Develop a Cheminformatics Platform with Mathematica

My first encounter with Mathematica happened more than 12 years ago. Since 2001, I have intensively used it as a tool in my research work. Till now, i virtually use it on a daily basis for many different tasks. I don't think I have every aspects of the tool, but I do think my understanding of Mathematica is beneficial to researchers who are interested in learning Mathematica. I feel the necessity to organize my previous codes into a tutorial for two reasons. The first is that there are no good if any books available on market on the application in the cheminformatics or bioinformatics, particularly for those intermediate users who have known the basics of Mathematica but want to sharpen their tools. The other reason is that I have the motive to clean up my codes and thoughts for the development of my research. This tutorial is intended to show the essentials of Mathematica through the anatomy of projects from design to implementation. I see many users (and some tutorials books as well) writing codes in the style of C, Fortran or other programming languages for which they have been familiar with. To me, a good programming style is extremely important to master the language, in terms of development time, efficiency and terseness. A rule of thumb is that the development process helps you to organize your thoughts and to let you understand the problems at a deeper level, instead of making you feel cumbersome and work as a laborer. On the surface, we could think Mathematica as an advanced dialect of Lisp. "Advanced" here means millions of built-in functions and packaged as the extension of the kernel delivered with the language.
My plan is to include the following chapters.
Chapter 1. Introduction
Chapter 2. Compounds collection database
Chapter 3. Graph theory representation of molecules and its applications
Chapter 4. Descriptor development, similarity comparison, and virtual screening
Chapter 5. CIF parser, molecular structural operations and interface to quantum mechanics calculation
Chapter 6. Spectra processing (including both Image and Graph)
Chapter 7. Schroedinger equation solutions
Appendices
Subject Index