Naming

I am using the latest version of JChem, in particular Marvin Sketch (5.3.2).   For example-sketch3.4, I can import anything, including the name that I type in.  However, I cannot export the IUPAC name as determined by Marvin.   Is this a bug, or a licensing issue.  (I can use the menu bar to generate the IUPAC name, I just cannot export it.)

What is the correct javascript to capture the name for the structure that the student enters? 

If the student enters some hydrogens (but not all) in order to specify stereochemistry at a chiral center, how are those treated in the smiles  or smarts string formats?

A related question.  I am developing tutorials for organic chemistry, and accurate stereochemical designation is important.  These are not complicated compounds.  However, in some programs I have tried, I have found that the smiles string varies, depending upon how the structure is presented on the page.  Since I cannot control how that is done by the student, I am looking for shortest but most accurate way to compare student input to my answer.  I have thought of 3:

smiles (but see the caveat above)

smarts (have not tried extensively)

IUPAC name

The last seems best from the viewpoint of my own trying to digest the meaning of the entries in my data files. (That simply says that I do not read smiles and smarts well).

Which of the three would you see as most accurate and unique in Sketch?

 

Phil

I assume the licence file is missing from your machine that's why Marvin do not export structure into IUPAC name format. Consult with sales guy about it.

About structure comparision: string comparision is not the best way to check matching of the target.

There are sophisticated tools in JChem package that can be useful for us for comparission.

I forward your topic to JChem guys. He can tell more about it.

Yes, it was a license problem and  now the example works.  It needs a comment to explain what the problem is for the uninitiated.

I await comments from the experts:-)

Hi Phil

One way is string matching indeed.

- Smiles should be fine for comparing molecules, smarts is used to represent queries. To avoid the problems you mentioned, additional format parameters should be used: You should use unique smiles (smiles:u) to canonicalize atom order, and remove explicit H-s (smiles:u-H). Unique smiles also aromatizes the molecule, so that different aromatic resonant forms are represented the same way.

See more: http://www.chemaxon.com/marvin/help/formats/smiles-doc.html#options

- I do not know how canonical the generated IUPAC names are. I guess that unique smiles above does a better job.

 

If you would like to consider other factors, like ignore stereochemistry, isotopes or tautomers, etc, You may consider doing duplicate matching using the MolSearch class in JChem. It offers many search options to change the default behaviour. For more details, see:

http://www.chemaxon.com/jchem/doc/dev/search/index.html#searchmem

 

Best regards,

Szabolcs

Thanks, I will give that a try, after I figure out how to embed the applet:-(

It has been a while since I worked with marvin so I got a license, downloaded and installed the latest version yesterday.  I have learned that the best way to learn how to do things is to look at what someone else has done and tinker with it.  So I went to the examples for sketch.  Number 1.1, the most basic.

I tried to open it in a text editor to see the code.  Nothing there.  Hmmm. So I view the source in my browser and see the code.   I copy it all, past it into my text editor, and save it with a new name in the examples directory.  Launch it.   No applet. 

What am I missing?  It is the same code as far as I can tell; it is located in the same place relative to the applet; but it will not load the applet.

All of the examples  in your directory work fine for me, but I can get none to work from what I think is identical source code from within the same directory. 

 

Using latest release of marvin on an intel mac running the latest version of snow leopard.

First of all, you need a web server where you can install the applet package.to.

Download the desired applet package from the site and setup to the web server.

I recommend to download the full applet package. If the package is installed properly to the server, Marvin applet examples in the package will display fine in your browser.

Please see the proper part of the documentation: Installation - Marvin Applets .

After that, you can start deploy your own applet examples. If you are not familiar with writting HTML pages, I recommend you consulting with a HTML tutorial.

If you have already a basic knowladge in web page writting, investigate the description in our first applet example.

It describes which code sniplet is required to embed applet in a web page. When you do it, take care to modify the references to codebase, since location of web page can be differ than the codebase where n marvin applet binaries (mostly jars) are located.

MarvinSketch Example - Embedding MarvinSketch applet in html pages