Tutorials: Analysis Tools

In this section, we will introduce the newly developed workflows that can be used in PySoftK for analysing polymers and other soft-matter systems. Tutorials for a new set of functionalities like estimation of densities, detection of ring-ring stacking enviorements, contact analysis have been developed.

• Tutorial on the usage of contacts
• Tutorial on the usage of ecc_micelle
• Tutorial on the usage of intrinsic_density_micelle tool
• Tutorial on the usage of micelle_whole tool
• Tutorial on the usage of rgyr_micelle
• Case example of MDAnalysis vs Pysoftk’s rgyr_micelle
• Tutorial on the Usage of the RSA Tool
• Tutorial: Analyzing $pi$-$pi$ Stacking in Proteins with RSA
• Tutorial on the usage of SCP tool
• Tutorial on the usage of hydration
• Tutorial on the usage of spherical_density tool
• Automated Kinetic State Discovery with PySoftK