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The workflow we've been using with OPLS doesn't work for most forcefields. In Amber, for example, non-bonded VdW and bonded interactions are specified through atomtyping but partial charges are assign…
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With this ```x.smi``` file: ```O=C(O)CCCCC``` I run this command:
```
obabel -i smi x.smi -o xyz -O x1.xyz --gen3d
```
The produced outputs are a little bit different with every run:
```
$ dif…
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**Is your feature request related to a problem? Please describe.**
Currently moltemplate users have to run ltemplify.py on the files created by VIPSTER, by typing this into the terminal/shell:
```
…
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## Problem/Concern
I discovered today that if you set the border width in the border atom to 8 or above, the secondary buttons on the Buttons Standard molecule start to become un-useable. With a…
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We run into performance problems / crashes when attempting to run NWX with large test data (>500 atoms). This issue is meant to track these problems as they show up and collect relevant repo-specific …
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#### API Porting Status
_We are slowly working towards exposing all the InCHI functions. PRs welcome._
A. Generation of InChI from structure
- [ ] GetINCHI | `int INCHI_DECL GetINCHI(inchi_In…
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The Copyright in the About dialog seems to have a problem. For example, see the screenshot below from the published version of Make A Ten. The version was published on 2024-04-03, but the copyright …
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Vulnerable Library - molecule-3.6.1-py3-none-any.whl
Path to dependency file: /requirements.txt
Path to vulnerable library: /requirements.txt
## Vulnerabilities
| CVE | Severity | CVSS | Depe…
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I am encountering a bit of strange behavior with the Transpiler recently. It always happens after activeRepos gets reloaded. Basically the problem is that after pull all, the transpiler freezes, and …
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Hello,
Thank you very much for your wonderful software.
I thought that if coot could be used with modern GUI app runtimes such as Flatpak or Snap, many people would be able to easily install wit…