CDPL Python Cookbook

This ‘cookbook’ provides a set of scripts that demonstrate how often occurring tasks in cheminformatics can be accomplished with Python code that utilizes functionality offered by the CDPL.

The scripts are all ready-to-run and have been designed to be executed on the command line. Most of the scripts require arguments to be specified (e.g. path to input/output files). Information on required/supported arguments can be obtained by running the scripts without arguments.

The source code provided by this cookbook can be used without restrictions for any purpose under the terms of the Zero-Clause BSD License (0BSD).

Note

The scripts require a properly set up installation of the CDPL Python bindings. Please visit section Installing CDPKit for further information.

• 1. Processing of Chemical Data
  • 1.1. Molecules
    • 1.1.1. Input and Output
      • 1.1.1.1. Sequential Input
      • 1.1.1.2. Retrieval and Processing of MDL SD-File Structure Data
    • 1.1.2. Fragmentation and Extraction of Substructures
      • 1.1.2.1. Extraction of Atom Environments
    • 1.1.3. Structure Standardization, Curation and Database Preparation
      • 1.1.3.1. ChEMBL Structure Curation Pipeline
      • 1.1.3.2. Generating Protonation States at Physiological pH
      • 1.1.3.3. Database Cleaning
    • 1.1.4. Substructure Search
      • 1.1.4.1. Testing for the Presence of Substructures
• 2. Pharmacophore Generation and Processing
  • 2.1. Input and Output
    • 2.1.1. Sequential Input
  • 2.2. Generation
    • 2.2.1. Plain Molecule Pharmacophores
    • 2.2.2. Ligand-receptor Interaction Pharmacophores
  • 2.3. Processing
    • 2.3.1. Retrieving Feature Properties
    • 2.3.2. Molecule to Reference Pharmacophore Alignment
• 3. Calculation of Molecule, Atom and Bond Properties
  • 3.1. Atomic Properties
    • 3.1.1. Connectivity Properties
    • 3.1.2. Chemical Element Properties
    • 3.1.3. Classification Properties
    • 3.1.4. Partial Charges And Other Electronic Properties
    • 3.1.5. Physicochemical Properties
• 4. Calculation of Molecule and Pharmacophore Descriptors
  • 4.1. Generation of Fingerprints
    • 4.1.1. Extended Connectivity Fingerprints (ECFPs)
    • 4.1.2. FAME Atom Environment Fingerprints
• 5. 3D Structure and Conformer Generation
  • 5.1. Single Low-energy 3D Structures
  • 5.2. Conformer Ensembles
  • 5.3. Torsion Driving
• 6. Force Field Calculations
  • 6.1. MMFF94 Atom Charges