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
>> >
>> ------------------------------------------------------------------------------
>> > Colocation vs. Managed Hosting
>> > A question and answer guide to determining the best fit
>> > for your organization - today and in the future.
>> > http://p.sf.net/sfu/internap-sfd2d
>> > _______________________________________________
>> > OpenBabel-discuss mailing list
>> > OpenBabel-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>> >
>>
>
>
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
36-37 Pembroke Street
Oxford
OX1 1BP
UK
(+44 / 0) 1865 262 034
This email and any files transmitted with it are confidential and intended
solely for the use of the individual or entity to whom they are addressed.
Any unauthorised dissemination or copying of this email or its attachments,
and any use or disclosure of any information contained in them, is strictly
prohibited and may be illegal. If you have received this email in error
please notify the sender and delete all copies from your system.
We and our group companies accept no liability or responsibility for
personal emails or emails unconnected with our business.
Internet communications including emails and access and use of web sites
cannot be guaranteed to be secure or error free as information can be
intercepted, corrupted, lost or arrive late. Furthermore, while we have
taken steps to control the spread of viruses on our systems, we cannot
guarantee that this email and any files transmitted with it are virus free.
No liability is accepted for any errors, omissions, interceptions, corrupted
mail, lost communications or late delivery arising as a result of receiving
this message via the Internet or for any virus that may be contained in it.
------------------------------------------------------------------------------
Colocation vs. Managed Hosting
A question and answer guide to determining the best fit
for your organization - today and in the future.
http://p.sf.net/sfu/internap-sfd2d
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
