It seems not possible to create a simple application were this issue happens.
As a context I'm reading in molecules, generating 3D coordinates and then
generate the Spectrophore. In a simple script-like snippet this works.
In the complete application the results are written to an output file, the
Just a hint: one common problem with the forcefield code is that you
forgot to check that Setup was successful (Setup can fail with crazy
molecules that are not supported by a particular forcefield). This can
result in any number of interesting segfaults if you call any other
forcefield methods aft
The code for generating the conformers is as below:
private void generateConformers(OBMol mol) {
OBConformerSearch conformerSearch = new OBConformerSearch();
OBConformerScore score = new OBEnergyConformerScore();
conformerSearch.SetScore(score);
if (!conformerSear
Hello,
Thank you all who are helping me with this openbabel. I have
difficultieswith conversion of pwscf files.Colleague of mine had the
same problem, but was able to fix it. But now we
cannot reproduce this "fix". But back to case, when I am wanted to convert
a valid pwscf file like this:
babel
PWSCF is a relatively new addition to the parser. So it's possible that it's a
new type of file that isn't read correctly. Can you send me an example file or
two?
Thanks very much,
-Geoff
On Dec 2, 2013, at 8:41 AM, Otto Kohulák wrote:
> Hello,
>
> Thank you all who are helping me with this
On Mon, Dec 2, 2013 at 5:41 AM, Otto Kohulák wrote:
>
> babel -i pwscf pw.out -o xyz out.xyz
>
> the result is always:
>
> 0 molecules converted
> 2 audit log messages
>
Can you convert from or to other formats? For example, can you do this?
echo "CCO" | obabel -i smi -o sdf
By the way, the
I can reproduce this on a different PC also running windows 7. The Windows
Event viewer generates an entry for this:
Faulting application name: java.exe, version: 7.0.450.18, time stamp:
0x525404d0
Faulting module name: ntdll.dll, version: 6.1.7601.18205, time stamp:
0x51db96c5
Exception code: 0xc
> Not sure if this helps at all. The whole issue is kind of confusing as
> again, the exact same code works when called from a simpler snippet that
> does not write results to a file and does not allow any options to be set.
When you say "does not allow any options to be set," do you mean the
OBC
Geoff Hutchison wrote
> When you say "does not allow any options to be set," do you mean the
> OBConformerScore isn't set?
No I meant that the options are not exposed as cli parameters and hence it
runs with default parameters (eg. nr of conformers, nr of children,
mutability,...)
--
View this
Dear list,
I have a bunch of .mol2 files.
I would like to count the number of atoms in each file
as: total number of atoms, number of polar atoms,
number of non polar atoms.
Is there a way to do this rather easily with Open Babel?
Thanks a lot,
Francois.
PS: I am not a chemist
---
This is confusing. This issue is some weird memory issue. At the end of this
post is the most simple code I could come up with that reproduces the
problem for me.
I can make the code work by removing or commenting just any of the following
lines (only one of them is enough):
- conformerSearch.Se
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