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Hi,
I am trying to run Fetch log files but I get the following error message:
---------------------------------------------------------------------------
NameError …
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The first step of this OpenBabel converter will be to convert OpenBabel OBMols to MDAnalysis AtomGroups. This will enable the indirect parsing of over 100 file types into a format that MDAnalysis tool…
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I'm wondering why the list of input file types is limited to SDF, MOL, MOL2, CML, InChI and SMILES? I would like to convert pdb to sdf which is possible on the commandline.
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sorry to ask you some weird question...
i use openbabel.js for smiles import plugin.but my smiles have some error ,can't generate.
i want to know how can i catch this warning to tell user smiles hav…
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Hello,
I installed OpenBabel and python-openbabel using apt (Ubuntu 19.04).
The problem is that after installing FragIt, I am getting the following error messages:
Error: OpenBabel could not…
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For some reason my graph is returning SMILES for aromatic groups that uses aromatic bond symbols e.g. `NC:1:N:N:C:[N]1N`.
RDKit does not recognize these symbols and it removes all the aromaticity …
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When installing "**PLIP**" via pip, the "**openbabel**" version mentioned in the requirements and to be installed shows a conflict. Given requirements shows a version of "~=3.0.0", but while installat…
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At the [web page](https://zarbi.chem.yale.edu/ligpargen/) of the web-based Ligpargen service, it is written "Maximum ligand size allowed is 200 atoms". This is understandable. However, I thought naive…
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Hi all. I am currently a Google Summer of Code Scholar working with MDAnalysis. My project involves the creation of a converter to convert between OpenBabel OBMols and MDAnalysis Universes. I am worki…
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## Environment Information
Open Babel version: 3.1.1
Operating system and version: Ubuntu 20.04.6 LTS
## Expected Behavior
```
$ obminimize -ff -h ChEMBL_Phase4_Drugs.sdf
```
The above c…