how to roll back to an older version JChem?

User 941c2467a3

20-11-2006 20:23:37

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

User 941c2467a3

22-11-2006 16:45:34

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

ChemAxon 9c0afc9aaf

22-11-2006 16:57:28

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

User 941c2467a3

22-11-2006 17:42:53

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

ChemAxon 9c0afc9aaf

22-11-2006 17:59:55

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

User 941c2467a3

22-11-2006 18:02:57

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!

User 941c2467a3

22-11-2006 21:29:07

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

ChemAxon e08c317633

23-11-2006 10:28:52

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