Getting Started with OpenAD

If you haven't yet done so, install OpenAD first.
When installing on macOS without a virtual environment, you may need to use python3 and pip3 instead of python and pip.
When updating to OpenAD 0.4.0 or above, first remove all toolkits by runnning list toolkits and then remove toolkit <toolkit_name>.

Getting Started - CLI

Enter the virtual environment

Note: If you just installed OpenAD, you probably already activated the virtual environment.
```
source ~/ad-venv/bin/activate
```
Enter the command shell
```
openad
```
Exit the command shell
Hit ctrl+c or run:
```
exit
```
Run a single command from outside the command shell
```
openad <command>
```
Exit the virtual environment
```
deactivate
```

To run a command in bash mode, prepend it with openad and make sure to escape quotes.

openad show molecules using file \'base_molecules.sdf\'

The following commands only need to be run once after installation:

Activate your virtual environment

Note: If you just installed OpenAD, you probably already activated the virtual environment.
```
source ~/ad-venv/bin/activate
```
Create an iPython kernel
This ports your virtual environment to Jupyter.
```
python -m ipykernel install --user --name=ad-venv
```
Note: To list your installed iPython kernels, you can run jupyter kernelspec list, and to remove the kernel you can run jupyter kernelspec uninstall ad-venv
Install the magic commands
This enables OpenAD commands to be run within a Jupyter Notebook.
```
init_magic
```
Alternative: Manually add magic commands
If you don't want to activate magic commands in all Notebooks, you can instead activate them for individual Notebooks.
- Run init_examples
- Copy the file ~/openad_notebooks/openad.ipynb to the same directory as the Notebook you wish to activate.
- In your Notebook, run this inside a code cell: !run openad.ipynb
Install example Notebooks
This installs our example Notebooks at ~/openad_notebooks.
```
init_examples
```

Open any Notebook
The following command will open up the example Notebook:
```
jupyter lab ~/openad_notebooks/Table_of_Contents.ipynb
```
Select the kernel
Make sure to select the "ad-venv" iPython kernel. You can do this under Kernel > Change Kernel, or in the latest versions of Jupyter by clicking the kernel name in the top right hand corner. If you don't see your iPython kernel, make sure you followed the Jupyter Setup instructions listed above.
Magic Commands
Magic commands let you access any OpenAD CLI command from within Jupyter. They are invoked by the %openad prefix.
```
%openad list files
```
If you wish to retrieve data from an OpenAD command, you can use the %openadd prefix instead. This will return raw, unstyled data for further processing.
```
my_data = %openadd display data 'my_data_file.csv'
```