r5589 - /1.3/prompt/palmer.py -- April 11, 2008 - 16:58

Author: semor
Date: Fri Apr 11 16:58:03 2008
New Revision: 5589

URL: http://svn.gna.org/viewcvs/relax?rev=5589&view=rev
Log:
Modified the 'nucleus' variable to its new designations as part of the move 
to the new design.


Modified:
    1.3/prompt/palmer.py

Modified: 1.3/prompt/palmer.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/palmer.py?rev=5589&r1=5588&r2=5589&view=diff
==============================================================================
--- 1.3/prompt/palmer.py (original)
+++ 1.3/prompt/palmer.py Fri Apr 11 16:58:03 2008
@@ -42,7 +42,7 @@
         self.__relax__ = relax
 
 
-    def create(self, dir=None, force=0, binary='modelfree4', 
diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=1, 
nucleus='15N', atom1='N', atom2='H'):
+    def create(self, dir=None, force=0, binary='modelfree4', 
diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=1, 
heteronuc_type='15N', atom1='N', atom2='H'):
         """Function for creating the Modelfree4 input files.
 
         Keyword Arguments
@@ -68,9 +68,9 @@
         constraints:  A flag specifying whether the parameters should be 
constrained.  The default
         is to turn constraints on (constraints=1).
 
-        nucleus:  A three letter string describing the nucleus type, ie 15N, 
13C, etc.
-
-        atom1:  The symbol of the X nucleus in the pdb file.
+        heteronuc_type:  A three letter string describing the heteronucleus 
type, ie 15N, 13C, etc.
+
+        atom1:  The symbol of the X heteronucleus in the pdb file.
 
         atom2:  The symbol of the H nucleus in the pdb file.
 
@@ -109,7 +109,7 @@
             text = text + ", trim=" + `trim`
             text = text + ", steps=" + `steps`
             text = text + ", constraints=" + `constraints`
-            text = text + ", nucleus=" + `nucleus`
+            text = text + ", heteronucleus=" + `heteronuc_type`
             text = text + ", atom1=" + `atom1`
             text = text + ", atom2=" + `atom2` + ")"
             print text
@@ -151,9 +151,9 @@
         if type(constraints) != int or (constraints != 0 and constraints != 
1):
             raise RelaxBinError, ('constraint flag', constraints)
 
-        # The nucleus argument.
-        if type(nucleus) != str:
-            raise RelaxStrError, ('nucleus', nucleus)
+        # The heteronucleus argument.
+        if type(heteronuc_type) != str:
+            raise RelaxStrError, ('heteronucleus', heteronuc_type)
 
         # The atom1 argument.
         if type(atom1) != str:
@@ -164,7 +164,7 @@
             raise RelaxStrError, ('atom2', atom2)
 
         # Execute the functional code.
-        palmer.create(dir=dir, force=force, binary=binary, 
diff_search=diff_search, sims=sims, sim_type=sim_type, trim=trim, 
steps=steps, constraints=constraints, nucleus=nucleus, atom1=atom1, 
atom2=atom2)
+        palmer.create(dir=dir, force=force, binary=binary, 
diff_search=diff_search, sims=sims, sim_type=sim_type, trim=trim, 
steps=steps, constraints=constraints, heteronuc_type=heteronuc_type, 
atom1=atom1, atom2=atom2)
 
 
     def execute(self, dir=None, force=0, binary='modelfree4'):