Author: bugman
Date: Sun Nov 5 10:29:59 2006
New Revision: 2751
URL: http://svn.gna.org/viewcvs/relax?rev=2751&view=rev
Log:
The function 'self.create_tensor_pdb()' has been modified for the new
'self.atomic_data' structure.
The centre of mass, vector distribution, and axes have been turned into
individual residues.
Modified:
branches/tensor_pdb/generic_fns/pdb.py
Modified: branches/tensor_pdb/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2751&r1=2750&r2=2751&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Nov 5 10:29:59 2006
@@ -276,7 +276,67 @@
R = self.centre_of_mass()
# Add the central atom.
- self.atom_add(atom_id='R', element='C', pos=R)
+ self.atom_add(atom_id='R', atom_name='R', res_name='COM',
chain_id=chain_id, res_num=res_num, pos=R, element='C')
+
+ # Increment the residue number.
+ res_num = res_num + 1
+
+
+ # Vector distribution.
+ ######################
+
+ # Print out.
+ print "\nGenerating the geometric object."
+
+ # Increment value.
+ inc = 20
+
+ # Get the uniform vector distribution.
+ print " Creating the uniform vector distribution."
+ vectors = self.uniform_vect_dist_spherical_angles(inc=20)
+
+ # Loop over the radial array of vectors (change in longitude).
+ for i in range(inc):
+ # Loop over the vectors of the radial array (change in latitude).
+ for j in range(inc/2+2):
+ # Index.
+ index = i + j*inc
+
+ # Atom id.
+ atom_id = 'T' + `i` + 'P' + `j`
+
+ # Rotate the vector into the diffusion frame.
+ vector = dot(self.relax.data.diff[self.run].rotation,
vectors[index])
+
+ # Set the length of the vector to its diffusion rate within
the diffusion tensor geometric object.
+ vector = dot(self.relax.data.diff[self.run].tensor, vector)
+
+ # Scale the vector.
+ vector = vector * scale
+
+ # Position relative to the centre of mass.
+ pos = R + vector
+
+ # Add the vector as a H atom of the TNS residue.
+ self.atom_add(atom_id=atom_id, atom_name=atom_id,
res_name='TNS', chain_id=chain_id, res_num=res_num, pos=pos, element='H')
+
+ # Connect to the previous atom (to generate the longitudinal
lines).
+ if j != 0:
+ prev_id = 'T' + `i` + 'P' + `j-1`
+ self.atom_connect(atom_id=atom_id, bonded_id=prev_id)
+
+ # Connect across the radial arrays (to generate the
latitudinal lines).
+ if i != 0:
+ neighbour_id = 'T' + `i-1` + 'P' + `j`
+ self.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
+
+ # Connect the last radial array to the first (to zip up the
geometric object and close the latitudinal lines).
+ if i == inc-1:
+ neighbour_id = 'T' + `0` + 'P' + `j`
+ self.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
+
+ # Increment the residue number.
+ res_num = res_num + 1
# Axes of the tensor.
@@ -297,11 +357,12 @@
Dpar_vect = R + Dpar_vect
Dpar_vect_neg = R + Dpar_vect_neg
- # Add the atom and connect it to the centre of mass.
- self.atom_add(atom_id='Dpar', element='C', pos=Dpar_vect)
- self.atom_add(atom_id='Dpar_neg', element='C', pos=Dpar_vect_neg)
- self.atom_connect(atom_id='Dpar', bonded_id='R')
- self.atom_connect(atom_id='Dpar_neg', bonded_id='R')
+ # Create the 'AXS' residue.
+ self.atom_add(atom_id='R_axes', atom_name='R', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=R, element='C')
+ self.atom_add(atom_id='Dpar', atom_name='Dpar', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dpar_vect, element='C')
+ self.atom_add(atom_id='Dpar_neg', atom_name='Dpar',
res_name='AXS', chain_id=chain_id, res_num=res_num, pos=Dpar_vect_neg,
element='C')
+ self.atom_connect(atom_id='Dpar', bonded_id='R_axes')
+ self.atom_connect(atom_id='Dpar_neg', bonded_id='R_axes')
# Print out.
print " Scaling factor: " + `scale`
@@ -330,80 +391,26 @@
Dy_vect_neg = R + Dy_vect_neg
Dz_vect_neg = R + Dz_vect_neg
- # Add the atoms and connect them to the centre of mass.
- self.atom_add(atom_id='Dx', element='C', pos=Dx_vect)
- self.atom_add(atom_id='Dy', element='C', pos=Dy_vect)
- self.atom_add(atom_id='Dz', element='C', pos=Dz_vect)
- self.atom_add(atom_id='Dx_neg', element='C', pos=Dx_vect_neg)
- self.atom_add(atom_id='Dy_neg', element='C', pos=Dy_vect_neg)
- self.atom_add(atom_id='Dz_neg', element='C', pos=Dz_vect_neg)
- self.atom_connect(atom_id='Dx', bonded_id='R')
- self.atom_connect(atom_id='Dy', bonded_id='R')
- self.atom_connect(atom_id='Dz', bonded_id='R')
- self.atom_connect(atom_id='Dx_neg', bonded_id='R')
- self.atom_connect(atom_id='Dy_neg', bonded_id='R')
- self.atom_connect(atom_id='Dz_neg', bonded_id='R')
+ # Create the 'AXS' residue.
+ self.atom_add(atom_id='R_axes', atom_name='R', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=R, element='C')
+ self.atom_add(atom_id='Dx', atom_name='Dx', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dx_vect, element='C')
+ self.atom_add(atom_id='Dy', atom_name='Dy', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dy_vect, element='C')
+ self.atom_add(atom_id='Dz', atom_name='Dz', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dz_vect, element='C')
+ self.atom_add(atom_id='Dx_neg', atom_name='Dx', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dx_vect_neg, element='C')
+ self.atom_add(atom_id='Dy_neg', atom_name='Dy', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dy_vect_neg, element='C')
+ self.atom_add(atom_id='Dz_neg', atom_name='Dz', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dz_vect_neg, element='C')
+ self.atom_connect(atom_id='Dx', bonded_id='R_axes')
+ self.atom_connect(atom_id='Dy', bonded_id='R_axes')
+ self.atom_connect(atom_id='Dz', bonded_id='R_axes')
+ self.atom_connect(atom_id='Dx_neg', bonded_id='R_axes')
+ self.atom_connect(atom_id='Dy_neg', bonded_id='R_axes')
+ self.atom_connect(atom_id='Dz_neg', bonded_id='R_axes')
# Print out.
print " Scaling factor: " + `scale`
print " Dx vector (scaled + shifted to R): " + `Dx_vect`
print " Dy vector (scaled + shifted to R): " + `Dy_vect`
print " Dz vector (scaled + shifted to R): " + `Dz_vect`
-
-
- # Vector distribution.
- ######################
-
- # Print out.
- print "\nGenerating the geometric object."
-
- # Increment value.
- inc = 20
-
- # Get the uniform vector distribution.
- print " Creating the uniform vector distribution."
- vectors = self.uniform_vect_dist_spherical_angles(inc=20)
-
- # Loop over the radial array of vectors (change in longitude).
- for i in range(inc):
- # Loop over the vectors of the radial array (change in latitude).
- for j in range(inc/2+2):
- # Index.
- index = i + j*inc
-
- # Atom id.
- atom_id = 'T' + `i` + 'P' + `j`
-
- # Rotate the vector into the diffusion frame.
- vector = dot(self.relax.data.diff[self.run].rotation,
vectors[index])
-
- # Set the length of the vector to its diffusion rate within
the diffusion tensor geometric object.
- vector = dot(self.relax.data.diff[self.run].tensor, vector)
-
- # Scale the vector.
- vector = vector * scale
-
- # Position relative to the centre of mass.
- pos = R + vector
-
- # Add the vector as a H atom.
- self.atom_add(atom_id=atom_id, element='H', pos=pos)
-
- # Connect to the previous atom (to generate the longitudinal
lines).
- if j != 0:
- prev_id = 'T' + `i` + 'P' + `j-1`
- self.atom_connect(atom_id=atom_id, bonded_id=prev_id)
-
- # Connect across the radial arrays (to generate the
latitudinal lines).
- if i != 0:
- neighbour_id = 'T' + `i-1` + 'P' + `j`
- self.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
-
- # Connect the last radial array to the first (to zip up the
geometric object and close the latitudinal lines).
- if i == inc-1:
- neighbour_id = 'T' + `0` + 'P' + `j`
- self.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
-
# Create the PDB file.
r2751 - /branches/tensor_pdb/generic_fns/pdb.py