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 >> > >> > ------------------------------------------------------------------------------ >> > 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