r15010 - in /1.3/generic_fns/structure: api_base.py internal.py main.py -- November 23, 2011 - 10:42

Author: bugman
Date: Wed Nov 23 10:42:13 2011
New Revision: 15010

URL: http://svn.gna.org/viewcvs/relax?rev=15010&view=rev
Log:
Added the validate_models() method to the structural API.

This is used to check that the models are 100% consistent.


Modified:
    1.3/generic_fns/structure/api_base.py
    1.3/generic_fns/structure/internal.py
    1.3/generic_fns/structure/main.py

Modified: 1.3/generic_fns/structure/api_base.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=15010&r1=15009&r2=15010&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Wed Nov 23 10:42:13 2011
@@ -630,6 +630,16 @@
             self.displacements.to_xml(doc, disp_element)
 
 
+    def validate_models(self):
+        """Check that the models are consistent with each other.
+
+        This checks that the primary structure is identical between the 
models.
+        """
+
+        # Raise the error.
+        raise RelaxImplementError
+
+
     def write_pdb(self, file, model_num=None):
         """Prototype method stub for the creation of a PDB file from the 
structural data.
 

Modified: 1.3/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=15010&r1=15009&r2=15010&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Wed Nov 23 10:42:13 2011
@@ -1245,6 +1245,47 @@
                     mol.z[i] = mol.z[i] + T[2]
 
 
+    def validate_models(self):
+        """Check that the models are consistent with each other.
+
+        This checks that the primary structure is identical between the 
models.
+        """
+
+        # Print out.
+        print("Validating models:")
+
+        # Loop over the models.
+        for i in range(len(self.structural_data)):
+            # Check the molecules.
+            if len(self.structural_data[0].mol) != 
len(self.structural_data[i].mol):
+                raise RelaxError("The number of molecules, %i, in model %i 
does not match the %i molecules of the first model." % 
(len(self.structural_data[i].mol), self.structural_data[i].num, 
len(self.structural_data[0].mol)))
+
+            # Loop over the molecules.
+            for j in range(len(self.structural_data[i].mol)):
+                # Alias the molecules.
+                mol = self.structural_data[i].mol[j]
+                mol_ref = self.structural_data[0].mol[j]
+
+                # Check the names.
+                if mol.mol_name != mol_ref.mol_name:
+                    raise RelaxError("The molecule name '%s' of model %i 
does not match the name '%s' of the first model." % (mol.mol_name, 
self.structural_data[i].num, mol_ref.mol_name))
+
+                # Loop over the atoms.
+                for k in range(len(mol.atom_name)):
+                    # Create pseudo-pdb formatted records (with no atomic 
coordinates).
+                    atom = "%-6s%5s %4s%1s%3s %1s%4s%1s   
%8s%8s%8s%6.2f%6.2f      %4s%2s%2s" % ('ATOM', mol.atom_num[k], 
self._translate(mol.atom_name[k]), '', self._translate(mol.res_name[k]), 
self._translate(mol.chain_id[k]), self._translate(mol.res_num[k]), '', '#', 
'#', '#', 1.0, 0, self._translate(mol.seg_id[k]), 
self._translate(mol.element[k]), '')
+                    atom_ref = "%-6s%5s %4s%1s%3s %1s%4s%1s   
%8s%8s%8s%6.2f%6.2f      %4s%2s%2s" % ('ATOM', mol_ref.atom_num[k], 
self._translate(mol_ref.atom_name[k]), '', 
self._translate(mol_ref.res_name[k]), self._translate(mol_ref.chain_id[k]), 
self._translate(mol_ref.res_num[k]), '', '#', '#', '#', 1.0, 0, 
self._translate(mol_ref.seg_id[k]), self._translate(mol_ref.element[k]), '')
+
+                    # Check the atom info.
+                    if atom != atom_ref:
+                        print(atom)
+                        print(atom_ref)
+                        raise RelaxError("The atoms of model %i do not match 
the first model." % self.structural_data[i].num)
+
+        # Final print out.
+        print("\tAll models are consistent")
+
+
     def write_pdb(self, file, model_num=None):
         """Method for the creation of a PDB file from the structural data.
 

Modified: 1.3/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=15010&r1=15009&r2=15010&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Nov 23 10:42:13 2011
@@ -563,6 +563,9 @@
     if method not in allowed:
         raise RelaxError("The superimposition method '%s' is unknown.  It 
must be one of %s." % (method, allowed))
 
+    # Validate the models.
+    cdp.structure.validate_models()
+
     # Create a list of all models.
     if models == None:
         models = []