The GLYCAM Molecular Modelling Library (GMML) assists in a variety of molecular modelling tasks, with a focus on the needs of carbohydrates.
Gmml was written in C++, an object orientated language that allows us to build large programs with compartmentalized code. The software is maintainable and expandable.
There is a central data structure (CDS) that contains atoms, residues, and assemblies. Any manipulation or measuring of atomic coordinates is carried out here. Information is fed into the CDS from classes that deal with reading, writing and manipulating different file types such as a PDB, PDBQT, or AMBER topology and coordinate files.
To learn more about its structure, see the online documentation by Doxygen. Another good option if you plan to edit/develop gmml is to navigate using Qtcreater (A C++ IDE). In gmml there is a makefile-main (do ./make.sh Qt) which creates gmml.pro, which you can open in Qtcreater.
The source for an initial version of GMML is also available. We started again from scratch, and the current GMML might not yet possess all the functionality of the old version.