Hello, I am using openbabel to convert the CIFs of the Crystallography
Open Database to SMILES and subsequently perform substructure searches.
I have pointed out several times in this forum the problems that I am
finding in such conversions and searches, many of them similar to that
your are hintin
Hi,
I asked the earlier question:
On 11/11/2012 04:01, Sarah Rodriguez wrote:
> Hello,
> I am wondering if I have 2 large databases that I want to compare the
> structures in, would I be able to do this in babel?
Thanks for your reply. I was really helpful. As a followup, is there anyway
to put
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 m
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 wrote:
> Hi all,
>
> Here are some introducto
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
Thanks Chris for the helpful comments. Sorry to keep on but I'm still left
with the problem on going from cif to smiles where the original number of
elements is not conserved. What I want is to be able to reliably represent
the original cif molecule as a smiles string and from there recreate the
mo
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 -
Hi all,
Here are some introductory slides to features and usage of Open Babel:
http://baoilleach.blogspot.co.uk/2012/12/intro-to-open-babel.html
Regards,
Noel
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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: C(=O)(O)C[C@
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) {
System.load("/Applications/OpenBab
Can you provide a complete program that exhibits the problem? Please
make it as small as possible.
On 4 December 2012 10:06, mpillong wrote:
> Ah yes, my bad! Of course, I have also tried different output formats, but
> the error remains the same!
>
>
>
> --
> View this message in context:
> htt
Ah yes, my bad! Of course, I have also tried different output formats, but
the error remains the same!
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Hi,
I was more curious about the output format, not the format of the input files.
If the problem is indeed in the writing, it would be interesting to know if it
is a specific format or something more general.
/Fredrik
4 dec 2012 kl. 10:44 skrev Max Pillong :
> Hey Fredrik,
>
> thanks for th
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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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 :
> Hmmm, sorry about that, I was using t
Hey Noel,
indeed I started with the SetOutFormat method. Unfortunately, both methods
(SetOut/SetInAndOut) return true, yet, the error during writing still
remains, so I'm guessing it's happening somewhere during the writing :/.
Thanks for your input!
Max
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htt
On 4 December 2012 09:16, mpillong wrote:
> Hmmm, sorry about that, I was using the < raw > Tag here ... but here's the
> original text.
>
> Hey everyone,
>
> I am currently running OpenBabel on a MacOSX 10.6.8 in Eclipse with Java.
> Recently, I encountered the following exception during using th
Hmmm, sorry about that, I was using the < raw > Tag here ... but here's the
original text.
Hey everyone,
I am currently running OpenBabel on a MacOSX 10.6.8 in Eclipse with Java.
Recently, I encountered the following exception during using the WriteFile()
Method in OBConversion:
'Invalid memory
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