KBS - Home
Chem. tools tutorials
File conversion
Visualization
Avogadro
OpenBabel
RASPA
LAMMPS
EQeq
Packmol
HostDesigner

Avogadro

Avogadro 2 is a cross-platform powerful molecular editor and visualization application.

Plug-ins

Avogadro 2 provides an easy to use plug-in interface. You can create your plug-in with just a few lines of Python code. The example below shows how you can use the plug-in interface to create a benzene molecule.

More examples can be seen in this repository as well as in the OpenChemistry Avogadro 2018 users group meeting repository.

Example 1: Add molecule

"""
Avogadro 2 basic plug-in example for adding a benzene molecule.
"""
import os
import sys
import json
import argparse

# Some globals:
debug = True
benzene_xyz = """12
benzene
C  -0.0000  1.4027  0.0000
H  -0.0000  2.4903  0.0000
C  -1.2148  0.7014  0.0000
H  -2.1567  1.2451  0.0000
C  -1.2148 -0.7014  0.0000
H  -2.1567 -1.2451  0.0000
C  -0.0000 -1.4027  0.0000
H  -0.0000 -2.4903  0.0000
C   1.2148 -0.7014  0.0000
H   2.1567 -1.2451  0.0000
C   1.2148  0.7014  0.0000
H   2.1567  1.2451  0.0000"""


def get_options():
    return {}


def run_command():
    # Read options from stdin
    stdin = sys.stdin.read()

    # Parse the JSON strings
    opts = json.loads(stdin)

    # Prepare the result
    result = {'append': True,
              'moleculeFormat': 'xyz',
              'xyz': benzene_xyz}
    return result


if __name__ == "__main__":
    parser = argparse.ArgumentParser('Add a benzene molecule')
    parser.add_argument('--debug', action='store_true')
    parser.add_argument('--print-options', action='store_true')
    parser.add_argument('--run-workflow', 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("Add Benzene")
    if args['menu_path']:
        print("&Build")
    if args['print_options']:
        print(json.dumps(get_options()))
    elif args['run_workflow']:
        print(json.dumps(run_command()))

Plug-in structure

Avogadro and your Python code communicates through json files. Basically they send each other some data by reading and writing json files.

User input: `get_options`

This function allows you to get options from the user. You can create a window with different input styles. In the example below there are no options for user to select.

List input

The function below creates a drow down list with strings. The selected entry is sent to the Python code.

def get_options():
    """User interface options."""
    user_options = {}
    user_options['mol'] = {'label': 'Molecules',
                           'type': 'stringList',
                           'default': 'C60',
                           'values': mol_list}
    return {'userOptions': user_options }

The selection can be read by:

stdin = sys.stdin.read()
opts = json.loads(stdin)
user_selection = opts['mol']

Number input

The function below creates a number input.

def get_options():
    """User interface options."""
    user_options = {}
    user_options['num'] = {'label': 'My Number',
                           'type': 'float',
                           'default': 1.0,
                           'precision': 3,
                           'toolTip': 'Some number we want'}
    return {'userOptions': user_options }

The selection can be read by:

stdin = sys.stdin.read()
opts = json.loads(stdin)
user_selection = opts['mol']

Return result: `run_command`

New molecule

The function below returns a new molecule in xyz format.

def run_command():
    stdin = sys.stdin.read()   # Read options from stdin
    opts = json.loads(stdin)   # Parse the JSON strings

    result = {'append': True,              # Prepare the result
              'moleculeFormat': 'xyz',
              'xyz': string_xyz}
    return result

Modify current molecule

The function below flattens all the z-coordinates of a molecule.

def run_command():
    stdin = sys.stdin.read()   # Read options from stdin
    opts = json.loads(stdin)   # Parse the JSON strings

    coords = opts['cjson']['atoms']['coords']['3d']
    for i in range(0, len(coords), 3):
        coords[i+2] = 0.0
    return opts