Hi,
You should probably test the result from SetInAndOutFormats, just to be sure.
If that step failed, you're in trouble. Do you get the error regardless of what
format you're using for output?
Kind regards,
Fredrik
4 dec 2012 kl. 10:16 skrev mpillong max.pill...@pharma.ethz.ch:
Hmmm, sorry
Hey Fredrik,
thanks for the input. The SetInAndOutFormat returns true, so I'm guessing
there's nothing worng here. I've experienced this error with several
inputfiles of varying format (pdb, sdf, mol2).
Best regards,
Max
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Ah yes, my bad! Of course, I have also tried different output formats, but
the error remains the same!
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Can you provide a complete program that exhibits the problem? Please
make it as small as possible.
On 4 December 2012 10:06, mpillong max.pill...@pharma.ethz.ch wrote:
Ah yes, my bad! Of course, I have also tried different output formats, but
the error remains the same!
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Sure thing! Is the code sufficient, or would you need a runnable jar?
package TestClasses;
import org.openbabel.OBConversion;
import org.openbabel.OBMol;
public class TestOBWriteFile {
public static void main(String[] args) {
Hi Chris,
Thanks for your reply and apologies for the delayed response. Converting
the cif to xyz and viewing the molecule shows the correct structure but
converting the xyz file to smi and then generating coordinates and viewing
shows the addition of a H atom.
The correct smiles is:
Scott
Your correct smiles is not right. The sum of the bond orders to the
charged nitrogen should be 4, and is only 3 (it has no H attached). The
correct SMILES is in my post below. Even with it, the round trip via xyz:
obabel -:C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1 -oxyz --gen3D
| obabel
Your problem is the incorrect conversion of a cif file, but you haven't
shown one yet. (Not that I know much about cif files, but others may.)
Conversions in OB go through an internal data structure, OBMol. It sound
like the problem is in the cif to OBMol part, not in the OBMol to SMILES.
Chris
Very nice ... thanks for doing this. Things like this should be available
in the OB documentation as a resource for those starting new projects or
trying to make a presentation to their management.
Craig
On Tue, Dec 4, 2012 at 3:31 AM, Noel O'Boyle baoille...@gmail.com wrote:
Hi all,
Here
Apologies, it was attached in the e-mail before last but had an identifier
name (SOXGES.search2.cif) and so may have caused confusion. I've attached
it again in this e-mail.
As a general question, is it possible to convert coordinates to smiles that
will always preserve the elements present (but
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