Contracted group link point

Hello,

  I hope everyone had a great time in San Diego.  I'm sorry I missed the fun!

  So, I'm drawing groups and contracting them but I do not like the way they look.  

  In Example 1, the link point is at the center of the group rather than at the link atom.  

  In Example 2, the subscript interferes with the bond making for a fuzzy picture.  

  I'm using JC4XL to make product flyers (example attached) but find I spend more time than I'd like tweaking the structures to minimize these effects.  Any suggestions would be most appreciated.

All the best,
Chris 

Hi Chris,

Yes, San Diego was great! Maybe next time you can join us.

The reason why your abbreviations are not displayed properly is that they are not included in the default abbreviated groups of Marvin, where the leftName (i.e. when abbreviated group label is on the left side) can be defined. You should extend the default.abbrevgroup file with the C3F7 and CO2CH3 groups as described here:

http://www.chemaxon.com/marvin/help/formats/abbrevgroup-doc.html

An axample for the behaviour of default abbrevgroups having leftName is CO2Me group. Please try it!

Best regards,

Akos

Howdy Akos,

  Thank you very much for the advice.  I found the file you mentioned, opened it with excel and it is read only.  It's not a problem to dance around that but I'd like to know how you would do it?

  Much appreciated!

Chris

Hi Chris,

i think we simply use wordpad, or wordpad++ to edit the file, and openoffice is also a good choice to open and edit a tab separated file. I did not tried it with current Excel versions, but as i remember the Excel in Office 2003 did not really understand that format, or at least it was not easy to even import a tab separated file in a proper way into Excel that times, and i never tried to do so after the first complications.

Regards,
Istvan

Hello,

  I added one entry to the file but none of my applications see the additional group.  Any suggestions?

Thanks,
Chris

Hi all,

  Just checking in on my last post.

  I hope all is well.

Thanks,
Chris 

Hi Chris,

sorry for the late answer, i missed your previous question unfortunatelly.

As far as i know, the order of the abbreviated groups in the file is important (it has to be ordered alphabetically by the smiles/smarts string of the structure) i assume this is why your structure does not show up.

It is misleading that this is not mentioned in the documentation, we will fix this either by remove the necessity of ordering the structures, or at least mention this in the documentation.

Regards,
Istvan

Hello Istvan,

  I did as you suggested with no luck.  When I parse the default file with marvin, it sees my group.  Anything else I can try?

Thanks,
Chris 

Hi again,

  From Istvan's post...

  "it has to be ordered alphabetically by the smiles/smarts string of the structure"

  This isn't the case in the default file, they are alphabetized by the contracted group name.  Either way, it isn't working for me.  Please, I would like to get this function to work.

  Thanks in advance for your assistance.

Sincerely,
Chris

PS - Maybe for the future you could add some way to interface with abbrevgroup files directly as they do contain structures.  It sure would be easy to create a table in IJC or JC4XL and export it as an abbrevgroup file.  

Hi Chris,

first of all, please forgive me for the very late answer, i was a bit overhelmed.

I have to ask a seemingly stupid question, but where your default.abbrevgroup file is located? I think may be that is not the one which is being used to load the abbreviations, and this information may help me to understand what is happening in your environment.

Regards,
Istvan

C:\Program Files\ChemAxon\JChem\marvin\chemaxon\marvin\templates

Thanks, Istvan.

Hi,

I tested a bit around this functionality, and i found that this is not as simple as i knew. So the default.abbrevgroup file is inside a jar file in Marvin, and the classloader prefers this file instead of the file that is in the same path from the classloader point of view but not in a jar file. This seems true also for JC4XL, where we use the .Net version of Marvin that is also based on Java with the help of IKVM.

It seems you have to add the abbrevgroup file path to your marvin.properties file to achive the loading of your custom file.

You have to add somthing like this line into your marvin.properties file under %USER_HOME%\chemaxon directory:

abbrevgroups=c\:\\Program Files\\Chemaxon\\JChem\\marvin\\chemaxon\\marvin\\templates\\default.abbrevgroup

to make it work.

We have a task in our issue tracker to improve the addition of user defined abbreviation groups in our software, but currently this is the way, and as i checked it in the documentation, it is not very well documented, so we are keen on to improve the documentation as a minimum until the improvements are ready, and released.

I hope this will solve the problem in your side.

Regards,
Istvan

I added as you suggested, no dice.  I attached my marvin.properties file.

Thanks,

Chris

Hi,

that sounds weird. Can you give me all installed Chemaxon Software with version? I'll create a test environment, and i will try to reproduce it there, because it is worked for me, so currently i have no clue.

Regards,
Istvan