drug-computing
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MobleyLab
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
Several notebooks do trajectory visualization with `nglview`; it would be helpful to migrate those to something which will work on Colab. The most important seem to be: - MD sandbox...
- The ligand-based design lecture and assignment have some inconsistencies and the code in the lecture is more helpful than the example code in the assignment, students report - Check...
Links referring to `Python_Linux_Vi` in the lectures [`README.md`](https://github.com/MobleyLab/drug-computing/blob/master/uci-pharmsci/lectures/README.md) are broken. Additionally, the links in the [`README.md`](https://github.com/MobleyLab/drug-computing/blob/master/uci-pharmsci/lectures/Python_Linux_Vi/README.md) file in the `Python_Linux_Vi` directory are also broken.
The visualization lecture added a couple very large files (Keynote files) which have to managed with git-lfs. A better procedure would be to just link to them (hosted elsewhere) and...
The notebooks and worked examples for lectures need updating, particularly, these cases: - [x] Python, Linux, and vi(m) - [x] 3D structure and shape methods (#25 ) - [x] **Molecular...
Currently, I do not have Jupyter notebooks for the following lectures, so I will need to create them (potentially from the slides), ideally also creating activities to try at the...
- Improve images/make sure all have suitable credit/attribution - Migrate to Jupyter notebook? Unsure if content lends itself to that, but would make for greater portability/easier updates.
Using Toolkit version 2023.1 and presumably OEDocking TK 4.2.1. In the notebook OEDocking.ipynb, section 3.4: I get the following error. --------------------------------------------------------------------------- NameError Traceback (most recent call last) Cell In[13], line...