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It seems forcefield_kwargs is not being propagated sometimes. I've fixed this error below by editing
```
File "openmmforcefields/generators/template_generators.py", line 1112, in generate_residue_t…
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Hello,
I have a polymer system that I constructed by
1. Building the molecule using Avogadro
2. Editing the atom identifiers for later step involving topology file
3. Creating a bulk system usin…
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**Is your feature request related to a problem? Please describe.**
I am trying to produce grid_esp and grid_properties alongside a number of one-electron properties (https://psicode.org/psi4manua…
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**Describe the bug**
Updating an atom's residue-relevant metadata does not update the same data on the corresponding residue object. Editing the residue also doesn't update the atom. I'm not sure…
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Hi @AspirinCode , very impressive list!
We have a series of works that are also related to molecule editing or lead optimization
- [GraphCG](https://openreview.net/forum?id=wyU3Q4gahM), unsupervis…
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These long function calls to `domain_decomposition(...)` with many lines of arguments doubled by the if test clause for the molecules being present is getting cumbersome. Look into rewriting this in a…
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I was playing around with the `crispr` module and came across a weird error where the cut coordinates of a `cas9` object were way larger than the target sequence.
```
from pydna.dseqrecord import …
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1- Two formula with different names may be mapped as equal if they have the same formula and the same references. I think this is an error
2- Formula check does not check for dimension. I also thin…
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In order to correctly execute the package, several requirements are needed.
The corresponding Conda environment containing all those requirements is created usign the **tidyscreen.yml** file present…
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Consider a case in which a water `Molecule` has arbitrary partial charges and is fed to a well-defined SMIRNOFF force field for 4-site water (in atoms have charges defined by a `LibraryCharges` and `V…