Thanks for the suggestion Greg. Unfortunately that did not work either. So I
bit the bullet and installed anaconda python 3 and then the example in your
blog works without modification.
I had some trouble installing rdkit and rdkit-postgresql with conda:
conda install -c rdkit rdkit-postgresql
Fetching package metadata ...........
Solving package specifications: .
UnsatisfiableError: The following specifications were found to be in conflict:
- python 3.6*
- rdkit-postgresql -> postgresql >=9.4,<9.5 -> python 2.7*
Use "conda info <package>" to see the dependencies for each package.
But I was able to install it this way:
conda install python=3.5.1
conda install --offline rdkit-2016.09.4-np111py35_1.tar.bz2
conda install --offline rdkit-postgresql95-2016.09.4-py35_1.tar.bz2
conda install --offline boost-1.56.0-py35_3.tar.bz2
condo install psycopg2
-Konrad
> On 5 Sep 2017, at 06:37, Greg Landrum <greg.land...@gmail.com> wrote:
>
> I know from the subsequent post that you've moved on from this, but it's
> probably worth responding here anyway:
>
> On Fri, Sep 1, 2017 at 9:36 AM, Konrad Koehler <konrad.koeh...@icloud.com
> <mailto:konrad.koeh...@icloud.com>> wrote:
>
> First problem: Null characters. When I run the example script (using the
> Sheridan bit vector fingerprints), I generate the following error message:
>
> curs.executemany('insert into fps values
> (%s,bfp_from_binary_text(%s))',[(x,DataStructs.BitVectToBinaryText(y)) for
> x,y in fps])
> ValueError: A string literal cannot contain NUL (0x00) characters.
>
> I am not sure what I should do here. I could strip the null characters from
> the binary text, but are the null characters supposed to be there? Should I
> use the bytea data type on PostgreSQL side?
>
>
> I guess that this could also be a Python 2.7 thing. If you try:
>
> curs.executemany('insert into fps values
> (%s,bfp_from_binary_text(%s))',[(x,bytes(DataStructs.BitVectToBinaryText(y)))
> for x,y in fps])
>
> It might work.
>
> -greg
>
>
> Second problem: convert numpy array into bit vector
>
> The linked example creates a fingerprint as a bit vector:
> fp =
> Sheridan.GetBTFingerprint(m,fpfn=rdMolDescriptors.GetHashedTopologicalTorsionFingerprintAsBitVect)
>
> whereas rdReducedGraphs.GetErGFingerprint method produces a numpy array:
> fp = rdReducedGraphs.GetErGFingerprint(m)
>
> Is there anyway of converting this numpy array into a bit vector?
>
>
> Any suggestions would be greatly appreciated. Thanks,
>
> Konrad
>
>
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