Visualization of Protein Ligand Graphs (VPLG) uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, usually alpha helices and beta strands) or ligand molecules, while the edges model contacts and relative orientations between them. The graphs can be visualized, written to a database, and saved in a text-based file format.
Pythonect is an experimental general-purpose dataflow programming language based on Python. It provides both a visual programming language and a text-based scripting language. The text-based scripting language aims to combine the quick and intuitive feel of shell scripting with the power of Python. The visual programming language is based on the idea of a diagram with “boxes and arrows”.