Hi Jameed,
I am guessing RDKit was too smart in guessing which database it should use and
decided to use PostgreSQL. Try set an environment variable to disable this
behavior: with bash, do
export RD_USESQLLITE 1
and then run your command again.
Regards,
Eddie
On Aug 8, 2012, at 9:00 AM, Jameed Hussain wrote:
> Hi,
>
> I am just trying to use DbCli tool in rdkit (RDKit_2012_06_1):
>
> http://code.google.com/p/rdkit/wiki/UsingTheDbCLI
>
> using the command (where junk.smi is a smiles file):
>
> python $RDBASE/Projects/DbCLI/CreateDb.py --dbDir=dhfr --molFormat=smiles
> junk.smi
>
> And I get these errors below. Does anyone have any ideas what is wrong ?
>
> Thanks
> Jameed Hussain
>
>
> [16:46:56] INFO: Reading molecules and constructing molecular database.
> [16:46:56] INFO: Generating molecular database in file dhfr/Compounds.sqlt
> [16:46:57] INFO: done 100
> [16:46:57] INFO: done 200
> [16:46:57] Warning: ring stereochemistry detected. The output SMILES is not
> canonical.
> [16:46:57] Warning: ring stereochemistry detected. The output SMILES is not
> canonical.
> [16:46:57] INFO: done 300
> [16:46:57] INFO: done 400
> [16:46:57] INFO: done 500
> [16:46:57] INFO: done 600
> [16:46:57] Warning: ring stereochemistry detected. The output SMILES is not
> canonical.
> [16:46:57] Warning: ring stereochemistry detected. The output SMILES is not
> canonical.
> [16:46:57] INFO: done 700
> [16:46:57] INFO: done 800
> [16:46:58] INFO: done 900
> [16:46:58] INFO: done 1000
> Traceback (most recent call last):
> File "/GWD/schem/apps/rdkit/default/Projects/DbCLI/CreateDb.py", line 456,
> in <module>
> CreateDb(options,dataFilename)
> File "/GWD/schem/apps/rdkit/default/Projects/DbCLI/CreateDb.py", line 212,
> in CreateDb
> lazySupplier=int(options.maxRowsCached)>0)
> File
> "/GWD/schem/apps/python/x86_64/python-2.7.0/lib/python2.7/site-packages/rdkit/Chem/MolDb/Loader_orig.py",
> line 152, in LoadDb
> curs = conn.GetCursor()
> File
> "/GWD/schem/apps/python/x86_64/python-2.7.0/lib/python2.7/site-packages/rdkit/Dbase/DbConnection.py",
> line 229, in GetCursor
> self.cn = DbModule.connect(self.dbName,self.user,self.password)
> File
> "/GWD/schem/apps/python/x86_64/python-2.7.0/lib/python2.7/site-packages/pyPgSQL/PgSQL.py",
> line 2210, in connect
> return Connection(connInfo, client_encoding, unicode_results)
> File
> "/GWD/schem/apps/python/x86_64/python-2.7.0/lib/python2.7/site-packages/pyPgSQL/PgSQL.py",
> line 2365, in __init__
> raise DatabaseError, m
> libpq.DatabaseError: could not translate host name "dhfr/Compounds.sqlt" to
> address: Name or service not known
>
>
>
>
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