r18495 - in /trunk/generic_fns/structure: main.py statistics.py -- February 18, 2013 - 21:20

Author: bugman
Date: Mon Feb 18 21:20:06 2013
New Revision: 18495

URL: http://svn.gna.org/viewcvs/relax?rev=18495&view=rev
Log:
Printout improvements for the structure.rmsd user function.


Modified:
    trunk/generic_fns/structure/main.py
    trunk/generic_fns/structure/statistics.py

Modified: trunk/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/main.py?rev=18495&r1=18494&r2=18495&view=diff
==============================================================================
--- trunk/generic_fns/structure/main.py (original)
+++ trunk/generic_fns/structure/main.py Mon Feb 18 21:20:06 2013
@@ -639,8 +639,7 @@
         coord[-1] = array(coord[-1])
 
     # Calculate the RMSD.
-    cdp.structure.rmsd = atomic_rmsd(coord)
-    print("RMSD:  %s" % cdp.structure.rmsd)
+    cdp.structure.rmsd = atomic_rmsd(coord, verbosity=1)
 
     # Return the RMSD.
     return cdp.structure.rmsd

Modified: trunk/generic_fns/structure/statistics.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/statistics.py?rev=18495&r1=18494&r2=18495&view=diff
==============================================================================
--- trunk/generic_fns/structure/statistics.py (original)
+++ trunk/generic_fns/structure/statistics.py Mon Feb 18 21:20:06 2013
@@ -23,11 +23,11 @@
 """Module for handling all types of structural statistics."""
 
 # Python module imports.
-from numpy import float64, sqrt, zeros
+from numpy import float64, mean, sqrt, std, zeros
 from numpy.linalg import norm
 
 
-def atomic_rmsd(coord):
+def atomic_rmsd(coord, verbosity=0):
     """Determine the RMSD for the given atomic coordinates.
 
     This is the per atom RMSD to the mean structure.
@@ -43,17 +43,17 @@
     M = len(coord)
     N = len(coord[0])
     model_rmsd = zeros(M, float64)
-    mean = zeros((N, 3), float64)
+    mean_str = zeros((N, 3), float64)
 
     # Calculate the mean structure.
-    calc_mean_structure(coord, mean)
+    calc_mean_structure(coord, mean_str)
 
     # Loop over the models.
     for i in range(M):
         # Loop over the atoms.
         for j in range(N):
             # The vector connecting the mean to model atom.
-            vect = mean[j] - coord[i][j]
+            vect = mean_str[j] - coord[i][j]
 
             # The atomic RMSD.
             model_rmsd[i] += norm(vect)**2
@@ -61,8 +61,18 @@
         # Normalise, and sqrt.
         model_rmsd[i] = sqrt(model_rmsd[i] / N)
 
+        # Print out.
+        if verbosity:
+            print("Model %2s RMSD:  %s" % (i, model_rmsd[i]))
+
+    # Calculate the mean and standard deviation.
+    rmsd_mean = mean(model_rmsd)
+    rmsd_sd = std(model_rmsd, ddof=1)
+    if verbosity:
+        print("\nGlobal RMSD:  %s +/- %s" % (rmsd_mean, rmsd_sd))
+
     # Return the average RMSD.
-    return sum(model_rmsd) / M
+    return rmsd_mean
 
 
 def calc_mean_structure(coord=None, mean=None):