3. Examples

This page includes a collection of examples that demonstrate how to use the pharmaforge library.

• 3.1. Adding SMILES codes to HDF5 Files
  • 3.1.1. Learning Objectives
  • 3.1.2. Required Files
  • 3.1.3. Tutorial
  • 3.1.4. Full Code
• 3.2. Building a MongoDB Database
  • 3.2.1. Learning Objectives
  • 3.2.2. Required Files
  • 3.2.3. Tutorial
  • 3.2.4. Full Code
• 3.3. Generating QDPi1 MongoDB Database
  • 3.3.1. Learning Objectives
  • 3.3.2. Required Files
  • 3.3.3. Full Code
• 3.4. Generating QDPi2 MongoDB Database
  • 3.4.1. Learning Objectives
  • 3.4.2. Required Files
  • 3.4.3. Full Code
• 3.5. Querying the MongoDB Database
  • 3.5.1. Learning Objectives
  • 3.5.2. Required Files
  • 3.5.3. Tutorial
  • 3.5.4. Full Code
• 3.6. Interfaces with ASE
  • 3.6.1. Learning Objectives
  • 3.6.2. Required Files
  • 3.6.3. Tutorial
  • 3.6.4. See Also
  • 3.6.5. Full Code
• 3.7. Running DeepMD-Kit with Pharmaforge
  • 3.7.1. Learning Objectives
  • 3.7.2. Required Files
  • 3.7.3. Tutorial
  • 3.7.4. Full Code
• 3.8. Relabeling Existing Data within the Database
  • 3.8.1. Learning Objectives
  • 3.8.2. Required Files
  • 3.8.3. Tutorial
  • 3.8.4. Full Code
• 3.9. Generating Free Energy Profiles
  • 3.9.1. Learning Objectives
  • 3.9.2. Required Files
  • 3.9.3. Tutorial
  • 3.9.4. Full Code