Added python module trajectory_analysis.py with a function

to smooth a vector or list of floats

modules/mol/alg/pymod/CMakeLists.txt

@@ -10,6 +10,7 @@ set(OST_MOL_ALG_PYMOD_MODULES
   "__init__.py"
   views.py
   superpose.py
+  trajectory_analysis.py
 )
 
 if (ENABLE_IMG)

modules/mol/alg/pymod/__init__.py

 from _ost_mol_alg import *
 from ost.mol.alg.superpose import *
-
+import ost.mol.alg.trajectory_analysis

modules/mol/alg/pymod/trajectory_analysis.py

+"""
+Some functions for analyzing trajectories
+
+Author: Niklaus Johner
+"""
+
+from ost import *
+import os
+
+def smooth(vec,n):
+#Function to smooth a vector or a list of floats
+#for each element it takes the average over itself and the
+#n elements on each side, so over (2n+1) elements
+  try:
+    vec2=vec.copy()
+  except:
+    vec2=vec[:]
+  for i in range(n):
+    v=0.0
+    count=1.0
+    v+=vec[i]
+    for j in range(n):
+      count+=1
+      v+=vec[i+j+1]
+    for j in range(i):
+      count+=1
+      v+=vec[i-(j+1)]
+    vec2[i]=v/float(count)
+  for i in range(1,n+1):
+    v=0.0
+    count=1.0
+    v+=vec[-i]
+    for j in range(n):
+      count+=1
+      v+=vec[-(i+j+1)]
+    for j in range(i-1):
+      count+=1
+      v+=vec[-i+j+1]
+    vec2[-i]=v/float(count)
+  for i in range(n,len(vec2)-n):
+    v=vec[i]
+    for j in range(n):
+      v+=vec[i+j+1]
+      v+=vec[i-j-1]
+    vec2[i]=v/float(2.*n+1.)
+  return vec2
+
+