Pysoftk v1.0 adds a complete standalone module for the analysis of soft matter systems. The new module described in this paper provides a set of interconnected tools that are useful for determining the physical properties of soft matter self-assembled aggregates as well as the molecular-scale interactions that underlie such emergent behavior. One of the key features of PySoftK v1.0 is that it properly accounts for periodic boundary conditions when determining the positions of atoms within the molecules that make up a soft matter aggregate, particularly if the aggregate is larger than half the size of the simulation box in one or multiple dimensions. Other software tools are not designed to account for molecular assemblies of such size. A thorough set of tests have been created to cover all code to ensure its correct functionality. Furthermore, PySoftK v1.0 is designed to provide maximum flexibility to the user, so most functions output the data per outputted configuration of the trajectory, so that the user can decide how to represent or further process the data. Although the initial version of PySoftK has a particular focus on polymers, the analysis module has been created such that it is fully chemically agnostic. The goal of this module is to create an open-source platform that allows users to analyse complex structures, dynamics and interactions in their simulations with minimal user input. PySoftK v1.0 contributes to the standardisation of molecular-scale simulation analysis, which will promote accurate comparisons across different simulations to support the rational in silico design of new soft materials.