Merge branch 'master' of https://gitlab.eps.surrey.ac.uk/mw00368/GromacsOnEUREKA

any2pdb.py

+#!/usr/bin/env python
+
+import argparse
+
+import mout # https://github.com/mwinokan/MPyTools
+import mcol # https://github.com/mwinokan/MPyTools
+# import mplot # https://github.com/mwinokan/MPyTools
+
+import asemolplot as amp # https://github.com/mwinokan/AseMolPlot
+
+import os
+
+##########################################################################
+
+argparser = argparse.ArgumentParser(description='Convert traj Coordinates to a Gromacs suitable PDB')
+
+argparser.add_argument("-i","--input",help="Input file")
+argparser.add_argument("-o","--output",help="Output file")
+
+args = argparser.parse_args()
+  
+##########################################################################
+
+if args.input is None:
+  mout.errorOut("No input file specified",fatal=True)
+
+if args.output is None:
+  pre, ext = os.path.splitext(args.input)
+  outfile = pre + ".pdb"
+  mout.warningOut("No output file specified, defaulted to "+mcol.file+outfile)
+else:
+  outfile = args.output
+
+try:
+  atoms = amp.read(args.input)
+except:
+  mout.errorOut("Could not read file!",fatal=True)
+
+amp.write("__temp__.pdb",atoms)
+
+os.system("grep -v MODEL __temp__.pdb | grep -v ENDMDL > "+outfile)
+
+os.system("rm __temp__*")
+