Molpher-lib: Systematic Chemical Space Exploration with Molecular Morphing

This library is essentially a fork of the de novo drug design framework Molpher. Molpher is a program developed to tackle systematic exploration of chemical space using an intuitive atom-based method called molecular morphing to sample new and potentially useful chemical structures. The task of Molpher is to bring the idea of molecular morphing to non-technical users. Therefore, it contains a rich graphical user interface with visualizations of chemical space and other GUI features that help to analyse and oversee the exploration.

Over the years, however, as we learnt more about this concept and its potential, the need to adjust certain parts of the exploration algorithm for different purposes became more imminent and Molpher-lib was born. It wraps the core idea of Molpher in a user-friendly programming interface (also available from Python) that can be used to drive the exploration in a more nuanced way or to implement entirely new use cases.

If you wish to jump right in, you can take a look at the tutorial. It showcases some of the typical tasks that the library was designed for and should get any new users acquainted with it quickly. If you wish to know more about molecular morphing itself and how this library can be useful in de novo drug design, you may continue reading the next section. To understand the concept of molecular morphing more in depth, you can check out the original paper on the Molpher software.

Warning

Please, note that the project is in early stage of development and so a lot of features mentioned in this documentation might change in the future and there might still be a considerable amount of bugs and other issues.

Note

If you find a bug or have a point to make regarding missing features or other things, do not hesitate to post on the project’s issue tracker.

Table of Contents

• Molpher-lib: Systematic Chemical Space Exploration with Molecular Morphing
• Molecular Morphing Introduction
  • What is Molpher?
  • What is Molpher-lib?
• Using the library
  • 1. Installation
    • 1.1. Installation with Anaconda
    • 1.2. Building and Installing from Source – Linux
      • 1.2.1. Prerequisites
      • 1.2.2. Building the Library
      • 1.2.3. Building the Documentation
      • 1.2.4. Building Conda Packages
  • 2. Tutorial
    • 2.1. Molecular Morphing Basics
      • 2.1.1. Molecules and Morphing Operators
      • 2.1.2. Creating Morphs in Bulk
      • 2.1.3. Substructure locking
      • 2.1.4. Summary
    • 2.2. Implementing Chemical Space Exploration with Molecular Morphing
      • 2.2.1. Creating an Exploration Tree and Setting Morphing Parameters
      • 2.2.2. Morph Generation and Exploration Tree Extension
        • 2.2.2.1. Morph Generation and Manipulation
        • 2.2.2.2. Sorting and Filtering
        • 2.2.2.3. Tree Extension
        • 2.2.2.4. Tree Pruning
      • 2.2.3. Summary
    • 2.3. Exploration Algorithms Implemented in Molpher-lib
      • 2.3.1. Classic (Original) Algorithm
      • 2.3.2. Bidirectional Algorithm
      • 2.3.3. Anti-decoys Algorithm
      • 2.3.4. Summary
    • 2.4. Advanced Topics
      • 2.4.1. Customized Morphing Operators
      • 2.4.2. Tree Operations
        • 2.4.2.1. Built-in Operations
      • 2.4.3. Tree Templates and Snapshots
      • 2.4.4. Summary
• Source Code Documentation
  • 1. Python
    • 1.1. molpher package
      • 1.1.1. Subpackages
        • 1.1.1.1. molpher.core package
        • 1.1.1.2. molpher.algorithms package
        • 1.1.1.3. molpher.swig_wrappers package
        • 1.1.1.4. molpher.examples package
      • 1.1.2. Module contents
  • 2. C++
    • 2.1. Compiling and running your programs
    • 2.2. Molpher API
      • 2.2.1. Core API Classes
      • 2.2.2. Callbacks
      • 2.2.3. Operations
    • 2.3. SAScore data file loader
• Glossary

Indices and Search

• Module Index
• Index
• Glossary