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pdb_corner/plot_bfactor_by_chain.py

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+# python3
+import argparse
+from biopandas.pdb import PandasPdb
+import matplotlib
+import matplotlib.pyplot as plt
+# input parameters
+ap = argparse.ArgumentParser()
+ap.add_argument("-in", "--input", required=True, help="input pdb file")
+ap.add_argument("-chain", "--chain", required=True, help="chain from pdb file to select")
+ap.add_argument("-col", "--col", required=True, help="colour of line in plot(write in '' or "" you can use hex colour codes)")
+ap.add_argument("-plot", "--plot", required=False, help="export plot to file")
+ap.add_argument("-dpi", "--dpi", default= 300, required=False, help="dpi of exported plot")
+ap.add_argument("-type", "--type", required=True, help="type of plot file(e.g png etc)")
+args = vars(ap.parse_args())
+# main
+ppdb = PandasPdb()
+ppdb.read_pdb(args['input'])
+ppdb.df['ATOM'] = ppdb.df['ATOM'][ppdb.df['ATOM']['chain_id'] == args['chain']]
+# export figure
+ppdb.df['ATOM']['b_factor'].plot(kind='line', color= args['col'])
+plt.title('B-Factors Along the Amino Acid Chain')
+plt.xlabel('Atom Number')
+plt.ylabel('B-factor in $A^2$')
+matplotlib.pyplot.savefig(args['plot'], dpi=int(args['dpi']), format=args['type'])