double shortcut groups

Hi, using Marvin 6.2.1, I'm now seeing double shortcut groups when I type them in the drawing window (see screenshots). I didn't see this phenomenon (or at least, I didn't notice it) in previous versions of Marvin. 

We have our own version of the abbreviated groups file, marvin/chemaxon/marvin/templates/ACE.abbrevgroups. The default abbreviated groups file is in the same directory, as well. Our applet launch includes the command,

msketch_param('abbrevgroups', 'chemaxon/marvin/templates/ACE.abbrevgroups');

I don't see the same doubling of groups if I use the Insert -> Groups menu.

Hello,

Indeed, it seems, that we parse the default.abbrevgroups, and after that we parse the given aggbrevgroup file which, in this case seems to have duplicates. We manage to handle this at the Insert Group, but in the case of shortcuts we do not care. I've checked, and this was the case in 6.1 and 6.0 too. This gets interesting when the user redefines an abbrevgroup with the same name.

Thank you for reporting, we will investigate this issue and get back to you if we found a solution.

Regards,

Tamas Fazekas-Vigh

tfazekas wrote:

This gets interesting when the user redefines an abbrevgroup with the same name.

In that case, there is only one solution. The user's definition MUST take precedent over the default definition.

Hi Bob,

the parameter you are using is designed to replace the default abbrevgroups file. It should load only the contents of the file.

The storage behind the abreviated groups is a map, where the name of the group is the key, so it should not contain duplicates. The problem could bein the file, or in the logic which shows the possible completions.

Can you please send me even in e-mail if it is confidential, the used ACE.abbrevgroups file to test the behaviour with it?

Regards,
Istvan 

It's not confidential. Here it is.

Just found another shortcut group problem. On my Mac 10.9.3 using Safari 7.0.4, when I type Ac, the actinium atom comes up, not the acetyl group. Seriously, I haven't seen this behavior since Marvin 2.

Dear Bob,

Thank you for reporting this isssue, we are working on a solution.

Regards,
István 

Just so you know, this isn't just an esthetic issue. Two students submitted the exact same response that contained a Bz group. One inserted the Bz group by typing it, and one used the Insert menu. One student's Bz group was in the aromatized (toilet bowl) form, the other's in the dearomatized (Kekulé) form. The responses were treated differently, even though they looked exactly the same.

Hi Bob,

Upon closer investigating this issue, we came to a conclusion, that it is your file what messes things up a little.

The problem is with you abbrevgroup file, that there are hidden duplicates inside. Abbrevgroups are usually defined with a right name (that will be the primary name) and preferably a left name. We parse the file and store the groups. When the user starts to type something in, we look into that storage, to find the corresponding group. But since the user can also type the left name of the group we also look for that too (and list them in the right upper corner).

This is where the problem comes from, since your file in some cases holds duplicates like this : 

CHEt2 CCCCC 3 leftName=Et2CH

Et2CH CCCCC 3 rightName=CHEt2 

And we use the first strings to be the primary name (thus being the primary key), but list the left names too, so that's how duplicates came to life.

 

In the case of Ac, this behavior was changed. You can still access the acetyl group, if you either type it lower case, or upper case (ac/AC). For example in the acetyl group case: if you type shift+'a' and 'c', you will get actinium atom, because in the case of upper case letters we prefer the Element over the group. If you type 'a' and 'c' we will prefer the group over the element thus acetyl group will show up at your cursor.

 

Regards,

Tamas Fazekas-Vigh

Ah, I see. This must be a relatively new behavior, since we didn't have this problem when we were using Marvin 5.4. OK, I will modify our shortcut group file. Or maybe I will just start using yours; there was a time when they were substantially different, but I don't think they are anymore.

As for Ac vs. ac, I urge you to abolish this feature. There is no way on God's green earth that students will remember whether to type Ac or ac, and there is no way they will notice that a brown Ac on the canvas means that they evoked actinium, not acetyl. 

Given that in organic chemistry, there is almost no call to draw compounds containing praseodymium or actinium, I really don't think you need to create confusion by having a shortcut to these atoms. One can always just bring up the periodic table menu.

Hi Bob,

Yes, it was introduced in 5.10, that was the point where we completely redesigned the storage of abreviations, but their handling from the UI is still on the shelf among many other ideas.

Regarding the Ac group please see my answer in the other topic.

Regards,
Istvan