ChemAxon Forum Archive » Structure manipulation: Reactor, Metabolizer

retain building block information when enumerating library

User c65f7ade2a

15-02-2008 14:52:59

How can I retain information on the parent building blocks (just the BB name/number would be sufficient) that had been combined for the respective product molecules when exporting the enumerated library as SD file?

ChemAxon d76e6e95eb

15-02-2008 17:14:50

If you are using the API or the react command line tool, you can generate a synthesis code for each product containing the ID of the reaction and the corresponding reactants. You can specify which SDfile field contains the ID of your compounds.





Code:
react -r r1.rdf -f sdf a1.sdf a2.sdf -i R1 -R ID,CD_ID -P PID






Do you need this feature in the Reactor application (GUI)?

User c65f7ade2a

15-02-2008 17:28:25

Thanks Gyuri, yes I was looking for this functionality in the Reactor application.

ChemAxon d76e6e95eb

15-02-2008 17:32:11

We will support this feature in the Reactor application in the next major JChem release (5.1).

User c65f7ade2a

16-02-2008 23:09:50

Trying to use the command line interface yields following error message





Registry key 'Software\JavaSoft\Java Runtime Environment\CurrentVersion'


has value '1.5', but '1.3' is required.


Error: could not find java.dll


Error: could not find Java 2 Runtime Environment.

ChemAxon e08c317633

18-02-2008 16:38:43

What Java version do you use? Please post the output of the


Code:
java -version



command.





How is the JAVA_HOME environmental variable set on your system?

ChemAxon 7c2d26e5cf

19-02-2008 00:07:16

Quote:
Registry key 'Software\JavaSoft\Java Runtime Environment\CurrentVersion'


has value '1.5', but '1.3' is required.


Error: could not find java.dll


Error: could not find Java 2 Runtime Environment.
This issue is not related to Marvin. It is a Java configuration problem.


Probably there are several Java version on your machine and they are in conflict with each other. Maybe an earlier version of Java is not removed properly that caused inconsistent state in your system registry.


Please read the linking topic about this problem from the Java forum of Sun:


New To Java - Newbie questions - registry key


In the refered topic, you can get tips how to solve it.


By the way, if you copy the above error message into google, you will get further hits about this problem.





Just a note about Marvin: newer version of Marvin does not support Java 1.3.1. Marvin and JChem products require Java 1.4.2 or higher version.


If you use Marvin / JChem installers with bundled Java, you can avoid conflict with other Java versions. This bundled Java is available only for Marvin / JChem applications. It is not registered in the system registry, so it has no effect to other Java applications on your machine.

User c65f7ade2a

19-02-2008 02:37:33

thanks guys!

User 9547aebe97

23-10-2008 18:23:11

Gyuri wrote:
We will support this feature (generate a synthesis code for each product containing the ID of the reaction and the corresponding reactants) in the Reactor application in the next major JChem release (5.1).
I just installed JChem 5.1.2 and I do not see where I can apply this feature in the Reactor application. Any suggestions?

ChemAxon e08c317633

27-10-2008 14:09:10

Unfortunately the Reactor application (GUI) does not support it yet, but we will add this feature to it very soon.





Till then you can use the react command line tool, which can generate the synthesis code for each product.
Quote:
If you are using the API or the react command line tool, you can generate a synthesis code for each product containing the ID of the reaction and the corresponding reactants. You can specify which SDfile field contains the ID of your compounds.





Code:
react -r r1.rdf -f sdf a1.sdf a2.sdf -i R1 -R ID,CD_ID -P PID



Sorry for the inconvenience.





Zsolt

ChemAxon d76e6e95eb

09-11-2010 07:21:55

The synthesis code generation feature has been added to the Reactor GUI that will be available in the upcoming 5.4 version in a few weeks.