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We previously included some functionality using `BumpyMatrix` to store molecule-based spatial transcriptomics data, along with an example dataset from the `seqFISH` platform in the `STexampleData` pac…
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**Describe the bug**
When I do
```
sudo pip install molecule
sudo gem install serverspec
molecule test
```
I got an error:
```
ERROR: 'molecule/default/molecule.yml' glob failed. E…
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Improve the contribution guide with details like below. Taken from a discussion, so reword to fit as a document:
--------
So in general we try to avoid introducing some new knobs in `eos_cli_con…
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According to this discussion, it should be possible to change MW of a molecule. E.g. the use case is - importing data for a molecule that is not present in the project. However, I do not see the respe…
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Hi folks,
please have a look at the following code:
```
import qcportal as ptl
import cmiles
print(ptl.__version__)
print(cmiles.__version__)
qc_client = ptl.FractalClient("https://api…
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THF in Martini is mapped as 2 beads but is a cyclic molecule. This is problematic because at the moment it is assumed that each meta-edge corresponds to one bond at the all-atom level
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## Environment Information
Open Babel version: 3.0.0
Operating system and version: Linux Ubuntu 20.04
## Expected Behavior
I tried to convert .smi file into .pdbqt file via .sdf converting. I go…
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Add a new argument `stateVariableParams` to the function, so `createSimulationBatch(simulation, parametersOrPaths = NULL, stateVariableParamsOrPaths = NULL, moleculesOrPaths = NULL)`.
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Currently MMSchema does not handle multi-conformers (whereas OpenFF toolkit does). What is the best way to handle this disrepancy?
1 - Add another dimension to `Molecule.geometry` ? This would make…
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