CDPL Python Tutorial

Welcome to the Chemical Data Processing Library (CDPL) Python tutorial!

The CDPL serves as foundation for CDPKit’s own applications and provides powerful basic functionality for the development of advanced cheminformatics and drug discovery software.

The subsequent sections will introduce the most important concepts, core data structures and method/algorithm implementations by means of short theory sections and runnable code snippets. The tutorial is based on a Jupyter notebook which can be downloaded and then executed step-by-step on your own computer.

By the end, you’ll be well-equipped to start crafting your own drug design software solutions using the CDPL Python bindings.

Tip

For a detailed description of a particular function, method or class please visit the CDPL Python API Documentation pages. There is also a a powerful search tool on the top right corner of the page that you can use to find particular functions or modules within the documentation.

• 1. Installing the CDPL Python Bindings
• 2. CDPL Package Overview
• 3. Basic Concepts
  • 3.1. Dynamic Properties
  • 3.2. Control-Parameters
  • 3.3. Data I/O Framework
• 4. Working with Molecules
  • 4.1. In-memory Representation of Molecular Structures
  • 4.2. Representation of Molecule Substructures
  • 4.3. Basic Operations on Molecule Objects
    • 4.3.1. Creation
    • 4.3.2. Querying Atom and Bond Counts
    • 4.3.3. Creating Atoms and Bonds
    • 4.3.4. Copying Atoms and Bonds
    • 4.3.5. Accessing Atoms and Bonds
    • 4.3.6. Removing all Atoms and Bonds
    • 4.3.7. Removing single Atoms and Bonds
    • 4.3.8. Removing multiple Atoms and Bonds
    • 4.3.9. Testing Atom and Bond Ownership
    • 4.3.10. Retrieving Atom and Bond Indices
    • 4.3.11. Processing Bonds
    • 4.3.12. Processing Atom Connections
  • 4.4. Basic Operations on Fragment Objects
    • 4.4.1. Creation
    • 4.4.2. Adding single Atoms and Bonds
    • 4.4.3. Adding multiple Atoms and Bonds
    • 4.4.4. Exchanging Atom and Bond Lists
    • 4.4.5. Removing single Atoms and Bonds
    • 4.4.6. Removing multiple Atoms and Bonds
  • 4.5. Input of Molecule Data
    • 4.5.1. Parsing String Data
    • 4.5.2. Reading Data Files
    • 4.5.3. Sequential Molecule Access
    • 4.5.4. Random Molecule Access
  • 4.6. Essential Properties
  • 4.7. Preparation for Downstream Processing
    • 4.7.1. Implicit Hydrogen Count Calculation
    • 4.7.2. Atomic Orbital Hybridization Perception
    • 4.7.3. Atom and Bond Ring Membership Perception
    • 4.7.4. SSSR Perception
    • 4.7.5. Atom and Bond Aromaticity Perception
    • 4.7.6. Molecular Graph Component Perception
    • 4.7.7. All-in-one Property Calculation
  • 4.8. Output of Molecule Data
    • 4.8.1. Direct String Output
    • 4.8.2. File Output