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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