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
  • 1.1.2.2. Rule-based Fragmentation
  • 1.1.2.3. Bemis-Murcko Framework Analysis
• 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
• 1.1.5. Generation of Isomers
  • 1.1.5.1. Enumeration of Stereoisomers