Sorry - our emails crossed. You don't say what OS you're using, but
it's a simple matter to check to go to its website to check what
version of Open Babel the bindings are linked against. It sounds like
it's 2.2.3 but you can verify with "print
pybel.ob.OBReleaseVersion()".
I think you'll have to compile the bindings yourself.
- Noel
On 18 March 2011 14:03, Bradley Calhoun <calhoun.resea...@gmail.com> wrote:
> I am using Open Babel 2.3.0 and the most recent apt-get version of
> python-openbabel, which I believe is where the openbabel python module is.
> I think this is version 2.2.3. My python is 2.6.6 (we have to keep this on
> the same page as python's scipy package).
> - Brad
>
>
> On Fri, Mar 18, 2011 at 8:57 AM, JP <jeanpaul.ebe...@inhibox.com> wrote:
>>
>> Maybe; you have a different version number than NoB than?
>>
>> Details!Details!
>>
>> On 18 March 2011 13:53, Bradley Calhoun <calhoun.resea...@gmail.com>
>> wrote:
>>>
>>> I have to wonder then what the difference is. I ran the code again to
>>> make sure, and the program sat for 30 minutes without any progress.
>>> I added a few other molecules that cause the same response. (seeming to
>>> hang)
>>> These are all real molecules. The Substance IDs 23587365, 34132506,
>>> and 34132507 can be searched at the PubChem website.
>>> ***
>>> import openbabel
>>> import sys
>>> obConversion = openbabel.OBConversion()
>>> obConversion.SetInAndOutFormats("smi", "can")
>>> mol = openbabel.OBMol()
>>> X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)cccc1Cl"
>>> a =
>>> "c1ccc2c(c1)ccc1cc3c4c(cccc4c4c5c6cc7ccc8ccccc8c7c7cccc(c67)c5c5c(c34)c3cccc4c6c(ccc7ccccc67)cc5c34)c21
>>> 23587365"
>>> b =
>>> "c1ccc2c(c1)sc1cc3sc4ccccc4n4c5ccc(cc5)c5ccc(cc5)n5c6cc7c(sc8ccccc8n7c7ccc(cc7)c7ccc(cc7)n2c1cc34)cc6sc1ccccc51
>>> 34132506"
>>> c =
>>> "c1ccc2c(c1)oc1cc3oc4ccccc4n4c5ccc(cc5)n5c6cc7c(oc8ccccc8n7c7ccc(cc7)n2c1cc34)cc6oc1ccccc51
>>> 34132507"
>>> obConversion.ReadString(mol, X)
>>> sys.stdout.write( 'x' )
>>> obConversion.ReadString(mol, a)
>>> sys.stdout.write( 'a' )
>>> obConversion.ReadString(mol, b)
>>> sys.stdout.write( 'b' )
>>> obConversion.ReadString(mol, c)
>>> sys.stdout.write( 'c' )
>>> ***
>>> - Brad
>>>
>>> On Fri, Mar 18, 2011 at 5:24 AM, Noel O'Boyle <baoille...@gmail.com>
>>> wrote:
>>>>
>>>> Hi Brad,
>>>>
>>>> It works for me, but it takes 10 seconds. It also uncovers a bug - the
>>>> system is not detected as aromatic.
>>>>
>>>> Is this a real molecule?
>>>>
>>>> - Noel
>>>>
>>>> On 17 March 2011 17:53, Bradley Calhoun <calhoun.resea...@gmail.com>
>>>> wrote:
>>>> > Hello,
>>>> > I am currently struggling with a particular interaction in openbabel.
>>>> > When I run the following python code, the obConversion object
>>>> > correctly
>>>> > reads X, but it just stalls on Y.
>>>> > ***
>>>> > import openbabel
>>>> > import sys
>>>> > obConversion = openbabel.OBConversion()
>>>> > obConversion.SetInAndOutFormats("smi", "can")
>>>> > mol = openbabel.OBMol()
>>>> > X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)cccc1Cl"
>>>> > obConversion.ReadString(mol, X)
>>>> > sys.stdout.write("X read\n")
>>>> > mol2 = openbabel.OBMol()
>>>> > Y =
>>>> >
>>>> > "c1ccc2c(c1)ccc1cc3c4c(cccc4c4c5c6cc7ccc8ccccc8c7c7cccc(c67)c5c5c(c34)c3cccc4c6c(ccc7ccccc67)cc5c34)c21"
>>>> > obConversion.ReadString(mol2, Y)
>>>> > sys.stdout.write("Y read\n")
>>>> > ***
>>>> > Is there an explanation or a fix for this?
>>>> > Thank you for your time,
>>>> > - Brad Calhoun, Washington University in St Louis, Pathology
>>>> >
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>>>
>>>
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>>
>>
>>
>> --
>>
>> Jean-Paul Ebejer
>> Early Stage Researcher
>> InhibOx Ltd
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