r5421 - /1.3/prompt/structure.py -- April 08, 2008 - 14:17

Author: bugman
Date: Tue Apr  8 14:17:30 2008
New Revision: 5421

URL: http://svn.gna.org/viewcvs/relax?rev=5421&view=rev
Log:
Created the structure.load_spins() user function.

The back end does not exist yet.


Modified:
    1.3/prompt/structure.py

Modified: 1.3/prompt/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=5421&r1=5420&r2=5421&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Tue Apr  8 14:17:30 2008
@@ -233,6 +233,60 @@
         generic_fns.structure.geometric.create_vector_dist(length=length, 
symmetry=symmetry, file=file, dir=dir, force=force)
 
 
+    def load_spins(self, spin_id='@N'):
+        """Load spins from the structure into the relax data store.
+
+        Keyword Arguments
+        ~~~~~~~~~~~~~~~~~
+
+        spin_id:  The spin identification string.
+
+
+        Description
+        ~~~~~~~~~~~
+
+        This function allows a sequence to be generated within the relax 
data store using the atomic
+        information from the structure already associated with this data 
pipe.  The spin_id string
+        is used to select which molecules, which residues, and which atoms 
will be recognised as
+        spin systems within relax.  If the empty string is supplied, then 
all molcules, residues,
+        and atoms will be placed within the data store.
+
+
+        Example
+        ~~~~~~~
+
+        For a model-free backbone amide nitrogen analysis, to load just the 
backbone N sequence from
+        the file '1F3Y.pdb' (which is a single protein), type the follow two 
user functions:
+
+        relax> structure.read_pdb('1F3Y.pdb')
+        relax> structure.load_spins(spin_id='@N')
+
+
+        For an RNA analysis of adenine C8 and C2, guanine C8 and N1, 
cytidine C5 and C6, and uracil
+        N3, C5, and C6, type the following series of commands (assuming that 
the PDB file with this
+        atom naming has already been read):
+
+        relax> structure.load_spins(spin_id=':A@C8&@C2')
+        relax> structure.load_spins(spin_id=':G@C8&@N1')
+        relax> structure.load_spins(spin_id=':C@C5&@C6')
+        relax> structure.load_spins(spin_id=':U@N3&@C5&@C6')
+
+        """
+
+        # Function intro text.
+        if self.__relax__.interpreter.intro:
+            text = sys.ps3 + "structure.load_spins("
+            text = text + "spin_id=" + `spin_id` + ")"
+            print text
+
+        # Spin identifier.
+        if spin_id != None and type(spin_id) != str:
+            raise RelaxNoneStrError, ('spin identifier', spin_id)
+
+        # Execute the functional code.
+        generic_fns.structure.main.load_spins(spin_id=spin_id)
+
+
     def read_pdb(self, file=None, dir=None, model=None, parser='scientific', 
load_seq=True, spin_id='@N'):
         """The pdb loading function.