Minor edits for python2/3 support, improved comments

examples/PACKAGES/cgdna/util/generate.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
@@ -16,16 +15,23 @@
 /* ----------------------------------------------------------------------
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
-"""
 
+Program: generate.py
 
-"""
-Import basic modules
+Generates a simple initial ssDNA or dsDNA configuration from a given sequence.
+For dsDNA the sequence should be preceded by the 'DOUBLE' keyword.
+
+Usage: 
+$$ python generate.py box_offset box_length sequence_file 
 """
 
 # for python2/3 compatibility
 from __future__ import print_function
+#!/usr/bin/env python
 
+"""
+Import basic modules
+"""
 import sys, os, timeit
 
 from timeit import default_timer as timer

examples/PACKAGES/cgdna/util/lmp2vis.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
@@ -32,6 +31,13 @@ The LAMMPS trajectory input file needs to contain the following data columns:
 id mol type x y z vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4]
 """
 
+# for python2/3 compatibility
+from __future__ import print_function
+#!/usr/bin/env python
+
+"""
+Import basic modules
+"""
 import sys, math, subprocess
 
 # converts quaternion DOF into local body reference frame

examples/PACKAGES/cgdna/util/nbps.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
@@ -17,16 +16,23 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-Program:
+Program: nbps.py
+
+Calculates the number of base pairs based on proximity of hydrogen bonding
+interaction sites in oxDNA2.
 
 Usage: 
-$$ python 
+$$ python nbps.py input_filename output_filename 
 
 Requirements:
 The LAMMPS trajectory input file needs to contain the following data columns:
 id mol type x y z c_quat[1] c_quat[2] c_quat[3] c_quat[4]
 """
 
+# for python2/3 compatibility
+from __future__ import print_function
+#!/usr/bin/env python
+
 import sys, math, subprocess
 
 # converts quaternion DOF into local body reference frame