r9150 - /branches/frame_order/specific_fns/frame_order.py -- June 25, 2009 - 14:24

Author: bugman
Date: Thu Jun 25 14:24:51 2009
New Revision: 9150

URL: http://svn.gna.org/viewcvs/relax?rev=9150&view=rev
Log:
Wrote the cone_pdb() and pivot() methods.


Modified:
    branches/frame_order/specific_fns/frame_order.py

Modified: branches/frame_order/specific_fns/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order/specific_fns/frame_order.py?rev=9150&r1=9149&r2=9150&view=diff
==============================================================================
--- branches/frame_order/specific_fns/frame_order.py (original)
+++ branches/frame_order/specific_fns/frame_order.py Thu Jun 25 14:24:51 2009
@@ -32,7 +32,11 @@
 # relax module imports.
 from float import isNaN, isInf
 from generic_fns import pipes
+from generic_fns.structure.geometric import cone_edge, generate_vector_dist, 
generate_vector_residues, stitch_cap_to_cone
+from generic_fns.structure.internal import Internal
 from maths_fns import frame_order_models
+from maths_fns.frame_order_matrix_ops import generate_vector
+from maths_fns.rotation_matrix import R_2vect
 from relax_errors import RelaxInfError, RelaxNaNError, RelaxNoModelError
 from specific_fns.base_class import Common_functions
 
@@ -264,6 +268,76 @@
         """
 
         yield None
+
+
+    def cone_pdb(self, scale=1.0, file=None, dir=None, inc=20, force=False):
+        """Create a PDB file containing a geometric object representing the 
Frame Order cone models.
+
+        @param scale:       The size of the geometric object is equal to 10 
Angstroms multiplied by
+                            this scaling factor.
+        @type scale:        float
+        @param inc:         The number of increments for the filling of the 
cone objects.
+        @type inc:          int
+        @param file:        The name of the PDB file to create.
+        @type file:         str
+        @param dir:         The name of the directory to place the PDB file 
into.
+        @type dir:          str
+        @param force:       Flag which if set to True will cause any 
pre-existing file to be
+                            overwritten.
+        @type force:        bool
+        """
+
+        # Test if the current data pipe exists.
+        pipes.test()
+
+        # Alias the current data pipe.
+        cdp = pipes.get_pipe()
+
+        # The cone axis. 
+        cone_axis = zeros(3, float64)
+        generate_vector(cone_axis, cdp.theta_axis, cdp.phi_axis)
+
+        # Cone axis from simulations.
+        cone_axis_sim = zeros((cdp.sim_number, 3), float64)
+        for i in range(cdp.sim_number):
+            generate_vector(cone_axis_sim[i], cdp.theta_axis_sim[i], 
cdp.phi_axis_sim[i])
+
+        # The rotation matrix (rotation from the z-axis to the cone axis).
+        R = zeros((3,3), float64)
+        R_2vect(R, array([0,0,1], float64), cone_axis)
+
+        # Create the structural object.
+        structure = Internal()
+
+        # Add a molecule.
+        structure.add_molecule(name='iso cone')
+
+        # Alias the single molecule from the single model.
+        mol = structure.structural_data[0].mol[0]
+
+        # Add the pivot point.
+        mol.atom_add(pdb_record='HETATM', atom_num=1, atom_name='R', 
res_name='PIV', res_num=1, pos=cdp.pivot, element='C')
+
+        # Generate the axis vectors.
+        print "\nGenerating the axis vectors."
+        res_num = generate_vector_residues(mol=mol, vector=cone_axis, 
atom_name='Axe', res_name_vect='AXE', sim_vectors=cone_axis_sim, res_num=2, 
origin=cdp.pivot, scale=scale)
+
+        # Generate the cone outer edge.
+        print "\nGenerating the cone outer edge."
+        cap_start_atom = mol.atom_num[-1]+1
+        cone_edge(mol=mol, res_name='CON', res_num=3, apex=cdp.pivot, R=R, 
angle=cdp.theta_cone, length=10, inc=inc)
+
+        # Generate the cone cap, and stitch it to the cone edge.
+        print "\nGenerating the cone cap."
+        cone_start_atom = mol.atom_num[-1]+1
+        generate_vector_dist(mol=mol, res_name='CON', res_num=3, 
centre=cdp.pivot, R=R, max_angle=cdp.theta_cone, scale=10, inc=inc)
+        stitch_cap_to_cone(mol=mol, cone_start=cone_start_atom, 
cap_start=cap_start_atom+1, max_angle=cdp.theta_cone, inc=inc)
+
+        # Create the PDB file.
+        print "\nGenerating the PDB file."
+        pdb_file = open_write_file(file, dir, force=force)
+        structure.write_pdb(pdb_file)
+        pdb_file.close()
 
 
     def create_mc_data(self, index):
@@ -481,6 +555,28 @@
         yield None
 
 
+    def pivot(self, pivot=None):
+        """Set the pivot point for the 2 body motion.
+
+        @param pivot:   The pivot point of the two bodies (domains, etc.) in 
the structural
+                        coordinate system.
+        @type pivot:    list of num
+        """
+
+        # Test if the current data pipe exists.
+        pipes.test()
+
+        # Alias the current data pipe.
+        cdp = pipes.get_pipe()
+
+        # Set the pivot point.
+        cdp.pivot = pivot
+
+        # Convert to floats.
+        for i in range(3):
+            cdp.pivot[i] = float(cdp.pivot[i])
+
+
     def return_error(self, index):
         """Return the alignment tensor error structure.