Author Archives: Lachele

Summary of main classes

GMML Main Classes MolecularModeling This contains the classes that make up the central data structure (CDS). It contains classes for atoms, residues (list of atoms), and assemblies (list of atoms). As you can see, our core unit is an atom. In OOP-speak, our atom class is a child of multiple parent classes including qmAtom, dockingatom, […]

Monosaccharide Naming Tables

The code used by these tables is documented here.  Note that the tables only contain ‘D’ sugars.  To generate the ‘L’ sugars, merely swap all the ‘up’ and ‘down’ components so that they are their opposite. Table of monosaccharides Table of derivatives

GlyCode: Internal Monosaccharide Representation

Overview This document describes the monosaccharide representation scheme used by GMML in its monosaccharide identification.  It is essentially a monosaccharide shorthand for humans to use when needing to translate a visual representation of a cyclic monosaccharide into its name.  Since it is also linearizable, it is similarly useful in computer programs. Rationales 1.  Ease of communication […]