Can you confirm that you are running OB 2.3.0?
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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