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Update README #48

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Dec 14, 2021
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Update README #48

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17 changes: 5 additions & 12 deletions README.md
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Expand Up @@ -22,18 +22,18 @@ All-against all comparison of structurally covered kinases using the [`kissim`](
│   ├── user_env.yaml
│   └── regenerate_readmes.py
│
├── docs <- A default Sphinx project; see sphinx-doc.org for details.
├── docs <- A default Sphinx project; see sphinx-doc.org for details (not used by us so far).
│
├── notebooks <- Jupyter notebooks.
│
├── reports <- Generated analysis as HTML, PDF, LaTeX, etc.
│   └── figures <- Generated graphics and figures to be used in reporting.
│
├── results <- Encodings (fingerprints) and comparisons.
├── results <- Encodings (fingerprints) and comparisons. Needs to be downloaded from zenodo as described in the installation section.
│
├── setup.py <- Makes project pip installable (pip install -e .) so src can be imported.
│
├── scripts <- KiSSim scripts.
├── scripts <- KiSSim and other scripts; includes README with details.
│
├── src <- Source code for use in this project.
│   ├── __init__.py <- Makes src a Python module.
Expand All @@ -49,7 +49,7 @@ All-against all comparison of structurally covered kinases using the [`kissim`](

## Installation

> We are assuming you have a working `mamba` installation in your computer. If this is not the case, please refer to their [official documentation](https://mamba.readthedocs.io/en/latest/installation.html#mamba).
> We are assuming you have a working `mamba` installation in your computer. If this is not the case, please refer to their [official documentation](https://mamba.readthedocs.io/en/latest/installation.html#mamba). If you installed `mamba` into an existing `conda` installation, also make sure that the `conda-forge` channel is configured by running `conda config --add channels conda-forge`.

1. Clone this repository.

Expand All @@ -72,14 +72,7 @@ All-against all comparison of structurally covered kinases using the [`kissim`](
pip install -e kissim_app
```

3. Download `kissim` fingerprints and distances to `results/` folder.

```
# Change to kissim_app directory (if you have not already)
cd /path/to/kissim_app

# TBA
```
3. Download (a) `kissim` fingerprints and distances to `results/` folder and (b) KLIFS structures to `data/external/structures` folder as described in our [zenodo release](https://doi.org/10.5281/zenodo.5774521) (some files were just not suitable upload to GitHub).

4. Open the notebooks, e.g. a [quick start](https://github.com/volkamerlab/kissim_app/blob/master/notebooks/001_quick_start/001_quick_start_kissim.ipynb) on how to load `kissim` results.

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