r14943 - in /1.3: generic_fns/structure/internal.py generic_fns/structure/main.py prompt/structure.py -- October 31, 2011 - 10:45

Author: bugman
Date: Mon Oct 31 10:45:33 2011
New Revision: 14943

URL: http://svn.gna.org/viewcvs/relax?rev=14943&view=rev
Log:
Created the structure.connect_atom user function to expose the back-end 
functionality.

This works with atom indices, so is not ideal for a user function.  In the 
future this should be
modified to handle atom ID strings instead.


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

Modified: 1.3/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14943&r1=14942&r2=14943&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Mon Oct 31 10:45:33 2011
@@ -822,6 +822,33 @@
         return data
 
 
+    def connect_atom(self, mol_name=None, index1=None, index2=None):
+        """Connect two atoms in the structural data object.
+
+        @keyword mol_name:  The name of the molecule.
+        @type mol_name:     str
+        @keyword index1:    The global index of the first atom.
+        @type index1:       str
+        @keyword index2:    The global index of the first atom.
+        @type index2:       str
+        """
+
+        # Test if the current data pipe exists.
+        pipes.test()
+
+        # Add the molecule, if it does not exist.
+        if cdp.structure.get_molecule(mol_name) == None:
+            cdp.structure.add_molecule(name=mol_name)
+
+        # Loop over each model.
+        for model in self.structural_data:
+            # Specific molecule.
+            mol = cdp.structure.get_molecule(mol_name)
+
+            # Add the atom.
+            mol.atom_connect(index1=index1, index2=index2)
+
+
     def delete(self):
         """Delete all the structural information."""
 

Modified: 1.3/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14943&r1=14942&r2=14943&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Mon Oct 31 10:45:33 2011
@@ -77,6 +77,26 @@
 
     # Add the atoms.
     cdp.structure.add_atom(mol_name=mol_name, atom_name=atom_name, 
res_name=res_name, res_num=res_num, pos=pos, element=element, 
atom_num=atom_num, chain_id=chain_id, segment_id=segment_id, 
pdb_record=pdb_record)
+
+
+def connect_atom(index1=None, index2=None):
+    """Connect two atoms.
+
+    @keyword index1:    The global index of the first atom.
+    @type index1:       str
+    @keyword index2:    The global index of the first atom.
+    @type index2:       str
+    """
+
+    # Test if the current data pipe exists.
+    pipes.test()
+
+    # Place the structural object into the relax data store if needed.
+    if not hasattr(cdp, 'structure'):
+        cdp.structure = Internal()
+
+    # Add the atoms.
+    cdp.structure.connect_atom(index1=index1, index2=index2)
 
 
 def delete():

Modified: 1.3/prompt/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14943&r1=14942&r2=14943&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Mon Oct 31 10:45:33 2011
@@ -78,9 +78,37 @@
         ["pdb_record", "The optional PDB record name, e.g. 'ATOM' or 
'HETATM'."]
     ]
     add_atom._doc_desc = """
-        This allows 
+        This allows atoms to be added to the internal structural object.
         """
     _build_doc(add_atom)
+
+
+    def connect_atom(self, index1=None, index2=None):
+        # Function intro text.
+        if self._exec_info.intro:
+            text = self._exec_info.ps3 + "structure.connect_atom("
+            text = text + "index1=" + repr(index1)
+            text = text + ", index2=" + repr(index2) + ")"
+            print(text)
+
+        # The argument checks.
+        arg_check.is_int(index1, 'index 1')
+        arg_check.is_int(index2, 'index 2')
+
+        # Execute the functional code.
+        generic_fns.structure.main.connect_atom(index1=index1, index2=index2)
+
+    # The function doc info.
+    connect_atom._doc_title = "Connect two atoms."
+    connect_atom._doc_title_short = "Atom connection."
+    connect_atom._doc_args = [
+        ["index1", "The global index of the first atom."],
+        ["index2", "The global index of the second atom."]
+    ]
+    connect_atom._doc_desc = """
+        This allows atoms to be connected in the internal structural object. 
 The global index is normally equal to the PDB atom number minus 1.
+        """
+    _build_doc(connect_atom)
 
 
     def create_diff_tensor_pdb(self, scale=1.8e-6, file='tensor.pdb', 
dir=None, force=False):