Example Plugin Script - Part 1

Let’s consider Alloy/Alchemy command as a reference for writing code for scripts or plugins

The Main function:

The main function is responsible for parsing command-line arguments . It serves as the entry point for the script , facilitates its interaction with the user and executes the appropriate actions.

Below is a detailed explanation of the main function:

if __name__ == "__main__":
    parser = argparse.ArgumentParser('Replace atoms of elements')
    parser.add_argument('--debug', action='store_true')
    parser.add_argument('--print-options', action='store_true')
    parser.add_argument('--run-command', action='store_true')
    parser.add_argument('--display-name', action='store_true')
    parser.add_argument('--menu-path', action='store_true')
    parser.add_argument('--lang', nargs='?', default='en')
    args = vars(parser.parse_args())

    debug = args['debug']

    if args['display_name']:
        print("Replace Elements")
    if args['menu_path']:
        print("&Build")
    if args['print_options']:
        print(json.dumps(getOptions()))
    elif args['run_command']:
        print(json.dumps(runCommand()))

Here’s a detailed breakdown of the main function:

1. Command-Line Argument Parsing: The argparse module is used to define command-line arguments and parse them.

2. Script Entry Points:

   • The script supports the following command-line arguments (Refer script entry points) :

     • --debug

     • --print-options

     • --run-command

     • --display-name

     • --menu-path

     • --lang [language]

3. Debug Mode: If the --debug flag is set, the debug variable is set to True. This can be used to control the script’s debugging behavior.

Input Arguments

1. Display Name: If the --display-name flag is provided, the script prints Replace Elements as the display name of the operation.

2. Menu Path: If the --menu-path flag is provided, the script prints &Build as the menu path where the operation can be found.

3. Print Options: If the --print-options flag is set, the script prints the available user UI options in JSON format using the getOptions function.

4. Run Command: If the --run-command flag is set, the script executes the runCommand function, which performs the element replacement operation and returns the modified molecular structure in JSON format.

getOptions() Function

def getOptions():
    userOptions = {}

    userOptions['Find'] = {}
    userOptions['Find']['label'] = 'Find Element'
    userOptions['Find']['type'] = 'stringList'
    userOptions['Find']['values'] = list(element_dict.keys())
    userOptions['Find']['default'] = "Carbon"

    .....
    return opts

The getOptions function is used to specify the script Interfaces or the pop-up menu for the script. For each option in the userOptions list, Avogadro will create appropriate labels, menus, text boxes, check boxes, etc. Interface will look something like this:

It is called in the command line when --print-options is given as the input argument.