Welcome to PharmaForge’s documentation!

This is the documentation for the PharmaForge package, which is designed to store, process, and query molecular data in MongoDB. The dataset inclused hierarchical molecular information, making a NoSQL database like MongoDB the ideal choice for scalability and flexibility.

The workflow includes:

• Storing molecular data in MongoDB

• Processing the data using the PharmaForge package

• Labeling the data with the help of the PharmaForge package (e.g., adding SMILES notation)

• Querying the data using MongoDB’s powerful query language

• Exporting the data to the DeepMD kit HDF5 format for MLP training.

• Relabeling data within the database using the PharmaForge package.

The design principles of the PharmaForge package are to make it easy to use, and flexible across a wide range of molecular systems, and easily queryable to find the data that you need.

The package includes a robust interface to a wide-variety of electronic structure codes, including XTB, DFTB+, Gaussian, Psi4, and direct interfaces to the DeepMD-kit library as well.

There is also a robust set of tools for querying the data within the database, through the querying api.

>>> from pharmaforge.queries.Query import Query
>>> query = "contains_elements only ['H', 'O']"
>>> q = Query(query)
>>> print(q.parsed_query)
{'contains_elements': {'$not': {'$elemMatch': {'$nin': ['H', 'O']}}}}

Folder Structure

The folder structure of the documentation is as follows:

Folder structure for the project.

Indices and tables

• Index

• Module Index

• Search Page

User Documentation

• 1. Installation
  • 1.1. Miniforge Instructions
  • 1.2. Git Instructions
  • 1.3. MongoDB Installation
    • 1.3.1. Linux Instructions
    • 1.3.2. MacOS Instructions (Apple Silicon)
  • 1.4. Interfaces to Other Codes
    • 1.4.1. Psi4 Interface
    • 1.4.2. XTB Interface
    • 1.4.3. DFTB+ Interface
    • 1.4.4. Gaussian Interface
    • 1.4.5. DeepMD-GNN Interface
• 2. Query Syntax
  • 2.1. Basic queries
  • 2.2. Advanced Query Syntax
  • 2.3. List of Query operators
  • 2.4. List of fields
• 3. Examples
  • 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
      • 3.6.3.1. Psi4 with Multiprocessing Interface Example
      • 3.6.3.2. Working Directly with queries
      • 3.6.3.3. Gaussian Interface Example
      • 3.6.3.4. XTB Interface Example
    • 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
      • 3.8.3.1. Relabeling only Query
      • 3.8.3.2. Chunking Large Relabeling Tasks
    • 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
      • 3.9.3.1. Ethane-Like Torsional Scan
      • 3.9.3.2. Torsional Scanning with XTB and a Database query
      • 3.9.3.3. Repeating the scan with Psi4 (Scan Parallelization)
      • 3.9.3.4. Plotting the Final Scan Data
    • 3.9.4. Full Code

Source Documentation

• 1. DataBase
  • DataBase
  • Loader
• 2. Recipes
  • 2.1. General Database
  • 2.2. QDPi1
  • 2.3. QDPi2
• 3. Input and Output Utilities
  • 3.1. pharmaforge.io.hdf5_utils
• 4. Labeling Utilities
  • 4.1. get_smiles
  • 4.2. smiles
  • 4.3. Relabeler Class
• 5. Database Utilities
  • 5.1. create_mongodb_collections
  • 5.2. mongo_utils
• 6. Interfaces
  • 6.1. Gaussian Input/Output interfaces
  • 6.2. Psi4 Input/Output interfaces
  • 6.3. Interface to DPData
  • 6.4. DeepMDIO Input/Output interfaces
  • 6.5. DFTB+ Input/Output interfaces
  • 6.6. XTB Input/Output interfaces
  • 6.7. Abstract Interface
  • 6.8. Scanning Interface
• 7. Query Utilities
  • 7.1. Query Class
• 8. Statistical Comparisons
  • 8.1. Comparator - Statistical Comparisons