When following the install guide on
http://open-babel.readthedocs.org/en/latest/Installation/install.html#requirements
Visual Studio 2013 Express will not build the release and have 86 errors
(see below)
What am I doing wrong?
Error 1 error C2039: 'min' : is not a member of 'std'
C:\ope
Is there a way to automatically convert undefined double bond stereo to
trans? This is for display purposes only as undefined double bonds (C=C)
will be displayed in the used tool as crossed double bond, eg like an X but
users prefer to see them displayed as trans.
Is there a chemically intelligen
Found the issue:
I recently installed Avogadro which ships with a different version of
openbabel-2.dll. Because Avogadro adds PATH information to System variables
in contrast to OpenBabel which uses user variables for PATH, the
openbabel-2.dll in Avogadro is picked up first.
My solution is to man
I just realized that the python extensions fails with the same error:
>>> import pybel
Traceback (most recent call last):
File "", line 1, in
File "C:\Python27\lib\site-packages\pybel.py", line 52, in
import openbabel as ob
File "C:\Python27\lib\site-packages\openbabel.py", line 37, in
I'm constantly getting an
UnsatisfiedLinkError: C:\Program Files\OpenBabel-2.3.2\openbabel_java.dll:
The specified procedure could not be found
exception when calling
System.loadLibrary("openbabel_java");
This used to work previously on the same laptop. Now it has been couple of
weeks since I
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
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
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
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
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 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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