bad clean2d option to catalina.out

Hi

We are using marvin v5.3.8 and tomcat 6.0.28 on linux box.

Somehow, marvin view suddenly started writing the following lines to the log.

Could you tell me what this mean and how I can stop it.

Do I need to change my setup on log4j?

Thanks,

yasushi

 

O: bad Clean2D option
1: bad Clean2D option
O: bad Clean2D option
1: bad Clean2D option
O: bad Clean2D option
1: bad Clean2D option
O: bad Clean2D option
1: bad Clean2D option
O: bad Clean2D option
1: bad Clean2D option
O: bad Clean2D option
1: bad Clean2D option
O: bad Clean2D option
1: bad Clean2D option
O: bad Clean2D option
1: bad Clean2D option

Hi,

The clean options 01 02 etc does not exist any more.

Please remove these options from the preferences or marvin properties file.

The property file is located at

$HOME/.chemaxon/marvin.properties

where $HOME is the home directory of the user running tomcat.

 

Andras

If I understand correclty the situation, you use Marvin View API on server side (under Tomcat).

Can you confirm this?

Do you have any special reason why you use viewer for molecule clean on server side? Marvin View is a graphical component (designed to integrate it into desktop solutions). If you work on structures on server side, I recommend MolImporter, MolExporter, Molecule API in Marvin Beans package.

Tamas wrote:

If I understand correclty the situation, you use Marvin View API on server side (under Tomcat). Can you confirm this? Do you have any special reason why you use viewer for molecule clean on server side? Marvin View is a graphical component (designed to integrate it into desktop solutions). If you work on structures on server side, I recommend MolImporter, MolExporter, Molecule API in Marvin Beans package.

Hi

We do not use marvin view API.  I thought this error came from marvin view, but I think it does not make sense. So, it might be from MarvinBeans or somewhere from server side using mavin related classes.

Can you tell me which class is throwing this error?.

volfi wrote:

Hi, The clean options 01 02 etc does not exist any more. Please remove these options from the preferences or marvin properties file. The property file is located at $HOME/.chemaxon/marvin.properties where $HOME is the home directory of the user running tomcat.   Andras

Hi Andras

Sorry, I missed your post.  We do not have marvin.properties in home direcotry, but only license.cxl exists.

Is it happening because someone is using old marvin + old preference on client side?  If so, why is the error captured in catalina.out? We are pusing marvin v5.3.8 to the client from server.

yasushi

webprd2:~ =>ls .chemaxon/
license.12.1.2010*  license.cxl.08.24.2010*  license.cxl.temp*  license_struct2name.cxl*
license.cxl*        license.cxl.12.13.2010*  licenses.dat

Hi,

You are right the problem may be on server side.

The marvin.properties file presents if you use MarvinView/Sketch applications/components. They read/write it automatically. If you process structures directly via the Marvin Beans API, you do not meet this properties file.

Are you sure that the deprecated clean option has not been hardcoded somewhere in your code?

There are several way to pass this option to molecule clean. Please read the following documentation that enumerates cases where clean options can be set: Cleaning options.

Please check these cases in your code whether the deprecated option still presents in an invoke.

Of course, we are also checking our code whether there is any reference  to the deprecated clean options.

Tamas wrote:

Hi, You are right the problem may be on server side. The marvin.properties file presents if you use MarvinView/Sketch applications/components. They read/write it automatically. If you process structures directly via the Marvin Beans API, you do not meet this properties file. Are you sure that the deprecated clean option has not been hardcoded somewhere in your code? There are several way to pass this option to molecule clean. Please read the following documentation that enumerates cases where clean options can be set: Cleaning options. Please check these cases in your code whether the deprecated option still presents in an invoke. Of course, we are also checking our code whether there is any reference  to the deprecated clean options.

Hi Tamas

Thanks for the info. I found a legacy code in one of our applications and you are right. It is passing depreciated option to the clean function.  So, could you tell me this deprecated "O1" option is replaced by which new option?

Thanks,

yasushi

2D options

• Base: (none available)


• Extra:
  

  e Keep verbose either flag

  
  
  
  If it is not possible to decide whether the double bond is CIS or TRANS, the double bond either flag (crossed double bond) is kept.
  Otherwise, the flag is removed and converted to double bond with a wiggly bond.
  
  
  

  E Error output:

  
  
  
  0 - no output (default)
  1 - error output to standard error
  
  
  

  d show debugging info

  
  

  2 try to keep actual 2D alignment

  
  

  p ignore parity setting

  
  
  
  do not set wedges, the parity information is lost.
  
  
  

  H add Hydrogens

  
  
  
  Add Hydrogen atoms to chiral centers
  having no terminal atoms.
  
  
  

  w wedge clean

  
  
  
  Do not try to keep the actual wedge arrangement,
  but rearrange the wedges also.
  
  
  

  W stereo clean

  
  
  
  Only rearrange the wedges of the molecule, but keep the original coordinates untouched.
  
  
  

  tX set time limit to X ms

  
  
  
  maximum time spent in the cleaning
  default value: 20000ms
  if X<1, no time limit used
  
  
  

  T{filename} ring system template file name

  
  
  
  Use the template file during ring system cleaning together with the local template file definition (which is located at the users home directory .chemaxon/cleantemplates.t).
  
  
  

 

Thanks for the feedback.

I pass your question to my colleague (Andras Volford). He can say which clean option is recommended in this case.

Hi,

The clean2D algorithm is working in a different way now, and the 'O1' option has no substitution in the new version.

So you don't need to use any option.

Andras