OpenAD Commands§
This is the full list of available commands.
Info
To run a commands in Jupyter Notebook, prepend it with %openad - more information here.
Table of Contents§
Macromolecules§
show mmol|protein <fasta> | '<pdb_id>'
Launch the molecule viewer to visualize your macromolecule and inspect its properties.
Examples
Show a protein by its PDBe ID:
Show a protein by its FASTA string:
General§
openad
Display the openad splash screen.
get status
Display the currently selected workspace and toolkit.
display history
Display the last 30 commands run in your current workspace.
clear sessions
Clear any other sessions that may be running.
Workspaces§
set workspace <workspace_name>
Change the current workspace.
get workspace [ <workspace_name> ]
Display details a workspace. When no workspace name is passed, details of your current workspace are displayed.
create workspace <workspace_name> [ description('<description>') on path '<path>' ]
Create a new workspace with an optional description and path.
remove workspace <workspace_name>
Remove a workspace from your registry. Note that this doesn't remove the workspace's directory.
list workspaces
Lists all your workspaces.
Toolkits§
set context <toolkit_name> [ reset ]
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.
Runs§
create run
Start recording a run.
remove run <run_name>
remove a run.
save run as <run_name>
Stop recording a run and save it.
run <run_name>
Execute a previously recorded run. This will execute every command and continue regardless of any failures.
list runs
List all runs saved in the current workspace.
display run <run_name>
Display the commands stored in a certain run.
Utility§
display data '<filename.csv>'
Display data from a csv file.
result save [as '<filename.csv>']
Save table data to csv file.
result open
Explore table data in the browser.
If you append -d to the end of the command result open -d display will result to data viewer.
result edit
Edit table data in the browser.
If you append -d to the end of the command result open -d display will result to data viewer.
result copy
Copy table data to clipboard, formatted for spreadheet.
result display
Display the result in the CLI.
If you append -d to the end of the command result open -d display will result to data viewer.
result as dataframe
Return the result as dataframe (only for Jupyter Notebook)
edit config '<json_config_file>' [ schema '<schema_file>']
Edit any JSON file in your workspace directly from the CLI. If a schema is specified, it will be used for validation and documentation.
GUI§
launch gui
Launch the OpenAD GUI (graphical user interface).
restart gui
Terminate and then restart the GUI server.
quit gui
Terminate the GUI server.
LLM§
tell me <how to do xyz>
Ask your AI assistant how to do anything in OpenAD.
set llm <language_model_name>
Set the target language model name for the tell me command.
clear llm auth
Clear the language model's authentication file.
File System§
list files [ path ]
List al directories and files in your current workspace.
import from '<external_source_file>' to '<workspace_file>'
Import a file from outside OpenAD into your current workspace.
export from '<workspace_file>' to '<external_file>'
Export a file from your current workspace to anywhere on your hard drive.
copy file '<workspace_file>' to '<other_workspace_name>'
Export a file from your current workspace to another workspace.
remove '<filename>'
Remove a file from your current workspace.
open '<filename>'
Open a file or dataframe in the graphical user interface.
Examples
Help§
intro
Display an introduction to the OpenAD CLI.
docs
Open the documentation webpage.
?
List all available commands.
? ...<soft>
List all commands containing "..."
... ?<soft>
List all commands starting with "..."
Model§
model auth list
List authentication groups that have been created.
model auth add group <auth_group> with '<auth_token>'
Create a new authentication group for model services to use.
Single quotes are required for your <auth_token> but optional for <auth_group> in case it contains a space or special character.
Authorization is required to connect to IBM-hosted models (IBM partners only). Using an auth group allows you to authorize multiple models at once, and is the recommended authorization method.
Example§
ATTENTION
- Copy your authentication token from the OpenAD portal:
- open.accelerate.science for most users
xxxx .accelerate.science custom subdomain if your company runs its own instance- Create an auth group, e.g. 'default':
model auth add group default with '<auth_token>' - Catalog your services with the auth_group provided:
model service catalog from remote 'https://open.accelerate.science/proxy' as gen using (inference-service=generation auth_group=default)
You can also add a cataloged model to a group after you've created it:
model auth add service gen to group default
model auth remove group <auth_group>
Remove an authentication group.
Single quotes are optional in case auth_group contains a space or special character.
Examples
model auth add service <service_name> to group <auth_group>
Ad a model service to an authentication group.
Single quotes are optional for both <service_name> and <auth_group> in case they contain a space or special character.
Examples
model auth remove service <service_name>
Detach a model service from an authentication group.
Single quotes are optional in case service_name contains a space or special character.
Examples
model service status
Get the status of your currently cataloged services.
model service describe <service_name>
Get a service's configuration details.
Single quotes are optional in case service_name contains a space or special character.
Examples
model catalog list
List your currently cataloged services.
uncatalog model service <service_name>
Uncatalog a model service.
Single quotes are optional in case service_name contains a space or special character.
Examples
catalog model service from [ remote ] '<path>|<github>|<service_url>' as <service_name> USING (<parameter>=<value> <parameter>=<value>)
Catalog a model service from a local path, from GitHub or from an hosted service URL.
Use the remote clause when cataloging from a hosted service URL.
Parameters
<path>|<github>|<service_url>
The location of the model service, to be provided in single quotes.
This can be a local path, a GitHub SSH URI, or a URL for an existing remote service:
<soft>...</soft>from '/path/to/service'
<soft>...</soft>from 'git@github.com:acceleratedscience/generation_inference_service.git'
<soft>...</soft>from remote '0.0.0.0:8080'
<service_name>
How you will be refering to the service when using it. Keep it short, e.g. prop for a service that calculates properties.
Single quotes are optional in case you want to used a space or special character.
The USING Clause
The parameters below are only needed when connecting to an IBM-hosted service (IBM partners only).
inference-service=<string> (required)
The name of the inference service you want to connect to, eg. generation ot molformer.
Authorization:
To authorize to an IBM-hosted service (IBM partners only), you have two options:
1. authorization='<auth_token>'
Provide your authorzation token directly.
Note: to use this option, auth_group can not be defined.
2. auth_group=<auth_group_name>
The name of an authorization group which contains your auth_token.
This is recommended if you will be using more than one model service.
For instructions on how to set up an auth group, run model auth add group ?
Note: to use this option, authorization can not be defined.
Examples
<span style="background: #dc0; color: #fff"> ATTENTION </span> <yellow>The proxy URL used in the examples may be different for you: open.accelerate.science/proxy --> for most users <soft>xxxx</soft>.accelerate.science/proxy --> custom subdomain if your company runs its own instance</yellow>
Catalog a model using SkyPilot deployment
catalog model service from 'git@github.com:acceleratedscience/generation_inference_service.git' as gen
Catalog a model using a authentication group
catalog model service from remote 'https://open.accelerate.science/proxy' as molf USING (inference-service=molformer auth_group=default)
Catalog a model using an authorization token
openad catalog model service from remote 'https://open.accelerate.science/proxy' as gen USING (inference-service=generation authorization='<auth_token>')
Catalog a remote service that was shared with you:
model service up <service_name> [ no_gpu ]
Launch a model service, after it was cataloged using model service catalog.
Single quotes are optional in case service_name contains a space or special character.
If you don't want your service to use GPU you can append the no_gpu clause.
Examples
model service local up <service_name> [ no_gpu ]
Launch a model service locally.
Single quotes are optional in case service_name contains a space or special character.
If you don't want your service to use GPU you can append the no_gpu clause.
Examples
model service down <service_name>
Deactivate a model service.
Single quotes are optional in case service_name contains a space or special character.
Examples
get model service <service_name> result '<result_id>'
Retrieve a result from a model service.
This is for async inference, which will return a <result_id> instead of a result.
Single quotes are optional in case service_name contains a space or special character.
Examples