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Copy file name to clipboardExpand all lines: commands.md
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@@ -134,85 +134,13 @@ Lists all your workspaces. <br>
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### Toolkits
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`ds4sd`{: .cmd }
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</summary>
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Display the splash screen for the DS4SD toolkit. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`rxn`{: .cmd }
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</summary>
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Display the splash screen for the RXN toolkit. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`list toolkits`{: .cmd }
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</summary>
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List all installed toolkits. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`list all toolkits`{: .cmd }
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</summary>
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List all available toolkits. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`add toolkit <toolkit_name>`{: .cmd }
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</summary>
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Install a toolkit. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`remove toolkit <toolkit_name>`{: .cmd }
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</summary>
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Remove a toolkit from the registry. <br>
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<b>Note:</b> This doesn't delete the toolkit code. If the toolkit is added again, a backup of the previous install is created in the toolkit directory at `~/.openad/toolkits`. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`update toolkit <toolkit_name>`{: .cmd }
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</summary>
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Update a toolkit with the latest version. It is recommended to do this on a regular basis. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`update all toolkits`{: .cmd }
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</summary>
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Update all installed toolkits with the latest version. Happens automatically whenever OpenAD is updated to a new version. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`set context <toolkit_name> [ reset ]`{: .cmd }
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</summary>
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Set your context to the chosen toolkit. By setting the context, the selected toolkit functions become available to you. The optional parameter `reset` can be used to reset your login information. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`get context`{: .cmd }
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</summary>
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Display the currently selected toolkit. <br>
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</details>
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<detailsmarkdown="block"class="cmd-wrap">
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<summarymarkdown="block">
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`unset context`{: .cmd }
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</summary>
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Exit your toolkit context. You will no longer have access to toolkit-specific functions. <br>
Copy file name to clipboardExpand all lines: index.md
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The OpenAD client is accessible from our command line interface, via Jupyter Notebook or our API. It provides unified access to a variety of tools and AI models for literature knowledge extraction, forward and retrosynthesis prediction, generative methods and property inference. OpenAD lets you train models on your own data, to then visualize and filter your candidate molecules.
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<br>
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## Latest Release Notes
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OpenAD has remove the RXN and Deep Search toolkits and replaced them with new and more user Friendly plugins !
2. Once inside the OpenAD client, you'll be prompted to authenticate when activating the Deep Search (DS4SD) toolkit. When running `set context ds4sd` :
-**API_key:** The DS4SD API key you obtained following the instructions above.
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3. You should get a message saying you successfully logged in.
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> **Note:** Your DS4SD auth config file is saved as `~/.openad/deepsearch_api.cred`. If you ever want to reset your DS4SD login information you can run `set context ds4sd reset`, or you can delete this file.<br>
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</div>
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</details>
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<details>
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<summary>Register with RXN</summary>
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<divmarkdown="block">
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1. First, you'll need to generate an API key on the RXN website.
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<br>
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- Sign up for an RXN account at [rxn.app.accelerate.science](https://rxn.app.accelerate.science)
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- Obtain your API key by clicking the user profile icon in the top right hand corner and select "Account", then select the "My keys" tab.<br>
You can create your first plugin in just minutes. This creates the ability for your own projects (or your favorite tools) to access OpenAD's powerful visualisation capabilities and more.
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2. When setting the context to RXN using `set context rxn` you'll be prompted to create a new auth configuration file:
-**API_key:** The RXN API key you obtained following the instructions above.
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3. You should get a message saying you successfully logged in.<br>
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> **Note:** Your RXN auth config file is saved as `~/.openad/rxn_api.cred`. If you ever want to reset your RXN login information you can run `set context rxn reset`, or you can delete this file.<br>
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</div>
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</details>
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<br><br>
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## Adding a Toolkit
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First install the toolkit, then set the context to this toolkit.
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