Getting Started with OpenAD§

Tl;dr§

Get started in your terminal:

Bash

openad

Get started with Jupyter Notebook examples:

Bash

init_magic

Bash

init_examples

Bash

jupyter lab ~/openad_notebooks/Table_of_Contents.ipynb

Warning

If you get an error when running init_magic, you may first need to setup the default iPython profile for magic commands.

Bash

ipython profile create

Getting Started - CLI§

Enter the virtual environment
Bash
```
source ~/ad-venv/bin/activate
```
Enter the command shell

Here you'll find further instructions on how to use OpenAD.
Bash
```
openad
```
Exit the command shell
Hit ctrl+c or run:
Bash
```
exit
```
Run a single command from outside the command shell
Bash
```
openad <command>
```
Exit the virtual environment
Bash
```
deactivate
```
Running Bash Commands

To run a command in bash mode, prepend it with openad and make sure to escape quotes.
Bash
```
openad show molecules using file \'base_molecules.sdf\'
```

Getting Started - Jupyter§

Setting up Jupyter§

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

Activate your virtual environment
Bash
```
source ~/ad-venv/bin/activate
```
Create an iPython kernel
This ports your virtual environment to Jupyter.
Bash
```
python -m ipykernel install --user --name=ad-venv
```
Note: List your installed iPython kernels: jupyter kernelspec list
Remove a kernel: jupyter kernelspec uninstall ad-venv
Install the magic commands
This enables OpenAD commands to be run within a Jupyter Notebook.
Bash
```
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.
Bash
```
init_examples
```

Launching OpenAD in Jupyter§

Open any Notebook
Launch Jupyter lab to create a fresh notebook, or get started with our example Notebook:
Bash
```
jupyter lab
```
Bash
```
jupyter lab ~/openad_notebooks/Table_of_Contents.ipynb
```
Select the kernel
Make sure to select the "ad-venv" iPython kernel you just created. You can do this under Kernel > Change Kernel, or 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. Try listing your files as a test:
Python
```
%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. For example:
Python
```
my_data = %openadd display data 'my_data_file.csv'

for item in my_data:
    print(item.smiles)
```
To see the available commands, you consult the Commands page, or you can request inline help:
Python
```
%openad ?
```