Molecule Processing Toolkit

Overview
Fuse
Clean2D
Replace add-in
Split add-in
Links
About me

Clean2D

The article describes a refined approach to laying out molecular graphs in the plane. The approach I developed over the last couple of years turned out to be pretty simple and straightforward, although it took me some time to figure out the solution of various technical issues. The major issue was to define what types of fragments to use as a separate unit to apply transformations to. The next step would be to define those transformations. The answer to the first question is the block graph of the molecular graph, i.e. the bipartite graph of its 2-connected components and cutvertices. The solution to the second issue is just a summary of transformation rules that are used most frequently when drawing molecules. The following figure gives an idea of what the process looks like.

Overview of the process

Implementation

Detailed specification of the application is in progress. The application will be written in Ruby.

Synopsis

Installation