target.toFormat("smiles") ERROR

To whom it concerns,





Here is a snippet of my code:





try{


MolImporter mi = new MolImporter("Individual.sdf");





Molecule target = null;


.


.


.


.





while((target = mi.read()) !=null)


{


.


.


String smForm = target.toFormat("smiles");


.


.


.


}


mi.close();


}catch(IOException ioe)


{ ioe.printStackTrace();


}





.


.


}


}





Now in most cases if the SMILES string is invalid for example





(CCCC(CCC)CCC





the code throws an exception which is caught and this piece of code is exited. But, in one particular case when the SMILES string is as follows;





C1CCCC2CCC3CCC3(C1CCCCC2)C21C21





the code was left 'hanging'


I know that this SMILES string is Invalid but, I'd like the code to be able to handle any Invalid SMILES string.





I would appreciate any suggestions as to how I can ensure that if an Invalid SMILES is found then the code exits and returns a message(e.g. -999) to the calling function.





Thanks,


Miriam O'Riordan

















....


String smForm = target.toFormat("smiles")

Dear Miriam,





There are some things which are not clear for me.


It seems from your code snippet that you import an sdf file and export it to SMILES format.


But later, if I understand well, you have problem with SMILES import.


So let me focus on the part which I think I have understood.





You have two invalid smiles strings


(CCCC(CCC)CCC


C1CCCC2CCC3CCC3(C1CCCCC2)C21C21


and the problem is that the code hangs.





I actually cannot reproduce the 'hanging', only exceptions.


I have written a simple test code which can handle invalid smiles strings by catching the exceptions.

Code:

java Test invalid.smi The 0th molecule is invalid smiles The 1th molecule is invalid smiles CCCC The 3th molecule is invalid smiles

Andras

Hi Andras,





Thanks for replying to my query. I'm sorry for not getting back to you sooner but, I've been away since the 22nd Aug.





When I compared you're code Test.java with mine the most obvious difference was the following;





MyCODE:


Molecule target ;


MolImporter mi = new MolImporter("Individual.sdf");





target = mi.read();





YourCODE:


Molecule m = new Molecule();


MolImporter molimp = new MolImporter(s);





if(!molimp.read(m));





WHY is the previous line of code NOT as follows





if(!m=molimp.read())





Thanks,


Miriam

Dear Miriam,





From the API documentation of MolImporter:


http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/formats/MolImporter.html#read(chemaxon.struc.Molecule)


Returns:


true after success, false at end of file





So the while loop continuously reads the file

Code:

while(true){

and we escape from it at the end of the file:

Code:

if (!molimp.read(m)){ // at the end of the file read() returns false so we negate    break; }

I hope it is clear now





Andras

Hi Andras,





Thanks for your explanation but,I'm confused with respect to the following point.





In your code Test.java the SMILES string is imported and 'stored' in the MolImporter data structure molimp. Then, an empty Molecule data structure 'm' is created.


In my opinion, the code snippet,


molimp.read(m);





is saying read the empty molecule m.





Thanks,


Miriam

Dear Miriam,





The read method reads the SMILES string into the molecule m.


In other word it parses the SMILES string and generates the molecule representation in molecule m.If the method reaches the end of the file it returns false otherwise true.

Quote:

molimp.read(m); is saying read the empty molecule m.

No it says parse the input and generate the corresponding molecule structure in m.





Andras

Hi Andras,





Thanks for that explanation. It makes sense to me now.





All the best,


Miriam

Hi Andras,





In my original message under this topic I had assumed that the problem originated at the line of code





String smForm = target.toFormat("smiles")





But, my problem has reappeared and it would seem to be located at the line





try{


mol = nmi.read();





When Individual.sdf is as follows;


Oc1cncc2C=CC(Cc3nccc4CCc5c(C=O)c(CONN(C(=O))SC(c7ccccc7)SCN)c(Cc3nccc4C(CF)NOc5\


cc(Cc7ccccc7)c(Nccc(C)CNcnc(C=N)cSC(C=N)C)c(c7ccccc7Cl)c5Nc43)c(C=N)c5N(C=N)c43\


)CC(Br)c2





I get the following message


java.io.IOException: Unmatched ring closure number 1 in SMILES string Oc1cncc2C=CC(Cc3nccc4CCc5c(C=O)c(CONN(C(=O))SC(c7ccccc7)SCN)c(Cc3nccc4C(CF)NOc5cc(Cc7ccccc7)c(Nccc(C)CNcnc(C=N)cSC(C=N)C)c(c7ccccc7Cl)c5Nc43)c(C=N)c5N(C=N)c43)CC(Br)c2


at chemaxon.marvin.modules.SmilesImport.readMol0(Unknown Source)


at chemaxon.marvin.modules.SmilesImport.readMol(Unknown Source)


at chemaxon.marvin.modules.SmilesImport.readMol(Unknown Source)


at chemaxon.formats.MolImporter.readMol(Unknown Source)


at chemaxon.formats.MolImporter.read(Unknown Source)


at chemaxon.formats.MolImporter.read(Unknown Source)


at chemaxon.marvin.calculations.My_MolCalculator_Two_Rack17.main(My_MolCalculator_Two_Rack17.java:56)





This is what I'd expect to happen.





The PROBLEM is


when the molecule(Individual.sdf) is as follows the system just hangs





Oc1cncc2C=CC(Cc3nccc4CCc5c(C=O)c(CONN(C(=O))SC(c7ccccc7)SCN)c(Cc3nccc4C(CF)NOc5\


cc(Cc7ccccc7)c(Nccc(C)CNcnc(C=N)cSC(C=N)C)c(c7ccccc7Cl)c5Nc43)c(C=N)c5N(C=N)c43\


)CC(Br)c21








I want to ensure that if an INVALID SMILES molecule is encountered by the Java code that it(the Java code) will exit. I am aware that in the both examples of the molecule above that the Rings are numbered correctly the CORRECT Molecule should be





Oc1cncc2C=CC(Cc3nccc4CCc5c(C=O)c(CONN(C(=O))SC(c7ccccc7)SCN)c(Cc6nccc7C(CF)NOc8\


cc(Cc7ccccc7)c(Nccc(C)CNcnc(C=N)cSC(C=N)C)c(c7ccccc7Cl)c8Nc76)c(C=N)c5N(C=N)c43\


)CC(Br)c21





This molecule is passed to the java code with no problems/exceptions.





I would be very grateful if you could suggest a way that I could guarantee that ANY Invalid SMILES would cause the Java code to exit/return an error message to the calling function.





Kind Regards,


Miriam

Hi Miriam,





The solution is simple: change the catch exception type from MolFormatException to Exception. In this case any type of exception will generate the error printout.





Please let me know if it solves your problem.





Andras

Hi Andras,





I tried that but, the code is still hanging.





thanks,


Miriam

Hi,





Could you attach the sdf file which contains the molecule that hangs.


In that case I can check the problem more deeply.





Andras

Hi Andras,


Please find attached the file Individual.sdf.





Thanks,


Miriam

Hi Andras,





I thought that my problem may be due to the version of MarvinBeans that I was running. When I tried to install version marvinbeans-5_1_01-linux.sh I got the following error message:





testing JVM in /usr ...


testing JVM in /usr/java/jre1.6.0_07 ...


No suitable Java Virtual Machine could be found on your system.


The version of the JVM must be at least 1.4.2.


Please define INSTALL4J_JAVA_HOME to point to a suitable JVM.


You can also try to delete the JVM cache file /home/miriam/.install4j





I tried everything but, I still can't install MarvinBeans. Have you any suggestions as to what I could do next?





thanks,


Miriam

Hi Miriam,





At first, the given Individual.sdf is not an sdf file but smiles, so you should rename it to Individual.smi to have Test.java working.


On the other hand, if you modify the Test.java as I we have discussed earlier:


form

Code:

} catch (chemaxon.formats.MolFormatException e){

to

Code:

} catch (Exception e){

then it works as you would expect:

Quote:

java Test Individual.smi The 0th molecule is invalid smiles

Andras

Hi Andras,





Thanks for that. It's working fine now. One other question when I tried to install version 5.1.1 of marvinbeans (current version is 4.1.13) I get the following Error message:





No suitable Java Virtual Machine could be found on your system.


The version of the JVM must be at least 1.4.2.


Please define INSTALL4J_JAVA_HOME to point to a suitable JVM.


You can also try to delete the JVM cache file /home/miriam/.install4j








I tried everything and I re-installed the latest version of Java.





Using version 4.1.13 I typed





javac -d ./ MyFile.java





now I get a list of WARNINGS(which I never got before) e.g.,





WARNING in MyFile.java (at line 4)





import chemaxon.marvin*;





The import chemaxon.marvin is never used.








When I then type





java chemaxon.marvin.calculations.MyFile





I get the Exception message that I'd expect for the molecule in Individual.smi.








Are the WARNINGS a result of the newer version of Java and is it ok to ignore the Warnings?





Thanks again for all your help it is very much appreciated.





Miriam

Hi,





I think you can ignore the warnings. These are rather java programming specific questions but Tamas will tell you more about this.





Andras

The Marvin Beans installer works fine for me on my Linux.


Probably, your default Java is not Sun distributed one or it is earlier than 1.4.2.


Please check your configuration. Type "java -version", you should get something like that:

Code:

vertset@asus-laptop:java -version java version "1.6.0_03" Java(TM) SE Runtime Environment (build 1.6.0_03-b05) Java HotSpot(TM) Client VM (build 1.6.0_03-b05, mixed mode, sharing)

This description can be also useful: Installation Guid for Marvin Beans


I also recommend to read the linking forum topics:


installation error on linux


installation error on Mandriva 2007


If you do not manage to launch installer, I can suggest to use the cross-platform version of Marvin Beans package.


http://www.chemaxon.com/marvin/download-user.html


It is a zip archive, just download and extract it somewhere.

Hi Tamas,





I checked the Java version (the message is below) and you're right it is not a SUN one.


I will try to install marvinbeans using the crossplatform version.





Thanks,


Miriam





java -version


java full version "kaffe-1.4.2"





kaffe VM "1.1.7"





Copyright (c) 1996-2005 Kaffe.org project contributors (please see


the source code for a full list of contributors). All rights reserved.


Portions Copyright (c) 1996-2002 Transvirtual Technologies, Inc.





The Kaffe virtual machine is free software, licensed under the terms of


the GNU General Public License. Kaffe.org is a an independent, free software


community project, not directly affiliated with Transvirtual Technologies,


Inc. Kaffe is a Trademark of Transvirtual Technologies, Inc. Kaffe comes


with ABSOLUTELY NO WARRANTY.





Engine: Just-in-time v3 Version: 1.1.7 Java Version: 1.4


Heap defaults: minimum size: 5 MB, maximum size: unlimited


Stack default size: 256 KB

Actually, downloading the crossplatform version is not enough.


Under Linux, Marvin uses the default Java in all cases.


Marvin (like any other ChemAxon product and the installer) does not support kaffe Java. It is not a Sun compatible Java distribution.


If kaffe is your default one, you can get unexpected errors by running Marvin.


See the System requirements





To be able to use Marvin, install a Sun distributed Java version and change the default Java to Sun's one.





The simplest way is the following:


Modify the PATH variable: start your PATH variable with the reference to Sun's Java. (In this case, This Java will be used instead of "/usr/bin/java".)


To do this, just modify your bash profile (if you use other shell modify the proper script of your shell):

Code:

export JAVA_HOME=/opt/jre1.6.0_07 export PATH=$JAVA_HOME/bin:$PATH