API Access

Use the API to run any command from a python script and capture the result for further processing.

This lets you integrate OpenAD into larger workflows involving other tools.

The Basics

Python

from openad import OpenadAPI

oad = OpenadAPI()
result = oad.request("<command goes here>")

print(result)

Example A - Workspace / File System

In this example we filter out all files in your workspace starting with "sample-" and move them into a folder "samples".

Open in Colab

Python

from openad import OpenadAPI
oad = OpenadAPI()

# Get dataframe with files in your workspace
files_df = oad.request("list files")

# Filter out all files starting with 'sample-'
files_df_filtered = files_df[files_df["File Name"].str.startswith("sample-")]

# Scan for files
filenames = []
for file in files_df_filtered["File Name"]:
    filenames.append(file)

# No relevant files found
if len(filenames) == 0:
    print("⛔️ No files found that start with 'sample-'")

# List relevant files
else:
    print("The following files will be moved to the 'samples' directory:")
    print('-----------------------------------------------')
    print("• " + "\n• ".join(filenames))

    # Ask for confirmation
    cont = input("\nAre you sure you want to continue? (y/n)")

    # Move files
    if cont == "y":
        for fn in filenames:
            oad.request(f"move '{fn}' to 'samples' force")
        print(f"\n✅ {len(files_df_filtered)} files were moved into the 'samples' directory")

    # Abort
    else:
        print("\n❌ (No files were moved)")

Example B - Molecule Working Set

In this example we'll use the Deep Search plugin to search scientific literature for molecules that are similar to a provided SMILES, and use RDKit to generate SVG images for each result.

Open in Colab

Python

import os
from rdkit import Chem
from IPython.display import SVG, display, HTML

from openad import OpenadAPI
oad = OpenadAPI()

# Use Deep Search to search for similar molecules
candidates = oad.request("ds search for molecules similar to CC(=CCC/C(=C/CO)/C)C")

# Get your workspace path
cmd_pointer = oad.request("cmd_pointer")
workspace_path = cmd_pointer.workspace_path()

# Generate SVG image for each result
for i, smiles in enumerate(candidates["smiles"], start=1):

  # Generate SVG string using RDKit
  mol_rdkit = Chem.MolFromSmiles(smiles)
  mol_drawer = Chem.Draw.MolDraw2DSVG(400, 300)
  mol_drawer.DrawMolecule(mol_rdkit)
  mol_drawer.FinishDrawing()
  svg_str = mol_drawer.GetDrawingText()

  # Store SVG to your workspace
  destination_path = os.path.join(workspace_path, f"candidate-{i}.svg")
  with open(destination_path, "w") as f:
    _ = f.write(svg_str)

  # Visualize the SVG in the notebook
  print(f"---\nCandidate #{i}\n{smiles}:")
  SVG(svg_str)