pDynamo consists of a large number of Python modules and associated files that are grouped as follows:
- pBabel — a package containing modules that handle the input, output and interconversion of different molecular data.
- pCore — a package containing modules that implement various fundamental computing and mathematical operations.
- pMolecule — a package containing modules concerned with the simulation of molecular systems.
- pMoleculeScripts — a package containing modules that automate various common simulation tasks.
The four packages are arranged hierarchically in the following order: pMoleculeScripts, pBabel, pMolecule and pCore. Items in the list depend uniquely upon those to the right and not those to the left. This means, for example, that pMoleculeScripts imports modules from pBabel, pCore and pMolecule, whereas pCore is independent of the others.
A fairly complete reference, in HTML format, for pDynamo is available from the Downloads page. To use it, download and unpack the archive, and then navigate to the file
index.html with a web browser.