User 17ae043cc4
15-04-2007 16:17:52
Hi,
I was trying to follow the synthesizer example using linear in database mode.
When I run the first few commands from the windows prompt, I do not get any errors. When I look directly at the database, I see new tables created and data stored. When I try to view the structures in JChemManager with Synthesizer I do not see any structures and it reports zero. After I run the synthesize command I get an Invalid Fetch Size error.
I am using an academic license. Below is the sequence of commands I entered on a Windows XP machine.
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize c -n syn
-c Synthesizer.xml
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize i -n syn
-s scaffold scaffold.smiles
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize i -n syn
-s alkyne alkynes.smiles
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize i -n syn
-s amine amines.smiles
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize i -n syn
-s carboxylic-acid carboxylic-acids.smiles
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize r -n syn
java.sql.SQLException: Invalid Fetch Size
at sun.jdbc.odbc.JdbcOdbcStatement.setFetchSize(Unknown Source)
at sun.jdbc.odbc.JdbcOdbcResultSet.setFetchSize(Unknown Source)
at chemaxon.reaction.SynthesisSetReader.fetchIDsIfNeeded(SynthesisSetRea
der.java:441)
at chemaxon.reaction.SynthesisSetReader.nextWithPrefetch(SynthesisSetRea
der.java:456)
at chemaxon.reaction.SynthesisSetReader.next(SynthesisSetReader.java:116
)
at chemaxon.reaction.synthesis.DbSetContent$DbMolIterator.next(DbSetCont
ent.java:107)
at chemaxon.reaction.synthesis.MultiMolSetCounter.next(MultiMolSetCounte
r.java:107)
at chemaxon.reaction.synthesis.LinearAlgorithm.step(LinearAlgorithm.java
:204)
at chemaxon.reaction.Synthesizer.step(Synthesizer.java:849)
at chemaxon.reaction.Synthesizer.run(Synthesizer.java:823)
at chemaxon.reaction.Synthesizer.dbmain(Synthesizer.java:1245)
at chemaxon.reaction.Synthesizer.main(Synthesizer.java:1424)
chemaxon.reaction.ReactionException: Invalid Fetch Size
chemaxon.reaction.ReactionException: Invalid Fetch Size
at chemaxon.reaction.synthesis.DbSetContent$DbMolIterator.next(DbSetCont
ent.java:110)
at chemaxon.reaction.synthesis.MultiMolSetCounter.next(MultiMolSetCounte
r.java:107)
at chemaxon.reaction.synthesis.LinearAlgorithm.step(LinearAlgorithm.java
:204)
at chemaxon.reaction.Synthesizer.step(Synthesizer.java:849)
at chemaxon.reaction.Synthesizer.run(Synthesizer.java:823)
at chemaxon.reaction.Synthesizer.dbmain(Synthesizer.java:1245)
at chemaxon.reaction.Synthesizer.main(Synthesizer.java:1424)
Caused by:
chemaxon.reaction.SynthesisSetReaderException: Invalid Fetch Size
at chemaxon.reaction.SynthesisSetReader.next(SynthesisSetReader.java:146
)
at chemaxon.reaction.synthesis.DbSetContent$DbMolIterator.next(DbSetCont
ent.java:107)
at chemaxon.reaction.synthesis.MultiMolSetCounter.next(MultiMolSetCounte
r.java:107)
at chemaxon.reaction.synthesis.LinearAlgorithm.step(LinearAlgorithm.java
:204)
at chemaxon.reaction.Synthesizer.step(Synthesizer.java:849)
at chemaxon.reaction.Synthesizer.run(Synthesizer.java:823)
at chemaxon.reaction.Synthesizer.dbmain(Synthesizer.java:1245)
at chemaxon.reaction.Synthesizer.main(Synthesizer.java:1424)
I was trying to follow the synthesizer example using linear in database mode.
When I run the first few commands from the windows prompt, I do not get any errors. When I look directly at the database, I see new tables created and data stored. When I try to view the structures in JChemManager with Synthesizer I do not see any structures and it reports zero. After I run the synthesize command I get an Invalid Fetch Size error.
I am using an academic license. Below is the sequence of commands I entered on a Windows XP machine.
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize c -n syn
-c Synthesizer.xml
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize i -n syn
-s scaffold scaffold.smiles
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize i -n syn
-s alkyne alkynes.smiles
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize i -n syn
-s amine amines.smiles
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize i -n syn
-s carboxylic-acid carboxylic-acids.smiles
C:\Program Files\ChemAxon\JChem\examples\synthesizer\linear>synthesize r -n syn
java.sql.SQLException: Invalid Fetch Size
at sun.jdbc.odbc.JdbcOdbcStatement.setFetchSize(Unknown Source)
at sun.jdbc.odbc.JdbcOdbcResultSet.setFetchSize(Unknown Source)
at chemaxon.reaction.SynthesisSetReader.fetchIDsIfNeeded(SynthesisSetRea
der.java:441)
at chemaxon.reaction.SynthesisSetReader.nextWithPrefetch(SynthesisSetRea
der.java:456)
at chemaxon.reaction.SynthesisSetReader.next(SynthesisSetReader.java:116
)
at chemaxon.reaction.synthesis.DbSetContent$DbMolIterator.next(DbSetCont
ent.java:107)
at chemaxon.reaction.synthesis.MultiMolSetCounter.next(MultiMolSetCounte
r.java:107)
at chemaxon.reaction.synthesis.LinearAlgorithm.step(LinearAlgorithm.java
:204)
at chemaxon.reaction.Synthesizer.step(Synthesizer.java:849)
at chemaxon.reaction.Synthesizer.run(Synthesizer.java:823)
at chemaxon.reaction.Synthesizer.dbmain(Synthesizer.java:1245)
at chemaxon.reaction.Synthesizer.main(Synthesizer.java:1424)
chemaxon.reaction.ReactionException: Invalid Fetch Size
chemaxon.reaction.ReactionException: Invalid Fetch Size
at chemaxon.reaction.synthesis.DbSetContent$DbMolIterator.next(DbSetCont
ent.java:110)
at chemaxon.reaction.synthesis.MultiMolSetCounter.next(MultiMolSetCounte
r.java:107)
at chemaxon.reaction.synthesis.LinearAlgorithm.step(LinearAlgorithm.java
:204)
at chemaxon.reaction.Synthesizer.step(Synthesizer.java:849)
at chemaxon.reaction.Synthesizer.run(Synthesizer.java:823)
at chemaxon.reaction.Synthesizer.dbmain(Synthesizer.java:1245)
at chemaxon.reaction.Synthesizer.main(Synthesizer.java:1424)
Caused by:
chemaxon.reaction.SynthesisSetReaderException: Invalid Fetch Size
at chemaxon.reaction.SynthesisSetReader.next(SynthesisSetReader.java:146
)
at chemaxon.reaction.synthesis.DbSetContent$DbMolIterator.next(DbSetCont
ent.java:107)
at chemaxon.reaction.synthesis.MultiMolSetCounter.next(MultiMolSetCounte
r.java:107)
at chemaxon.reaction.synthesis.LinearAlgorithm.step(LinearAlgorithm.java
:204)
at chemaxon.reaction.Synthesizer.step(Synthesizer.java:849)
at chemaxon.reaction.Synthesizer.run(Synthesizer.java:823)
at chemaxon.reaction.Synthesizer.dbmain(Synthesizer.java:1245)
at chemaxon.reaction.Synthesizer.main(Synthesizer.java:1424)