PubChemPy relies entirely on the PubChem database and chemical toolkits provided via their PUG REST web service1. This service provides an interface for programs to automatically carry out the tasks that you might otherwise perform manually via the PubChem website.
This is important to remember when using PubChemPy: Every request you make is transmitted to the PubChem servers, evaluated, and then a response is sent back. There are some downsides to this: It is less suitable for confidential work, it requires a constant internet connection, and some tasks will be slower than if they were performed locally on your own computer. On the other hand, this means we have the vast resources of the PubChem database and chemical toolkits at our disposal. As a result, it is possible to do complex similarity and substructure searching against a database containing tens of millions of compounds in seconds, without needing any of the storage space or computational power on your own local computer.
You don't need to worry too much about how the PubChem web service works, because PubChemPy handles all of the details for you. But if you want to go beyond the capabilities of PubChemPy, there is some helpful documentation on the PubChem website.
- PUG REST Tutorial: Explains how the web service works with a variety of usage examples.
- PUG REST Specification: A more comprehensive but dense specification that details every possible way to use the web service.
Footnotes
That's a lot of acronyms! PUG stands for "Power User Gateway", a term used to describe a variety of methods for programmatic access to PubChem data and services. REST stands for Representational State Transfer, which describes the specific architectural style of the web service.↩