Hi Noel,
Here a link to a zip file containing the compiled jar, mols.smi and windows
cmd file:
https://drive.google.com/file/d/0B1KuZlTEmhZNV2l5clhoVlZ5blk/edit?usp=sharing
This application fails on 2 different Windows 7 PCs (one 32, the other 64
bit but both run java and OB 32-bit).
I now real
The test file didn't make it here, but I did succeed in compiling and
running the code on Windows without any problems. What OS are you
using?
- Noel
On 4 December 2013 05:24, Joos Kiener wrote:
> Hi Noel,
>
> this is a test file with 10 molecules only. memory consumption of the
> java.exe is 20
Hi Noel,
this is a test file with 10 molecules only. memory consumption of the
java.exe is 20-25 mb, so not a problem. Moving the builder outside of the
loop does not help with the issue. I also moved the OBConformerScore outside
of the loop. But does not help either.
--
View this message in co
How many molecules are in mols.smi? Have you looked at task manager to
see memory usage while running this?
You should move the initialisation of OBBuilder outside the loop. I
have a feeling you are eating up memory by creating this multple
times.
- Noel
On 3 December 2013 06:43, Joos Kiener wr
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
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
> 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
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
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
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
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
Can you give an example of a complete Java program (as short as
possible) that reproduces the problem?
On 29 November 2013 11:18, Joos Kiener wrote:
> Just using
>
> OBConformerSearch conformerSearch = new OBConformerSearch();
>
> works. However I want to use different scoring than RMSD, which se
Just using
OBConformerSearch conformerSearch = new OBConformerSearch();
works. However I want to use different scoring than RMSD, which seems to be
the default (not really documented).
If I do this
OBConformerSearch conformerSearch = new OBConformerSearch();
OBConformerScore score = new OBEner
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