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Take a look at example 7 here:
https://www.programcreek.com/python/example/110781/rdkit.Chem.AllChem.EmbedMolecule
Possibly an improvement to the SmilesWidget in aiidalab-widget-base.
But need a …
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Add relative energies to Singlepoint_fragments. Useful when we have multiple isomers (conformers, spin-state isomers etc.) and want to see their relative energies with respect to the lowest one.
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**Describe the bug**
Generating a conformer for this SMILES fails in both OE/RD, but it seems like all stereocenters are specified:
```
from openforcefield.topology.molecule import Molecule
mol =…
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@mmarianski reported an odd behavior of populations having same members after a while (all low energy conformers? Must provide examples and check this behaviour.
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I hit this while working on the failed test in https://github.com/rdkit/rdkit/pull/7426:
```python3
from rdkit import Chem
atropTestFile = '../Code/GraphMol/FileParsers/test_data/atropisomers/R…
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**Tool:**
http://172.26.0.2/cb (local DevEnv)
**Bug Description:**
When the project.zip archive is uncompressed, there are no symbolic links. This means two things: 1. It isn't possible to te…
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Dear OpenFF-Bespokefit Team,
First and foremost I would like to say thank you for the great work you did with BespokeFit!
I would like to ask for you help regarding a bug/problem I am facing testi…
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Dear XTB Team,
First of all, thank you for this great software, which I can enjoy even as an experimental chemist.
I frequently use Minimum Hopping, as it is sometimes superior to CREST. However…
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Currently, in qFit, removing conformers below a certain density level is defined as:
if any voxel in the conformed has a density intensity =5 atoms lack support (or somewhere around there).
This s…
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```
Done generating conformers in AutoTST...
80 conformers found
Skipping unconverged shell 1
Skipping unconverged shell 22
Skipping unconverged shell 49
Traceback (most recent call last):
Fi…