect to see an OH- anion there, which has 3 lone-pairs.


So, my initial request to disable autocalculate and autodisplay through some command-line option is still what I need to make this work in an educational setting.

Hi Michiel,

Quote:

I think the suggestion to use the SMARTS or the MRV format was given to avoid the automatic calculation of lone electrons in the SMILES import, which is not a bug. E.g. try to import [OH]; do you expect a lone electron here or not?

  


As a teacher, I would not expect to see a single dot there under most circumstances. Most students would expect to see an OH- anion there, which has 3 lone-pairs.


So, my initial request to disable autocalculate and autodisplay through some command-line option is still what I need to make this work in an educational setting. 





This is the problem I think. According to the specification of SMILES (http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) [OH] means an oxygen with exactly one hydrogen and no charge, consequently there has to be a radical electron. So Marvin correctly imports the SMILES, but you (and the students) expect something else. Again, I think another fileformat would better suits you.











Best regards,











Akos

Quote:

Hi Michiel, Quote: I think the suggestion to use the SMARTS or the MRV format was given to avoid the automatic calculation of lone electrons in the SMILES import, which is not a bug. E.g. try to import [OH]; do you expect a lone electron here or not?      As a teacher, I would not expect to see a single dot there under most circumstances. Most students would expect to see an OH- anion there, which has 3 lone-pairs. So, my initial request to disable autocalculate and autodisplay through some command-line option is still what I need to make this work in an educational setting.  This is the problem I think. According to the specification of SMILES (http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) [OH] means an oxygen with exactly one hydrogen and no charge, consequently there has to be a radical electron. So Marvin correctly imports the SMILES, but you (and the students) expect something else. Again, I think another fileformat would better suits you. Best regards, Akos

As a teacher, I give incomplete structures at best and sometimes no structure input at all. So maybe SMILES is not the correct way to give information to a student, but I expect to obtain a complete SMILES string from the student using the GUI. By turning autocalculate and autodisplay off when giving the incomplete structure I am prompting the student to complete the picture. This doesn't go through a database query and match mechanism, so I can't really match SMARTS/SMIRKS up with SMILES. I didn't ask for a modification of the interpretation of the SMILES-code, but for the option to disable the autocalculate and autodisplay modes. If that can't be done, I think we're pretty much done with MSketch as an educational tool because I want students to think for themselves whether lone-pairs and radicals need to be specified: there shouldn't be any undue prompting by the software. I understand that it can be hugely benificial under different circumstances to prompt the end-user with all sorts of visual information, but in this case it shouldn't.