The current structure of the Yup package is diagrammed below (showing module names not file names): Yup Data Energy Methods Models Taro Tools YupSee Yammp Constants Null Orihedron rrDNAv1 rrRNAv1 VirPack Worm Angles Bonds ElectroI ElectroX Hooke Impropers Noens SoftSphereI SoftSphereX Torsions VanderWaalsI VanderWaalsX EnerMinim MolDynam MolMech MonteCarlo Null Orihedron rrDNAv1 rrRNAv1 VirPack Worm AtomMap AtomVect Model Potential AVRecords Atoms AutoGen Brookhaven Chains ChemNames FFA Groups LinSeq MakeGraph MakeLine ParmTop PolytopeNets TraceChain Topology misc AtomViewData ConsoleModule DialogModule EventHandler FileMenu Globals MenuFactory SettingsMenu SimulateMenu TreeModule YupSeeFrame ModelGUIModules WormModule DNAModule lib StringModule Tree appl constr contra dynam environ line minim monte nonbond setup yammp ympshell Note the following codes: name of directory name of C module name of Python module The file name is exactly as written on the label and by (Python package) convention, directory names are capitalized. The boxes below the label enclose the contents of the directory. The file name depends on the operating system, on Linux a compiled module named "A" has a file name "Amodule.so" or simply "A.so" The source file name extension is .py and there is usually a compiled module file with the file name extension of either .pyc or .pyo or both variants are present.