User 78821debe8
28-01-2005 19:58:33
Whenever I try to export a new table I created (n jcman under linux), I get a:
SQL warning
SQLSTATE: 42000
Message: you have an error in your SQL syntax. Check the manual that corresponds to your MySQL server version for the right syntax to use near') ORDER BY CD_ID' at line 3
Vendor: 1064
the thing is, I have no SQL of my own, I want all the records out. This worked for sure in 3.0.5
Thanks
Art
ChemAxon 9c0afc9aaf
31-01-2005 11:03:02
Hi,
So far we could not reproduce the problem.
Please let me know the following details:
- Exact version of MySQL
- Exact version of the JDBC driver, e.g: "mysql-connector-java-3.0.10-stable-bin.jar"
- Where did you get this error ? (GUI, API, command line, JSP, etc ...)
-The structure of your table:
jcman -t <table_name>
Szilard
User 78821debe8
31-01-2005 15:35:15
Hi,
Mysql ver 12.22 Distrib 4.0.20 for mandrake-linux-gnu
mysql-connector-java-3.1.5
Error was in GUI export
Structure is in the next post...
Art
User 78821debe8
31-01-2005 15:36:03
[art@xps art]$ jcman -t babelall
Table uses default standardization.
Column name Type name
1 cd_id INTEGER
2 cd_structure MEDIUMBLOB
3 cd_smiles TEXT
4 cd_formula VARCHAR
5 cd_molweight DOUBLE
6 cd_hash INTEGER
7 cd_flags VARCHAR
8 cd_timestamp DATETIME
9 cd_fp1 INTEGER
10 cd_fp2 INTEGER
11 cd_fp3 INTEGER
12 cd_fp4 INTEGER
13 cd_fp5 INTEGER
14 cd_fp6 INTEGER
15 cd_fp7 INTEGER
16 cd_fp8 INTEGER
17 cd_fp9 INTEGER
18 cd_fp10 INTEGER
19 cd_fp11 INTEGER
20 cd_fp12 INTEGER
21 cd_fp13 INTEGER
22 cd_fp14 INTEGER
23 cd_fp15 INTEGER
24 cd_fp16 INTEGER
25 HEKPic50P1 DOUBLE
26 HEKPci50PX DOUBLE
27 HEKTarget VARCHAR
28 HTEPPic50 DOUBLE
29 HTEPPeak VARCHAR
30 HTEPTarget VARCHAR
31 SDFULLBlOCK DOUBLE
32 SDPeak VARCHAR
33 SDTarget VARCHAR
34 RegNumber VARCHAR
ChemAxon 9c0afc9aaf
01-02-2005 11:42:51
We still could not reproduce the problem yet.
Please write me the following:
1. the full stack trace
2. the output of the following:
mysql -u root (this will get you to the mysql console)
use <database_name>;
describe <table_name>;
exit; (with this you can exit from the console)
3. Your CLASSPATH setting:
echo $CLASSPATH
NOTE: jchem.jar should NOT be in the CLASSPATH.
4. Let me know what fields you have selected for export if you have changed the default selection.
5. Does the error persists if you try it on a new table ?
Regards,
Szilard
User 78821debe8
01-02-2005 17:36:36
Hi,
I have an SDF file that imports fine, but I can't export smiles (even from a new table) (fails in at least one of the compounds) I can send it privately, but I can't post it in the forum (it is from a commercial library).
Let me know what email to send it to...
Thanks
Art
ChemAxon 9c0afc9aaf
01-02-2005 17:58:51
Hi,
There are certain features in SDFiles and other MDL formats which are not supported by SMILES.
It's very likely that your SDFile contains such a feature.
You can find more on file types at the following address:
http://www.chemaxon.com/marvin/doc/dev/formats.html
If you are unsure, you may send the file to our support e-mail address displayed under the forum title.
Szilard
User 78821debe8
01-02-2005 18:43:39
Sent SDF file by mail...
Art
ChemAxon 9c0afc9aaf
02-02-2005 08:19:36
Hi Art,
You have at least structure in your SDF that contains radicals.
Radicals are not supported by SMILES, that's why the export fails.
Once you have MOL/SDF input, it's better to export in MOL / SDFile formats.
Is there a special reason to export to smiles ?
Regards,
Szilard
ChemAxon 25dcd765a3
02-02-2005 10:23:21
The next Marvin release will support radicals.
I hope that helps.
ChemAxon 9c0afc9aaf
04-02-2005 16:42:11
Hi,
I think you should try to delete those lines from the database table, where cd_smiles is NULL.
("DELETE FROM <table> WHERE cd_smiles IS NULL;")
Since the format of the cd_smiles column is cxsmiles (ChemAxon Extended SMILES) this will not guarantee for 100% that you can export everything in SMILES, but you will have a better chance for that.
Please let me know if it helps, we will find out something if it doesn't.
Best regards,
Szilard