Tutorial on the usage of RSA tool ================================= This tutorial illsutrates how to use the RSA tool. Before starting any analysis, load the neccesary modules for this class. .. code:: ipython3 from pysoftk.pol_analysis.tools.utils_mda import MDA_input from pysoftk.pol_analysis.tools.utils_tools import * from pysoftk.pol_analysis.make_micelle_whole import micelle_whole from pysoftk.pol_analysis.ring_ring import RSA import numpy as np import pandas as pd .. parsed-literal:: /home/raquellrdc/.local/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm 1. Select your trajectory files, it is recommended to use a tpr file for the topology and xtc file for the trajectory. Note that any MDAnalysis supported file can be used here. .. code:: ipython3 topology='data/f8bt_slab_quench.tpr' trajectory='data/1_frame_traj.xtc' The simulation where we are going to perform the analysis is on this very big system. Since the system is very big, we will only perform the analysis on one frame. .. figure:: images/ring_system.png :alt: Image Alt Text Which is a simulation box filled with this polymer: .. figure:: images/ring_1_polymer.png :alt: Image Alt Text This class requires minimal user input. Only the angle, distance cutoff, start, stop and step frames are needed, as well as the name of the output file. .. code:: ipython3 #name output file results='data/rsa.parquet' #angle cutoff - angle range (val < ang_c or val> 180-ang_c). ang_c=30 #distance cutoff - distance between two rings to be considered stacked dist_c=5 #start frame start=0 #stop frame stop=1 #step frame step=1 Now, let’s run the RSA stacking analysis!-This run will take a bit of time, it is mainly because our system is very large! .. code:: ipython3 rsa=RSA(topology, trajectory).stacking_analysis(dist_c, ang_c, start, stop, step, results) .. parsed-literal:: Ring Stacking analysis has started .. parsed-literal:: 0%| | 0/300700 [00:00