more shortcut group suggestions

SO3H OS(=O)=O 2


HO3S OS(=O)=O 2


SO2Cl ClS(=O)=O 2


ClSO2 ClS(=O)=O 2


SO2NH2 NS(=O)=O 2


H2NSO2 NS(=O)=O 2

Thanks, we will add these missing abbreviations!

I have some more shortcut group suggestions.

Code:

A   NC1=C2N=CN([C@@H]3O[C@H](CO)[C@@H](O[PH]([O-])=O)[C@H]3O)C2=NC=N1   11   14 dA   NC1=C2N=CN([C@H]3C[C@H](O[PH]([O-])=O)[C@@H](CO)O3)C2=NC=N1   16   11 G   NC1=NC2=C(N=CN2[C@@H]3O[C@H](CO)[C@@H](O[PH]([O-])=O)[C@H]3O)C(=O)N1   13   16 dG   NC1=NC2=C(N=CN2[C@H]3C[C@H](O[PH]([O-])=O)[C@@H](CO)O3)C(=O)N1   18   13 Ct   NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O[PH]([O-])=O)[C@H]2O   13   16 dC   NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O[PH]([O-])=O)[C@@H](CO)O2   18   13 Ur   OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[PH]([O-])=O)N2C=CC(=O)NC2=O   1   10 dT   CC1=CN([C@H]2C[C@H](O[PH]([O-])=O)[C@@H](CO)O2)C(=O)NC1=O   14   9

These groups will allow the user to construct DNA and RNA strands from 5' to 3'. I needed to use Ct and Ur instead of C or Cy and U because the latter abbreviations were already taken.

Thanks, Bob. I added them to the abbreviation list!

I have been trying to put the new shortcut groups in my local version of Marvin, but no luck. Here's what I'm doing:





unjar marvin.jar


copy chemaxon/marvin/templates/default.abbrevgroup to my own computer


copy new abbreviated groups into the bottom of default.abbrevgroup


copy default.abbrevgroup back to its original location


change default.abbrevgroup from Mac to Unix format


rejar marvin.jar





But nothing is changing when I go back to the Web site and use Marvin. The new groups don't appear, even after I quit, restart, and empty my cache. Am I doing anything wrong?

You have been choosen a very complicated way to append your shortcuts to "default.abbrevgroup".


I suggest you a more simple way:


1. Take a copy about "default.abbrevgroup" in your marvin directory.


2. Edit the copied version of "default.abbrevgroup" to append your shortcuts to the list.


3. Define "abbrevgroups" parameter in your applet example:

Code:

msketch_begin("../..", 460, 380); msketch_param("abbrevgroups","mydefault.abbrevgroup"); msketch_end();

where "mydefault.abbrevgroup" is the modified version in the "marvin" directory.





Take care to use the '\t' (tabulator) character as delimiter in the abbrevgroup file. Also avoid empty lines in this file because it can cause problem at reading data.


If you use Linux, Unix or OS X, you can check the special character in your files: just type the "od -c" command in a terminal window:

Code:

od -c mydefault.abbravgroup

The tail of the file should look like this (by displaying it with the "od -c" command):

Code:

0040160   O  \t   5  \t   6  \n   Z  \t   O   =   C   O   C   C   1   = 0040200   C   C   =   C   C   =   C   1  \t   2  \n   Z   N   H  \t   N 0040220   C   (   =   O   )   O   C   C   1   =   C   C   =   C   C   = 0040240   C   1  \t   1 0040244

As you see, there is not any '\n' character after the last record. Use '\n' (Unix end line) character to close lines.

I tried what you suggested. I got this error message:

Code:

java.util.NoSuchElementException    at java.util.StringTokenizer.nextToken(StringTokenizer.java:259)    at chemaxon.marvin.modules.AbbrevgroupImport.readMol(Unknown Source)    at chemaxon.marvin.util.MolLoader.a(Unknown Source)    at chemaxon.marvin.util.MolLoader.n(Unknown Source)    at chemaxon.marvin.util.MolLoader.run(Unknown Source)    at java.lang.Thread.run(Thread.java:552)

My jsp file had the following line in the Marvin applet definition:





msketch_param("abbrevgroups","ACE.abbrevgroups");





I put the ACE.abbrevgroups file in the Marvin directory, marvin4.0.5, the same one in which the jar file is found. Is that correct? I tried it both before and after converting the file (which I edited on my Mac) from Mac to Unix format. Here is how the last two lines from od -c read:

Code:

0041320   =   C   C   =   C   1  \t   1  \n  \n 0041332

Modify the last line like this:

Code:

0041320   =   C   C   =   C   1  \t   1 0041332

Great, that worked much better. Thanks.





You might see about making the abbrevgroups file tolerant of blank lines....

OK, I will make a bug report to myself and try to implement it in the near future.

Tamas wrote:

You have been choosen a very complicated way to append your shortcuts to "default.abbrevgroup". I suggest you a more simple way: 1. Take a copy about "default.abbrevgroup" in your marvin directory. 2. Edit the copied version of "default.abbrevgroup" to append your shortcuts to the list. 3. Define "abbrevgroups" parameter in your applet example: Code: msketch_begin("../..", 460, 380); msketch_param("abbrevgroups","mydefault.abbrevgroup"); msketch_end(); where "mydefault.abbrevgroup" is the modified version in the "marvin" directory.

How do I point Marvin Beans (desktop application) to my own abbreviated groups file?

Also, I tried using your instructions for adding user-defined groups to the My Template window. I was able to create a new group with an attachment point, but when I added it to My Templates, the attachment point was lost, so it was only a standalone molecule. Is it possible to add a user-defined group with an attachment point to My Templates?





Also, when I quit Marvin and restarted, the group I added to My Templates had disappeared. Wasn't the addition supposed to be permanent?

Indeed. We will fix it.

Quote:

Also, I tried using your instructions for adding user-defined groups to the My Template window. I was able to create a new group with an attachment point, but when I added it to My Templates, the attachment point was lost, so it was only a standalone molecule. Is it possible to add a user-defined group with an attachment point to My Templates? Also, when I quit Marvin and restarted, the group I added to My Templates had disappeared. Wasn't the addition supposed to be permanent?

It is working. Before you paste my templates to the canvas please select "Expand" option in the My Templates window. You can specify there in which status paste the template. The default value is ungroup. In this case, the compound is pasted (and group info like group name and attachment point is lost). By "expand" and "contract" options, these data are preserved.