Molpher-lib: a C++/Python Library For Systematic Chemical Space Exploration

This library is a fork of Molpher, a program for exploration of chemical space with molecular morphing. Molpher mostly targets non-technical users. Therefore, it contains a rich graphical user interface with visualizations of chemical space and supports various platforms.

However, Molpher is not very friendly when it comes to developers who usually require access to a computer program via an API or would like to easily alter the implementation so that it suits better to their needs. We have become more and more aware of the shortcomings of Molpher during our research where we would often like to implement new ways of filtering the generated morphs or evaluating their ‘fitness’, but there was no easy way to do that, because the underlying C++ implementation is not very flexible and user-friendly.

The goal of this project is to make molecular morphing more accessible to programmers, developers and scientists alike by providing a flexible and extensible programming interface that can also be used from a high-level programming language such as Python.

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.

Table of Contents

• Molpher-lib: a C++/Python Library For Systematic Chemical Space Exploration
• 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 Conda Packages
      • 1.2.4. Building the Documentation
  • 2. Tutorial
    • 2.1. The Morphing Algorithm
    • 2.2. Creating an Exploration Tree and Setting Morphing Parameters
    • 2.3. Generating Morphs and Extending the Exploration Tree
      • 2.3.1. Generating and Manipulating Morphs
      • 2.3.2. Sorting and Filtering Morphs
      • 2.3.3. Extending and Pruning
    • 2.4. Tree Operations
      • 2.4.1. Built-in Operations
        • 2.4.1.1. Traversing the Tree
    • 2.5. Tree Templates and Snapshots
    • 2.6. Implementing a Chemical Space Exploration Algorithm
    • 2.7. Summary
  • 3. Exploration Algorithms
    • 3.1. Classic (Original) Algorithm
    • 3.2. Bidirectional Algorithm
    • 3.3. Anti-decoys Algorithm
    • 3.4. 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