User 779e37e0e6
18-01-2013 19:21:54
Hello everyone,
I am facing a though and urgent situation here, and I really need you help
I would like to integrate superstructure search in one of my projects. I am thus using JChem Base. I would like to input a query molecule 'Q' and return all structures/structure patterns contained in that query molecule 'Q'. The structure patterns might be actual structures or patterns expressed in smarts (with unspecified bond topology, explicit Hydrogen atoms, atom type =A, Q, M, etc...)
I tried different methods: I implemented a code for superstructure search, simply using a JChemSearch object with searchtye= JChemSearch.SUPERSTRUCTURE (6). Moreover, I tried the jcsearch command line. Surpisingly, I got different outcomes.
(1) I first created a table called struct_p, of type "Any Query".
When Q1='C1=CC=C2C(=C1)C=CC(=O)O2', I get all the hits from my structure database, without any error.
However, when I used the command line "jcsearch -q 'C1=CC=C2C(=C1)C=CC(=O)O2' DB:struct_patterns -t:u", I got the following error:
**************
c1ccccc1
O=c1cccco1
O=c1ccc2ccccc2o1
chemaxon.marvin.io.MolExportException:
Some features of *~1~*~*~*~*~*~1 cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.
at chemaxon.marvin.io.formats.smiles.SmilesExport.throwMolExportExceptionSMILES(SmilesExport.java:6145)
at chemaxon.marvin.io.formats.smiles.SmilesExport.appendBond(SmilesExport.java:2857)
at chemaxon.marvin.io.formats.smiles.SmilesExport.generateSmilesString(SmilesExport.java:2626)
at chemaxon.marvin.io.formats.smiles.SmilesExport.singleMolToSMILES(SmilesExport.java:1101)
at chemaxon.marvin.io.formats.smiles.SmilesExport.toSMILES(SmilesExport.java:941)
at chemaxon.marvin.io.formats.smiles.SmilesExport.convert(SmilesExport.java:760)
at chemaxon.formats.MolExporter.write(MolExporter.java:776)
at chemaxon.jchem.Search.write(Search.java:1433)
at chemaxon.jchem.Search.searchInDatabase(Search.java:1661)
at chemaxon.jchem.Search.convert(Search.java:1244)
at chemaxon.jchem.Search.run(Search.java:2024)
at chemaxon.jchem.Search.runSearch(Search.java:2094)
at chemaxon.jchem.Search.main(Search.java:2113)
The program will exit with exit code: 1
**************
I am wondering why I did not get this error when using the code, which is actually really simplistic.
I tried using both the code I wrote and the jcsearch command line for other query compounds, and I got the same problems. For example, for Q2='[#6]C-,=CO!@-C!@-C(!@-C!@-OP(O)(O)=O)!@-O!@-C(!@-[#6])!@=O', The error message, when using the command line was the following:
************
chemaxon.marvin.io.MolExportException:
Some features of [#6]C-,=CO!@-C!@-C(!@-C!@-OP(O)(O)=O)!@-O!@-C(!@-[#6])!@=O cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.
at chemaxon.marvin.io.formats.smiles.SmilesExport.throwMolExportExceptionSMILES(SmilesExport.java:6145)
.....
************
---> Can you help me understand why I get errors when using the jcsearch command line?
(2) Because the problem apparently lies in the conversion to smiles format, and this is not always feasible, I crated a new table call smarts_p, with the type="Query Structures" this time. The documentation says that the structures here a saved in smarts format, and that this type is actually more appropriate for SUPERSTRUCTURE SEARCH. An I try the to search each of the two aformentioned query molecules with each of the two methods.
- When using the code I wrote:
For Query Q1, I had no error, and the same results.
For Query 2, I had some errors this time, incl. chemaxon.jchem.db.JChemSearch handleQTCError (see atached file: search_errors)
- When using the jcsearch command-line jcsearch -q $Query DB:smarts_patterns -t:u, I had some errors, incl. chemaxon.jchem.db.JChemSearch handleQTCError (see atached file: search_errors)
-->Could you please explain to me what is going one? What are those handleQT errors.
Why am I this time having problem using my code on some query structure when I am using the smarts_p table (although with the same query, I did not have this problem while searching the struct_p table).
What is the best table to use here?
What precautions should I take?
What options should I add?
Thank you.
Yannick D.
ChemAxon 9c0afc9aaf
18-01-2013 21:08:31
Hi,
(1)
(1) I first created a table called struct_p, of type "Any Query".
I suppose you mean Any Structures ?
You can always check with
jcman t <table>
chemaxon.marvin.io.MolExportException:
Some features of *~1~*~*~*~*~*~1 cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.
The search was executed fine, but the program is having problems exporting the results into SMILES format (which is the default).
You can use "-f" to choose a different output format and -o to send the ouput to a file if desired.
https://www.chemaxon.com/jchem/doc/user/Jcsearch.html
For example:
jcsearch -q 'C1=CC=C2C(=C1)C=CC(=O)O2' DB:struct_patterns -t:u -f mrv -o results.mrv
(2)
Regarding the other excptions with the Query table type, please send us
- the file you have imported into the DB id possible (you can send to support _at_ chemaxon.com if confidential)
- the output of "jcman t <table>"
- the exact JChem version (executing "jcsearch" w/o arguments prints a help, it starts with the version)
- an example of the the exact jcsearch command throwing the exception
In genneral the Query table type is recommended for best results.
BR,
Szilard
User 779e37e0e6
21-01-2013 02:12:01
Hi,
Thank you for your quick reply.
Regarding the first issue, I now just ask jcsearch to give the id's of the hits as output. I understand now how to deal with the output options.
Regarding issue 2:
- The table characteristics are the following:
Table type: Query structures
Table version: 5110000
Uses tautomers for duplicate search: No
Filters out the duplicate structures: Yes
Fingerprint settings:
Length (bits): 512
Pattern length: 6
Bits per pattern: 2
Table uses default standardization.
Column name Type name
1 CD_ID INT
2 CD_STRUCTURE MEDIUMBLOB
3 CD_SMARTS MEDIUMBLOB
4 CD_FORMULA VARCHAR
5 CD_SORTABLE_FOR VARCHAR
6 CD_MOLWEIGHT DOUBLE
7 CD_HASH INT
8 CD_FLAGS VARCHAR
9 CD_TIMESTAMP DATETIME
10 CD_PRE_CALCULAT TINYINT
11 CD_FP1 INT
12 CD_FP2 INT
13 CD_FP3 INT
14 CD_FP4 INT
15 CD_FP5 INT
16 CD_FP6 INT
17 CD_FP7 INT
18 CD_FP8 INT
19 CD_FP9 INT
20 CD_FP10 INT
21 CD_FP11 INT
22 CD_FP12 INT
23 CD_FP13 INT
24 CD_FP14 INT
25 CD_FP15 INT
26 CD_FP16 INT
- The exact JChem version
JChem Search Utility 5.11.5, (C) 2000-2013 ChemAxon Ltd.
-An example of the the exact jcsearch command throwing the exception
jcsearch -q "[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC=O)C([H])([H])OC(=O)CCCC" DB:mini_smarts_base -t:u -f smarts
(With the table being of type Query Structures), do I do not neet specifying the output format? I assume not since the files are stored as smarts.)
************
Jan 20, 2013 7:08:37 PM chemaxon.sss.search.Search logException
INFO: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Jan 20, 2013 7:08:38 PM chemaxon.jchem.db.JChemSearch handleQTCError
SEVERE: <?xml version="1.0"?><cml version="ChemAxon file format v5.10.0, generated by v5.11.5">
<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24" elementType="C O C O C C C O C O C O C O C O C O C O C C C C"></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"></bond><bond atomRefs2="a2 a3" order="1"></bond><bond atomRefs2="a3 a4" order="1"></bond><bond atomRefs2="a4 a5" order="1"></bond><bond atomRefs2="a5 a6" order="1"></bond><bond atomRefs2="a5 a7" order="1"></bond><bond atomRefs2="a7 a8" order="1"></bond><bond atomRefs2="a7 a9" order="1"></bond><bond atomRefs2="a9 a10" order="1"></bond><bond atomRefs2="a9 a11" order="1"></bond><bond atomRefs2="a3 a11" order="1"></bond><bond atomRefs2="a11 a12" order="1"></bond><bond atomRefs2="a1 a13" order="1"></bond><bond atomRefs2="a13 a14" order="1"></bond><bond atomRefs2="a14 a15" order="1"></bond><bond atomRefs2="a15 a16" order="2"></bond><bond atomRefs2="a13 a17" order="1"></bond><bond atomRefs2="a17 a18" order="1"></bond><bond atomRefs2="a18 a19" order="1"></bond><bond atomRefs2="a19 a20" order="2"></bond><bond atomRefs2="a19 a21" order="1"></bond><bond atomRefs2="a21 a22" order="1"></bond><bond atomRefs2="a22 a23" order="1"></bond><bond atomRefs2="a23 a24" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument>
</cml>
Jan 20, 2013 7:08:38 PM chemaxon.jchem.db.JChemSearch handleQTCError
SEVERE: chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Jan 20, 2013 7:08:38 PM chemaxon.jchem.db.status.observers.LogObserver report
SEVERE: QT search error Query=<?xml version="1.0"?><cml version="ChemAxon file format v5.10.0, generated by v5.11.5">\n<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24" element ... (1152 more characters) CD_ID=9 index=8
chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:632)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:623)
at chemaxon.jchem.db.JChemSearch.isMatching(JChemSearch.java:5506)
at chemaxon.jchem.db.JChemSearch.access$2200(JChemSearch.java:160)
at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:912)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 37
at chemaxon.sss.search.SmartsBondMatcher.prepareSMARTSTrees(SmartsBondMatcher.java:66)
at chemaxon.sss.search.StructureSearch.initMolecule(StructureSearch.java:2315)
at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1475)
at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6524)
at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:7040)
at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:7034)
at chemaxon.sss.search.AromatizedSearch.isMatching(AromatizedSearch.java:522)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:600)
... 3 more
Jan 20, 2013 7:08:38 PM chemaxon.jchem.db.JChemSearch$ABASThread run
SEVERE: Error during ABAS in table "mini_smarts_base" for cd_id: 9
chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:632)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:623)
at chemaxon.jchem.db.JChemSearch.isMatching(JChemSearch.java:5506)
at chemaxon.jchem.db.JChemSearch.access$2200(JChemSearch.java:160)
at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:912)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 37
at chemaxon.sss.search.SmartsBondMatcher.prepareSMARTSTrees(SmartsBondMatcher.java:66)
at chemaxon.sss.search.StructureSearch.initMolecule(StructureSearch.java:2315)
at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1475)
at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6524)
at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:7040)
at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:7034)
at chemaxon.sss.search.AromatizedSearch.isMatching(AromatizedSearch.java:522)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:600)
... 3 more
Error during search chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Caused by:
An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Caused by:
37
chemaxon.jchem.db.DatabaseSearchException: chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Caused by:
An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Caused by:
37
at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:2212)
at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2236)
at chemaxon.jchem.Search.runDBSearch(Search.java:1758)
at chemaxon.jchem.Search.searchInDatabase(Search.java:1554)
at chemaxon.jchem.Search.convert(Search.java:1244)
at chemaxon.jchem.Search.run(Search.java:2024)
at chemaxon.jchem.Search.runSearch(Search.java:2094)
at chemaxon.jchem.Search.main(Search.java:2113)
Caused by: chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:632)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:623)
at chemaxon.jchem.db.JChemSearch.isMatching(JChemSearch.java:5506)
at chemaxon.jchem.db.JChemSearch.access$2200(JChemSearch.java:160)
at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:912)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 37
at chemaxon.sss.search.SmartsBondMatcher.prepareSMARTSTrees(SmartsBondMatcher.java:66)
at chemaxon.sss.search.StructureSearch.initMolecule(StructureSearch.java:2315)
at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1475)
at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6524)
at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:7040)
at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:7034)
at chemaxon.sss.search.AromatizedSearch.isMatching(AromatizedSearch.java:522)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:600)
... 3 more
The program will exit with exit code: 1
************
The file with the structures I imported is attached below.
Thank you,
MrYan
ChemAxon abe887c64e
23-01-2013 11:42:48
Hello Mr Yan,
Thank you for the detailed information. We start to investigate this issue and will inform you about the results.
Best regards,
Krisztina
ChemAxon abe887c64e
23-01-2013 13:31:37
User 779e37e0e6
26-01-2013 00:27:44
Thanks for replying,
I have upated the sructure table to contain only one pattern, namely P1.
I still get errors for the superstructure query, both with P1 and P2
(P1) jcsearch -q "[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC=O)C([H])([H])OC(=O)CCCC" DB:mini_smarts_base -t:u
------
Jan 25, 2013 5:26:53 PM chemaxon.sss.search.Search logException
INFO: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Jan 25, 2013 5:26:53 PM chemaxon.jchem.db.JChemSearch handleQTCError
SEVERE: <?xml version="1.0"?><cml version="ChemAxon file format v5.10.0, generated by v5.11.5">
<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24" elementType="C O C O C C C O C O C O C O C O C O C O C C C C"></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"></bond><bond atomRefs2="a2 a3" order="1"></bond><bond atomRefs2="a3 a4" order="1"></bond><bond atomRefs2="a4 a5" order="1"></bond><bond atomRefs2="a5 a6" order="1"></bond><bond atomRefs2="a5 a7" order="1"></bond><bond atomRefs2="a7 a8" order="1"></bond><bond atomRefs2="a7 a9" order="1"></bond><bond atomRefs2="a9 a10" order="1"></bond><bond atomRefs2="a9 a11" order="1"></bond><bond atomRefs2="a3 a11" order="1"></bond><bond atomRefs2="a11 a12" order="1"></bond><bond atomRefs2="a1 a13" order="1"></bond><bond atomRefs2="a13 a14" order="1"></bond><bond atomRefs2="a14 a15" order="1"></bond><bond atomRefs2="a15 a16" order="2"></bond><bond atomRefs2="a13 a17" order="1"></bond><bond atomRefs2="a17 a18" order="1"></bond><bond atomRefs2="a18 a19" order="1"></bond><bond atomRefs2="a19 a20" order="2"></bond><bond atomRefs2="a19 a21" order="1"></bond><bond atomRefs2="a21 a22" order="1"></bond><bond atomRefs2="a22 a23" order="1"></bond><bond atomRefs2="a23 a24" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument>
</cml>
Jan 25, 2013 5:26:53 PM chemaxon.jchem.db.JChemSearch handleQTCError
SEVERE: chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Jan 25, 2013 5:26:53 PM chemaxon.jchem.db.status.observers.LogObserver report
SEVERE: QT search error Query=<?xml version="1.0"?><cml version="ChemAxon file format v5.10.0, generated by v5.11.5">\n<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24" element ... (1152 more characters) CD_ID=9 index=0
chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:632)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:623)
at chemaxon.jchem.db.JChemSearch.isMatching(JChemSearch.java:5506)
at chemaxon.jchem.db.JChemSearch.access$2200(JChemSearch.java:160)
at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:912)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 37
at chemaxon.sss.search.SmartsBondMatcher.prepareSMARTSTrees(SmartsBondMatcher.java:66)
at chemaxon.sss.search.StructureSearch.initMolecule(StructureSearch.java:2315)
at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1475)
at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6524)
at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:7040)
at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:7034)
at chemaxon.sss.search.AromatizedSearch.isMatching(AromatizedSearch.java:522)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:600)
... 3 more
Jan 25, 2013 5:26:53 PM chemaxon.jchem.db.JChemSearch$ABASThread run
SEVERE: Error during ABAS in table "mini_smarts_base" for cd_id: 9
chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:632)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:623)
at chemaxon.jchem.db.JChemSearch.isMatching(JChemSearch.java:5506)
at chemaxon.jchem.db.JChemSearch.access$2200(JChemSearch.java:160)
at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:912)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 37
at chemaxon.sss.search.SmartsBondMatcher.prepareSMARTSTrees(SmartsBondMatcher.java:66)
at chemaxon.sss.search.StructureSearch.initMolecule(StructureSearch.java:2315)
at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1475)
at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6524)
at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:7040)
at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:7034)
at chemaxon.sss.search.AromatizedSearch.isMatching(AromatizedSearch.java:522)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:600)
... 3 more
Error during search chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Caused by:
An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Caused by:
37
chemaxon.jchem.db.DatabaseSearchException: chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Caused by:
An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
Caused by:
37
at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:2212)
at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2236)
at chemaxon.jchem.Search.runDBSearch(Search.java:1758)
at chemaxon.jchem.Search.searchInDatabase(Search.java:1554)
at chemaxon.jchem.Search.convert(Search.java:1244)
at chemaxon.jchem.Search.run(Search.java:2024)
at chemaxon.jchem.Search.runSearch(Search.java:2094)
at chemaxon.jchem.Search.main(Search.java:2113)
Caused by: chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 37
Query:[#6]CCCC(=O)OCC(COC1OC([#6])C(O)C(O)C1O)OC=O
Target:Molecule can be seen on the logger output at level FINE
Caused by:
37
at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:632)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:623)
at chemaxon.jchem.db.JChemSearch.isMatching(JChemSearch.java:5506)
at chemaxon.jchem.db.JChemSearch.access$2200(JChemSearch.java:160)
at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:912)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 37
at chemaxon.sss.search.SmartsBondMatcher.prepareSMARTSTrees(SmartsBondMatcher.java:66)
at chemaxon.sss.search.StructureSearch.initMolecule(StructureSearch.java:2315)
at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1475)
at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6524)
at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:7040)
at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:7034)
at chemaxon.sss.search.AromatizedSearch.isMatching(AromatizedSearch.java:522)
at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:600)
... 3 more
The program will exit with exit code: 1
-----
Thanks,
MrYan
ChemAxon abe887c64e
28-01-2013 09:35:36
Hi MrYan,
Sorry, but I can't reproduce the error if only P1 is in the database, could you repeat with a newly created database ?
jcman c q_p1_only --t:query //create table
jcman a q_p1_only p1.mrv //import
jcsearch -q "[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC=O)C([H])([H])OC(=O)CCCC" DB:q_p1_only -t:u
[H]C([H])(OC=O)C([H])(OC=O)C([H])([H])OC1OC(C)C(O)C(O)C1O
We will further investigate the cause of the errors, and find a solution.
Best regards,
Krisztina
User 779e37e0e6
28-01-2013 19:00:19
Thanks Krisztina,
I tried it again and it works.
However, I still have to make sure it works when I have structures with and other without explicit H atoms in the same table.
I would like to also mention that the problem with explicit atoms and the one with the QTHandle errors are two different problems.
Please, let's exchange emails according to that, in order to make it more understandable to other users.
Cheers,
Yannick
ChemAxon abe887c64e
29-01-2013 10:06:10
Hi MrYan,
We will schedule fixing the bug causing the reported errors. As I've written before the possible reason is the incorrect handling of bond query features (chn) during superstructure search in Query tables. At the moment our only suggestion is to remove 'chn' and add R0 property to the atoms.
Best regards,
Krisztina
ChemAxon d4fff15f08
16-09-2013 15:39:57
Hi Yannick,
I am happy to inform you that JChem 6.1 has been released with a fix to this problem.
Please test it, and return to us if you are experiencing any misbehavior.
Best regards,
Norbert