-
Hi! I'm using openbabel v. 2.3.0 with a GNU/Linux OS (Ubuntu 10.10). I have the following problem on adding hydrogens with babel:
I have a structure contaning only certain hydrogen atoms (in my case …
-
## Actual Behavior
When I create OBMol of the same protein downloaded from the PDB archive in two different formats and try to protonate it using AddHydrogens(), I get completely different results. E…
-
Increasing hydrogen masses while removing mass from the parent heavy atom can cause instabilities, so we should offer an alternative (perhaps by default) where we increment the hydrogen masses without…
-
Forwarding from Dale E.T. (edited):
//
I was looking over 7np8 in the PDB and comparing the deposited model to the PDB-REDO model. It looks to me that REDO has refined the model with a problematic …
-
Thank you for providing the latest code updates! I've been exploring the force_matching.ipynb notebook, and I noticed that the loss value obtained during the training seems quite large, reaching aroun…
-
We want to ensure that incoming SMILES have unambiguous protonation / tautomer states.
There are several issues to look out for:
1. SMILES reader (Openeye or RDKit) preserve the protonation state…
-
- [ ] `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] …
-
I am having trouble with executing codes with `Hydrogen`. I have tried #1538 but had no luck. I am trying to setup Atom on my new Mac hence running into this issue.
1. Download Atom from https:/…
-
## Summary
tqdm.auto progress bar does not update if the codes are running in a Atom IDE with hydrogen
## Additional details
- I run the NiMARE package which it uses tqdm.auto
- NiMARE versi…
-
There is a keybinding conflict with Ctrl-Shift-W with word selection in Atom's core `atom-text-editor` selector.
I think the key bindings rbox uses are way too broad:
```
'atom-text-editor:not(…