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Use atomlite and stko for databasing and analysis. Add angle term. #12

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Nov 17, 2023
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10 changes: 10 additions & 0 deletions .github/workflows/tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,16 @@ jobs:
name: l5-plot
path: l5.png

- uses: actions/upload-artifact@v3
with:
name: uff-plot
path: uff_angle_test.png

- uses: actions/upload-artifact@v3
with:
name: uff2-plot
path: uff_angle_test2.png

- uses: actions/upload-artifact@v3
with:
name: rt-plot
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3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -130,4 +130,5 @@ dmypy.json

# Version.
src/cgexplore/_version.py
testff_iterations.json
testff_iterations.json
.vscode
10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ The code can be installed following these steps:
conda activate NAME
```

5. From `CGExplore` directory, install pip environment:
4. From `CGExplore` directory, install pip environment:
```
pip install .
```
Expand All @@ -32,7 +32,7 @@ or for development, use [just](https://github.com/casey/just) to install a dev e
just dev
```

6. Install `OpenMM` [docs](https://openmm.org/):
5. Install `OpenMM` [docs](https://openmm.org/):
```
mamba install openmm
```
Expand All @@ -41,7 +41,7 @@ or
conda install -c conda-forge openmm
```

7. Install `openmmtools` [docs](https://openmmtools.readthedocs.io/en/stable/gettingstarted.html):
6. Install `openmmtools` [docs](https://openmmtools.readthedocs.io/en/stable/gettingstarted.html):
```
mamba install openmmtools
```
Expand All @@ -51,7 +51,7 @@ conda config --add channels omnia --add channels conda-forge
conda install openmmtools
```

8. Update directory structure in `env_set.py` if using example code.
7. Update directory structure in `env_set.py` if using example code.

The library implements some analysis that uses:

Expand All @@ -60,7 +60,7 @@ The library implements some analysis that uses:
# Usage

* The directory `cgexplore` contains the actual source code for the package. **Warning**: This package is still very much underdevelopment and many changes are expected.
* The directory `first_paper_example` contains the code to generate the cages and data for DOI: XX. This series of examples uses the classes and tools in `CGExplore`.
* The directory `first_paper_example` contains the code to generate the cages and data for DOI: [10.1039/D3SC03991A](https://doi.org/10.1039/D3SC03991A). This series of examples uses the classes and tools in `CGExplore`. I would no longer recommend using it as a perfect example as many changes, including using databasing have been introduced without optimising these scripts. [This testing repository is a good example](https://github.com/andrewtarzia/cg_model_test/blob/main/cg_model_test.py).
* `generate_XX.py` generates cage structures for different topology sets
* `env_set.py` sets a specific environment for file outputs
* `plot_XX.py` produces images and figures, and performs analysis
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