PyMKS is an open source, pythonic implementation of the methodologies developed under the aegis of Materials Knowledge System (MKS) to build salient process-structure-property linkages for materials science applications. PyMKS provides for efficient tools for obtaining a digital, uniform grid representation of a materials internal structure in terms of its local states, and computing hierarchical descriptors of the structure that can be used to build efficient machine learning based mappings to the relevant response space.