Hello All,
I just recently started using RDKit and am trying to test it on a small test
set of 6630 molecules (The exact test set is available at
http://www.drugbank.ca/downloads). I tried using the DbCLI to create a
database but it terminated with an error. I have included here the command
exactly as I entered it and the error.
python /usr/share/RDKit/Projects/DbCLI/CreateDb.py --dbDir=drugbank
--maxRowsCached=1000 --molFormat=sdf drugbank_6630.sdf
Traceback (most recent call last):
File "/usr/share/RDKit/Projects/DbCLI/CreateDb.py", line 456, in <module>
CreateDb(options,dataFilename)
File "/usr/share/RDKit/Projects/DbCLI/CreateDb.py", line 212, in CreateDb
lazySupplier=int(options.maxRowsCached)>0)
File "/usr/lib64/python2.6/site-packages/rdkit/Chem/MolDb/Loader_orig.py",
line 163, in LoadDb
curs.executemany('insert into %s values (%s)'%(regName,qs),rows)
sqlite3.ProgrammingError: You must not use 8-bit bytestrings unless you use
a text_factory that can interpret 8-bit bytestrings (like text_factory =
str). It is highly recommended that you instead just switch your application
to Unicode strings.
I know it is failing on the 1004 molecule in the file and that all the
characters in the file are alphanumeric or punctuation. I have tried a few
edits, but to no avail. If anyone has seen this problem or knows how to
resolve it, I would greatly appreciate some insight.
Scott Mottarella
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