Christoph Clement

Tertiary structure preprocessing

4

Hi, thanks for putting this online, it is really nice to work with! I have a question regarding the preprocessing step of the tertiary structure that you mentioned [here](https://github.com/OpenProtein/openprotein/issues/15#issuecomment-485516443). The...

Hi, why is padding before and after masking in preprocessing.py needed? It seems to me that padding after masking would be enough. Best Christoph

G4Exception : Cache001

10

Hi, I am getting the following error at the end of my simulation: ``` -------- EEEE ------- G4Exception-START -------- EEEE ------- *** G4Exception : Cache001 issued by : G4CacheReference::Destroy Internal...

Why is DiceCELoss2 used in auto3dseg segresnet template?

1

Hi, I was just wondering why you are using `loss.DiceCELoss2` instead of the normal MONAI `DiceCELoss` in the [auto3dseg segresnet template](https://github.com/Project-MONAI/research-contributions/blob/main/auto3dseg/algorithm_templates/segresnet/configs/hyper_parameters.yaml)? [`DiceCELoss2`](https://github.com/Project-MONAI/research-contributions/blob/main/auto3dseg/algorithm_templates/segresnet/scripts/loss.py) seems to be the same as [`DiceCELoss` ](https://docs.monai.io/en/stable/_modules/monai/losses/dice.html#DiceCELoss)...

Hello, thank you for creating this nice package! It is really helpful and the Python bindings work great. I was wondering whether it would be possible to provide property files...

Fix #427

4

#### Reference Issues/PRs Fixes #427 #### Pull Request Checklist - [ ] Added a note about the modification or contribution to the `./CHANGELOG.md` file (if applicable) - [x] Added appropriate...

Add num_heavy_atoms as node features

1

**Is your feature request related to a problem? Please describe.** There are already a lot of nice molecule node features, but I was missing the number of heavy atoms as...

It would be great to have add_bond_type_one_hot as an edge features for molecules. Something similar to ```python def add_bond_type_one_hot( u: str, v: str, d: Dict[str, Any], return_array: bool = True,...

H coords are not included when constructing molecule graph from SDF file

1

**Describe the bug** H atoms are not included in `coords` when constructing molecule graph with `add_hs=True` and `path`. **To Reproduce** Colab reproducing the bug: https://colab.research.google.com/drive/122CTepC6O_-R-jbLArcbdqSQOiQseB-H?usp=sharing **Expected behavior** If `config.add_hs` is...