Thankyou Eddie - typing:
export RD_USESQLLITE=1
Before running the command fixed the problem.
Cheers
Jameed
From: Eddie Cao [mailto:[email protected]]
Sent: 08 August 2012 18:09
To: Jameed Hussain
Cc: [email protected]
Subject: Re: [Rdkit-discuss] DbCli error
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<http://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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