how to roll back to an older version JChem?

We installed the JChem3.2, found the react speed is slow, and now decide to roll back to JChem 3.1.7. I reinstalled the Jchem code, but I dont know how to "regenerate" the database from 3.2 to 3.1.7.





When I use try to add or edit the compound(our servlet codes), there is an exception called "The structure table contains newer data version that this program version can handle. Please use a later version." As well as I execute the jcman (version 3.1.7) to regenerate compound table, the exception also appears.





I also try to move back the compound table (backup file under 3.1.7) in MySQL database, but it doesn't help. (The above excetption still appear.)





Any sugguestions on this issue? Thank you in advance!





Jeff

JeffGao wrote:

We installed the JChem3.2, found the react speed is slow, and now decide to roll back to JChem 3.1.7. I reinstalled the Jchem code, but I dont know how to "regenerate" the database from 3.2 to 3.1.7. When I use try to add or edit the compound(our servlet codes), there is an exception called "The structure table contains newer data version that this program version can handle. Please use a later version." As well as I execute the jcman (version 3.1.7) to regenerate compound table, the exception also appears. I also try to move back the compound table (backup file under 3.1.7) in MySQL database, but it doesn't help. (The above excetption still appear.) Any sugguestions on this issue? Thank you in advance! Jeff

Solution:





First, find the table JChemProperties, change the fields table.compound.version, table.rxn.version from 32 to 17.


Then, regenerate the tables with jcman(3.1.7).


(Don't forget to backup tables - JChemProperties, compound, rxn).





Everything seems OK now. Thanks for Dave Roe's help!





Jeff

Jeff,

Quote:

We installed the JChem3.2, found the react speed is slow, and now decide to roll back to JChem 3.1.7.

I rather wanted to suggest you an upgrade (but it seems I'm just a bit late):


AFAIK the Reactor is slower because it has a more "clever" reaction mapping algorithm.


This new algorithm seems to be slow, we plan to speed it up soon.


We have just released JChem 3.2.1 a couple of minutes ago, where you can specify the

Code:

-a changing

flag again to imitate the old behaviour as a temporary measure.


(I'm not a Reactor expert, my colleagues will correct me soon if necessary)





Downgrade in general:


This is not officially supported.


The method you have described works between certain versions (if there were no changes in the JChem table structure).


3.2 and 3.1.7 are compatible in this sense, but this is not recommended as a general practice.





Best regards,





Szilard

Szilard wrote:

Jeff, Quote: We installed the JChem3.2, found the react speed is slow, and now decide to roll back to JChem 3.1.7. I rather wanted to suggest you an upgrade (but it seems I'm just a bit late): AFAIK the Reactor is slower because it has a more "clever" reaction mapping algorithm. This new algorithm seems to be slow, we plan to speed it up soon. We have just released JChem 3.2.1 a couple of minutes ago, where you can specify the Code: -a changing flag again to imitate the old behaviour as a temporary measure. (I'm not a Reactor expert, my colleagues will correct me soon if necessary) Downgrade in general: This is not officially supported. The method you have described works between certain versions (if there were no changes in the JChem table structure). 3.2 and 3.1.7 are compatible in this sense, but this is not recommended as a general practice. Best regards, Szilard

Thanks, Szilard. Your suggestion with using "-a" is helpful.





We are still looking forward to see a new version jchem with the react speed improvement. Thanks again!





Jeff

Hi,

Quote:

Unfortunately, it seems there is no improvement on the speed of react of this new version Jchem.

It seems you cave missed the crucial part of my advice:

Quote:

We have just released JChem 3.2.1 a couple of minutes ago, where you can specify the -a changing flag again to imitate the old behaviour in 3.2.1 as a temporary measure.

So please use

Code:

-a changing

flag to obtain the same behaviour in 3.2.1 that was the default for 3.1.7.





For example:





react -a changing -v -r bt0088.mrv "CC(C)(C)C(=O)SCCNC(=


O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(


O)=O)n2cnc3c(N)ncnc23"





Of course we plan to speed up the new default behaviour too.





Best regards,





Szilard

Szilard wrote:

Hi, Quote: Unfortunately, it seems there is no improvement on the speed of react of this new version Jchem. It seems you cave missed the crucial part of my advice: Quote: We have just released JChem 3.2.1 a couple of minutes ago, where you can specify the -a changing flag again to imitate the old behaviour in 3.2.1 as a temporary measure. So please use Code: -a changing flag to obtain the same behaviour in 3.2.1 that was the default for 3.1.7. For example: react -a changing -v -r bt0088.mrv "CC(C)(C)C(=O)SCCNC(= O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)( O)=O)n2cnc3c(N)ncnc23" Of course we plan to speed up the new default behaviour too. Best regards, Szilard

That's helpful. Thanks again!

Szilard wrote:

Hi, Quote: Unfortunately, it seems there is no improvement on the speed of react of this new version Jchem. It seems you cave missed the crucial part of my advice: Quote: We have just released JChem 3.2.1 a couple of minutes ago, where you can specify the -a changing flag again to imitate the old behaviour in 3.2.1 as a temporary measure. So please use Code: -a changing flag to obtain the same behaviour in 3.2.1 that was the default for 3.1.7. For example: react -a changing -v -r bt0088.mrv "CC(C)(C)C(=O)SCCNC(= O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)( O)=O)n2cnc3c(N)ncnc23" Of course we plan to speed up the new default behaviour too. Best regards, Szilard

At the same time, can I use


reactor.setMappingStyle(0)


in my code to set changing mapping-style?





I found this API was deprecated in Jchem3.2.1. There is a warning when compile the code. Any suggestions? Thank you!





Jeff

Hi,

JeffGao wrote:

At the same time, can I use reactor.setMappingStyle(0) in my code to set changing mapping-style? I found this API was deprecated in Jchem3.2.1. There is a warning when compile the code. Any suggestions? Thank you! Jeff

Yes, you can use it. We will not remove this method from the Reactor API until this speed issue with reaction mapping algorithm is fixed.





Best regards,


Zsolt