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Thanks for you opening our source code and the fantastic works.
I have a few questions I’d like to ask.
Firstly, the protein-ligand complexes in MISATO likely come primarily from the PDBbind dat…
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Issue to go with branch orientational_entropy.
Adding a simple orientational entropy calculation based on the number of neighbours. This will ignore hydrogen bonds (that will be future work!).
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**Steps to Reproduce**
1. Go to Macro - Flex mode
2. Load from file: [Copy_paste operation works wrong (copy only two hydrogen bonds and drops others).zip](https://github.com/user-attachments/files/…
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A common nuisance for hydrogen bonds is selecting the donor atom for each hydrogen. Ideally there could be a convenience function in `analysis.hbonds` which does this. So the signature would be:
…
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**Describe the bug**
Adding/Removing hydrogens changes layout of molecule (and lenght of bonds) if molecule contains bond of non-default length
**Steps to Reproduce**
1. Put simple bond on the ca…
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Here's an MWE and the corresponding output:
```{bash}
!wget https://files.rcsb.org/download/1AKI.pdb
```
```{python}
from openmm import app
pdb_file = '1AKI.pdb'
pdb = app.PDBFile(pdb_fil…
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**Describe the bug**
A minor issue is found that during featurization, a higher-level function can sometimes override featurizer (mol, atom, bond) logic that can yield unexpected behavior.
**Exam…
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## Theoretical background - What are antisense chains?
The central dogma of molecular biology states that the genetic information inside the cell flows in one direction: information stored within D…
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- [ ] `nointrares` keyword?
- [x] bridging time series?
- [x] Ignore UA - V -UA bridges with nointramol hbond
- [x] allow bridges within one residue
- [x] hbond bridging track atom numbers
- [x] …
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Dear David,
I hope this message finds you well.
I am encountering problems while generating the combinatorial pharmacophore library. I have successfully acquired the super_pharmacophore.pml file…