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

This is the documentation of Molpher-lib, a computer library for exploration of chemical space with molecular morphing. It is essentially a fork of Molpher – a free open source software developed for the same purpose.

The original Molpher is mostly aimed at users. Therefore, it contains a rich graphical user interface with visualizations of chemical space and many facilities to directly affect the exploration process. However, it is not very friendly when it comes to developers who usually prefer access to the facilities of a computer program via an API or would even like to alter the implementation so that it suits their needs. We have become more and more aware of these shortcomings during our research where we would often like to implement new ways of filtering the generated morphs or evaluating their ‘fitness’, but the monolithic implementation in C++ would make it difficult and time-consuming.

Therefore, the goal of this project is to make Molpher more accessible to programmers, developers and scientists alike by providing a flexible and extensible programming interface including a Python package that exposes most of the features of Molpher-lib to the Python programming language as well.

Warning

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

Table of Contents

• Molpher-lib: C++/Python Library For 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
      • 1.2.1. Prerequisites
      • 1.2.2. Building Molpher and Its Dependencies
  • 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. Example Exploration Algorithm Implementations
      • 2.6.1. Using the Tutorial to Implement a Search Algorithm
      • 2.6.2. Implementing a Bidirectional Search Algorithm
    • 2.7. 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.swig_wrappers package
        • 1.1.1.3. 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. Morphing Functions
• Glossary

Indices and Search

• Module Index
• Index
• Glossary