r20088 - /trunk/pipe_control/interatomic.py -- June 13, 2013 - 11:44

Author: bugman
Date: Thu Jun 13 11:44:23 2013
New Revision: 20088

URL: http://svn.gna.org/viewcvs/relax?rev=20088&view=rev
Log:
Improved the functionality of the interatom.read_dist user function.

The file data is now stripped using lib.io.strip to remove comments and blank 
lines.  And now if the
iteratomic data container cannot be found, it is created instead of raising a 
RelaxError.


Modified:
    trunk/pipe_control/interatomic.py

Modified: trunk/pipe_control/interatomic.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/interatomic.py?rev=20088&r1=20087&r2=20088&view=diff
==============================================================================
--- trunk/pipe_control/interatomic.py (original)
+++ trunk/pipe_control/interatomic.py Thu Jun 13 11:44:23 2013
@@ -36,7 +36,7 @@
 from pipe_control.mol_res_spin import Selection, count_spins, 
exists_mol_res_spin_data, return_spin, spin_loop
 from pipe_control import pipes
 from lib.errors import RelaxError, RelaxInteratomInconsistentError, 
RelaxNoInteratomError, RelaxNoSpinError
-from lib.io import extract_data, write_data
+from lib.io import extract_data, strip, write_data
 from lib.warnings import RelaxWarning, RelaxZeroVectorWarning
 
 
@@ -152,7 +152,7 @@
             raise RelaxInteratomInconsistentError(pipe1, pipe2)
 
 
-def create_interatom(spin_id1=None, spin_id2=None, pipe=None):
+def create_interatom(spin_id1=None, spin_id2=None, pipe=None, verbose=False):
     """Create and return the interatomic data container for the two spins.
 
     @keyword spin_id1:  The spin ID string of the first atom.
@@ -161,9 +161,15 @@
     @type spin_id2:     str
     @keyword pipe:      The data pipe to create the interatomic data 
container for.  This defaults to the current data pipe if not supplied.
     @type pipe:         str or None
+    @keyword verbose:   A flag which if True will result printouts.
+    @type verbose:      bool
     @return:            The newly created interatomic data container.
     @rtype:             data.interatomic.InteratomContainer instance
     """
+
+    # Printout.
+    if verbose:
+        print("Creating an interatomic data container between the spins '%s' 
and '%s'." % (spin_id1, spin_id2))
 
     # The data pipe.
     if pipe == None:
@@ -451,8 +457,9 @@
     if not exists_mol_res_spin_data():
         raise RelaxNoSequenceError
 
-    # Extract the data from the file.
+    # Extract the data from the file, and clean it up.
     file_data = extract_data(file, dir, sep=sep)
+    file_data = strip(file_data)
 
     # Loop over the RDC data.
     data = []
@@ -490,9 +497,9 @@
         # Get the interatomic data container.
         interatom = return_interatom(spin_id1, spin_id2)
 
-        # No container found.
+        # No container found, so create it.
         if interatom == None:
-            raise RelaxNoInteratomError(spin_id1=spin_id1, spin_id2=spin_id2)
+            interatom = create_interatom(spin_id1=spin_id1, 
spin_id2=spin_id2, verbose=True)
 
         # Store the averaged distance.
         interatom.r = ave_dist