Activity for Wolfgang Verestek
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Wolfgang Verestek modified a comment on a wiki page
Hi all, I didn't manage to get ChemTrayzer running properly. Therefore, I fumbled some python together while using NetworkX as graph library. With this i don't have the problem in analyzing "large" molecules anymore and can extract the reactions from reaxff simulations. At the moment, this is just some basic code and obviously cannot extract to smiles or do some fancy analysis. But it is creating some simple figures before and after reaction. In case anybody is having issues with chemtrayzer, or...
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Hi all, I didn't manage to get ChemTrayzer running properly. Therefore, I fumbled some python together while using NetworkX as graph library. By this i don't have the problem in analyzing "large" molecules anymore and can extract the reactions from reaxff simulations. At the moment, this is just some basic code and obviously cannot extract to smiles or do some fancy analysis. But, is creating some simple figures before and after reaction. In case anybody is having issues with chemtrayzer, or when...
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Hi Enia, yes, i played around a little bit more last night, but was too tired to post. Basically, i did as you said and included sys.setrecursionlimit(10000) after the imports in processing.py. However, as i am running a newer version of openbabel there was another error in processing.py around line 790 with atom.SetImplicitValence(...) Unlike the other functions, see post above, where it was just a change of the function name and easy to resolve, this one doesn't have a replacement though. So as...
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After the example worked i tried my own molecule (PPEK + O) and get an error message. First Question: I have several types of O (coming from the classical force field one is in the aromatic rings, etc. should sth like this work (multiple mappings to C, H and O)? python ~/Downloads/ChemTraYzer_2.1/processing.py bonds.reaxff.dump -gen -dp 0.2 -i 1:6 -i 2:1 -i 3:1 -i 4:8 -i 5:8 -i 6:8 -i 7:8 -i 9:1 -i 10:6 -i 11:6 -i 12:6 -i 13:6 -i 14:8 I get an error message: Is there a known limit to the molecule...
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Hi Enia Mudimu, that was a mistake on my side. Sorry for misunderstanding the instructions. However, I am getting a new error on OBBOndObject (see below). It seems the API to OpenBabel has changed the function name GetBO to GetBondOrder. Running sed -i "s/GetBO()/GetBondOrder()/g" *.py on the python scripts solved the issue. Thanks for the support. Regards Wolfgang wolfgang@L18001:~/Downloads/ChemTraYzer_2.1$ wolfgang@L18001:~/Downloads/ChemTraYzer_2.1$ wolfgang@L18001:~/Downloads/ChemTraYzer_2.1$...
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Hi all, I don't even get the example running. Has anybody seen this error before? No idea why max(reactions) should be empty. It's the example and expected to get some output. Regards Wolfgang wolfgang@L18001:~/Downloads/ChemTraYzer_2.1$ python analyzing.py -gen -dp -step 1000 -main test example/bonds.tatb Fri Nov 22 20:36:52 2024 / UTC !-------------- ChemTraYzer 2 - ReaxFF Data Analyzing ---------------! ! ! ! Version 2018-11-29 ! ! Author Malte Doentgen, LTT RWTH Aachen University ! ! Email chemtrayzer@ltt.rwth-aachen.de...
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