MarvinSpace WS parameters

Hi,





I am trying to integrate MarvinSpace with my web application using java web start. This was chosen because applets were crashing my browser on unload (the known issue).





Anyways, here's my question. I was trying to look for some documentation regarding the MSpace class but unfortunately found none in the javadoc provided.





Specifically, I need to load up 2 files, pdb and sdf to be specific, and display all the molecules inside one cell. (It would also be helpful if I could find out from anyone how not to trigger the popup of loading multiple molecules into one cell confirmation)





Using the examples provided on the chemaxon page, here's what I have in my jnlp file..





<application-desc main-class="chemaxon.marvin.space.gui.MSpace">


<argument>http://url.to.get/molecule.pdb </argument>


<!-- the top and bottom line cannot coexist, removing either one works! -->


<argument>http://url.to.get/molecules.sdf</argument>;


<argument>-s</argument>


<argument>-p</argument>


<argument>Ligand.DrawType</argument>


<argument>Stick</argument>


<argument>-p</argument>


<argument>Water.DrawType</argument>


<argument>Ball</argument>


<argument>-p</argument>


<argument>MacroMolecule.ColorType</argument>


<argument>Residue</argument>


<argument>-p</argument>


<argument>MacroMolecule.DrawType</argument>


<argument>Stick</argument>


<argument>-p</argument>


<argument>Ligand.ColorType</argument>


<argument>Constant</argument>


<argument>-p</argument>


<argument>ShowSurface</argument>


<argument>Connolly</argument>


<argument>-p</argument>


<argument>Surface.DrawType</argument>


<argument>Transparent</argument>


</application-desc>








Any help is much appreciated. Thanks in advance!

Hi,





the GUI of MarvinSpace is not fully elaborated, that's why MSpace and MSpaceApplet class are not public yet. Brief information about the application and its arguments can be found at http://www.chemaxon.com/marvin/doc/user/mspace.html





I created a jnlp file similar to yours (but with different files) and it loaded them just fine. Unfortunately I was unable to reproduce the problem you mention.


By the way I found a display error on the selection panel, ligands were not displayed there just when you loaded them first and the pdb afterwards. Is it possible that this was the problem? If not, could you please specify it?





About not triggering the popup: MarvinSpace has bean updated today. In case of downloading or using http://www.chemaxon.com/shared/MarvinSpace/mspace.jar the required function is available by using the --singleCell argument. The --multiCell argument is also available.





Thank you for your suggestion! Any more ideas are welcome.

Thanks for your reply. I found out that the problem was with one of my urls to the structures, mspace wasn't liking the file that was spit out from the url and hung there indefinitely, unable to proceed to the next file.





as for the --singleCell --multiCell option, is it included in the jnlp file as something like :


<argument>--singleCell</argument>


??





Another question, the list of arguments that was specified in the jnlp file on your examples, is there a place where i can an enumerated option list? For example, the MacroMolecule.DrawType and the list of its available options.





Thank you.

Thank you for the feedback. The hanging up will be handled soon.





Yes, you can use them like <argument>--singleCell</argument>. Arguments have a short and a long version, like -h and --help. This new argument does not have a short version yet.





You can find information from the gui's view in the MarvinSpace Help at http://www.chemaxon.com/marvin/chemaxon/marvin/help/space-index.html


More advanced information can be found in the API, search for

Code:

public void setDrawProperty(java.lang.String propertyName,java.lang.String propertyValue)

functions mainly in MoleculeComponent, MacroMoleculeComponent, MolecularSurfaceComponent classes.


As I checked it now, part of the description in the MacroMoleculeComponent apidoc is missing. It will be compensated soon.

Hi,





I am trying to set the ligand color type to cpk via jnlp code.


I was trying the following..


<argument>-p</argument>


<argument>Ligand.ColorType</argument>


<argument>Colors.CPK_MODE</argument>





I also tried <argument>CPK</argument> or <argument>CPK_MODE</argument> but to no avail. Any help here would be much appreciated :)





Thank you!

Hi,





the possible settings of ligands can be found in the API of the MoleculeComponent.setDrawProperty(String, String) function. The proper value is


<argument>-p</argument>


<argument>Ligand.ColorType</argument>


<argument>CPK</argument>





The settings of other visualizers (water, protein chains and ions) are unfortunately missing from the API, or more precisely they are not public yet.





Until then, I will create a quick collection of the properties, it will be linked here soon (hopefully tomorrow).

Hi,


That did not work. If i manually set it inside the program, it works like a charm, always. If i do it from the jnlp file, then it fails. Here is my jnlp file:





<application-desc main-class="chemaxon.marvin.space.gui.MSpace">


<argument>url.link.to/1azm.pdb</argument>


<argument>url.link.to/solutions.sdf</argument>


<argument>--singleCell</argument>


<argument>-s</argument>


<argument>-p</argument>


<argument>Ligand.DrawType</argument>


<argument>Stick</argument>


<argument>-p</argument>


<argument>Ligand.ColorType</argument>


<argument>CPK</argument>


<argument>-p</argument>


<argument>Water.DrawType</argument>


<argument>Ball</argument>


<argument>-p</argument>


<argument>MacroMolecule.ColorType</argument>


<argument>Residue</argument>


<argument>-p</argument>


<argument>MacroMolecule.DrawType</argument>


<argument>Stick</argument>


<argument>-p</argument>


<argument>Ligand.ColorType</argument>


<argument>Constant</argument>


<argument>-p</argument>


<argument>ShowSurface</argument>


<argument>Connolly</argument>


<argument>-p</argument>


<argument>Surface.DrawType</argument>


<argument>Transparent</argument>


</application-desc>








perhaps its something to do with the input files?

No, it is simpler:)


You set the color type to cpk, and a few arguments later you set it to constant. It's the third argument from the back.


The default color type of ligands is cpk, so you don't need to specify it as an argument.

oops :)


my bad!! many thanks!!!

The list of the MarvinSpace options is available here, and this link can also be found at the Documentation section at the MarvinSpace homepage.