r2645 - /1.3/generic_fns/pdb.py -- October 17, 2006 - 06:41

Author: bugman
Date: Tue Oct 17 06:41:14 2006
New Revision: 2645

URL: http://svn.gna.org/viewcvs/relax?rev=2645&view=rev
Log:
Fixes for a number of bugs caused by the changes for task #3838.

Task #3838 is located at https://gna.org/task/?3838 and more information is 
given at
https://mail.gna.org/public/relax-users/2006-10/msg00002.html (Message-id:
<7f080ed10610032153o4571935bq138d2739f55ca3bd@xxxxxxxxxxxxxx>).

Part of the problem, the failure of two of the tests of the test suite was 
reported by Alex Hansen
(viochemist _at_ gmail _dot_ com) in the post located at
https://mail.gna.org/public/relax-devel/2006-10/msg00095.html (Message-id:
<481156b20610130720u39a93e30k6d4603efd8730c96@xxxxxxxxxxxxxx>).  Another 
failure was reported by
Alex at https://mail.gna.org/public/relax-devel/2006-10/msg00096.html 
(Message-id:
<481156b20610130728jb6aa76ag3d9487a20397391b@xxxxxxxxxxxxxx).

The first fix, which was a missing run argument, is described at
https://mail.gna.org/public/relax-devel/2006-10/msg00099.html (Message-id:
<7f080ed10610130741j146721c8w512ba61bac3644c7@xxxxxxxxxxxxxx>).

The second problem was that the residue number and residue name was being 
referred to as 'num' and
'name' when they should have been 'res_num' and 'res_name'.

The third problem was an index for selecting the residue.  Rather than using 
the real index 'i', the
index 'j' was being used.


Modified:
    1.3/generic_fns/pdb.py

Modified: 1.3/generic_fns/pdb.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pdb.py?rev=2645&r1=2644&r2=2645&view=diff
==============================================================================
--- 1.3/generic_fns/pdb.py (original)
+++ 1.3/generic_fns/pdb.py Tue Oct 17 06:41:14 2006
@@ -190,7 +190,7 @@
         self.relax.data.res[run][res].xh_vect = xh_vect
 
 
-    def vectors(self, heteronuc=None, proton=None, res_num=None, 
res_name=None):
+    def vectors(self, run=None, heteronuc=None, proton=None, res_num=None, 
res_name=None):
         """Function for calculating/extracting the XH unit vector from the 
loaded structure."""
 
         # Arguments.
@@ -206,18 +206,18 @@
             raise RelaxNoSequenceError, run
 
         # Test if the residue number is a valid regular expression.
-        if type(num) == str:
+        if type(res_num) == str:
             try:
-                compile(num)
+                compile(res_num)
             except:
-                raise RelaxRegExpError, ('residue number', num)
+                raise RelaxRegExpError, ('residue number', res_num)
 
         # Test if the residue name is a valid regular expression.
-        if name:
+        if res_name:
             try:
-                compile(name)
+                compile(res_name)
             except:
-                raise RelaxRegExpError, ('residue name', name)
+                raise RelaxRegExpError, ('residue name', res_name)
 
         # Test that the nuclei have been correctly set.
         if self.heteronuc == self.proton:
@@ -262,16 +262,16 @@
                     continue
 
                 # Skip the residue if there is no match to 'num'.
-                if type(num) == int:
-                    if not data.num == num:
+                if type(res_num) == int:
+                    if not data.num == res_num:
                         continue
-                elif type(num) == str:
-                    if not match(num, `data.num`):
+                elif type(res_num) == str:
+                    if not match(res_num, `data.num`):
                         continue
 
                 # Skip the residue if there is no match to 'name'.
-                if name != None:
-                    if not match(name, data.name):
+                if res_name != None:
+                    if not match(res_name, data.name):
                         continue
 
                 # Find the corresponding residue in the PDB.
@@ -326,24 +326,24 @@
 
         # Average the vectors and convert xh_vect from an array of vectors 
to a vector.
         for i in xrange(len(self.relax.data.res[self.run])):
-            # Remap the data structure 'self.relax.data.res[self.run][j]'.
-            data = self.relax.data.res[self.run][j]
+            # Remap the data structure 'self.relax.data.res[self.run][i]'.
+            data = self.relax.data.res[self.run][i]
 
             # Skip unselected residues.
             if not data.select:
                 continue
 
             # Skip the residue if there is no match to 'num'.
-            if type(num) == int:
-                if not data.num == num:
+            if type(res_num) == int:
+                if not data.num == res_num:
                     continue
-            elif type(num) == str:
-                if not match(num, `data.num`):
+            elif type(res_num) == str:
+                if not match(res_num, `data.num`):
                     continue
 
             # Skip the residue if there is no match to 'name'.
-            if name != None:
-                if not match(name, data.name):
+            if res_name != None:
+                if not match(res_name, data.name):
                     continue
 
             # No vectors.