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
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