Author: bugman
Date: Thu Feb 21 14:40:05 2008
New Revision: 5105
URL: http://svn.gna.org/viewcvs/relax?rev=5105&view=rev
Log:
Shifted the code for generating the diffusion tensor geometric object into
generate_vector_dist().
The code has been abstracted so that it can also be used to generate cone
caps, or any other PDB
objects which can be generated by rotating and warping a sphere.
Modified:
1.3/generic_fns/structure.py
Modified: 1.3/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure.py?rev=5105&r1=5104&r2=5105&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Thu Feb 21 14:40:05 2008
@@ -466,10 +466,10 @@
#################
# Calculate the centre of mass.
- R = centre_of_mass()
+ CoM = centre_of_mass()
# Add the central atom.
- atom_add(atomic_data=atomic_data, atom_id='R'+atom_id_ext,
record_name='HETATM', atom_name='R', res_name='COM', chain_id=chain_id,
res_num=res_num, pos=R, element='C')
+ atom_add(atomic_data=atomic_data, atom_id='R'+atom_id_ext,
record_name='HETATM', atom_name='R', res_name='COM', chain_id=chain_id,
res_num=res_num, pos=CoM, element='C')
# Increment the residue number.
res_num = res_num + 1
@@ -481,56 +481,8 @@
# Print out.
print "\nGenerating the geometric object."
- # Increment value and initial atom number.
- inc = 20
- atom_num = 1
-
- # Get the uniform vector distribution.
- print " Creating the uniform vector distribution."
- vectors = 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` + atom_id_ext
-
- # Rotate the vector into the diffusion frame.
- vector = dot(pipe.diff.rotation, vectors[index])
-
- # Set the length of the vector to its diffusion rate within
the diffusion tensor geometric object.
- vector = dot(pipe.diff.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.
- atom_add(atomic_data=atomic_data, atom_id=atom_id,
record_name='HETATM', atom_name='H'+`atom_num`, 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` + atom_id_ext
- atom_connect(atomic_data=atomic_data, 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` + atom_id_ext
- atom_connect(atomic_data=atomic_data, 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` + atom_id_ext
- atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=neighbour_id)
-
- # Increment the atom number.
- atom_num = atom_num + 1
+ # The distribution.
+ generate_vector_dist(atomic_data=atomic_data, res_name='TNS',
res_num=res_num, centre=CoM, R=pipe.diff.rotation, warp=pipe.diff.tensor,
scale=scale, inc=20)
# Increment the residue number.
res_num = res_num + 1
@@ -757,6 +709,87 @@
# Close the file.
tensor_pdb_file.close()
+
+
+def generate_vector_dist(atomic_data=None, res_name=None, res_num=None,
centre=zero(3, float64), R=eye(3), warp=eye(3), max_angle=None, scale=1.0,
inc=20):
+ """Generate a uniformly distributed distribution of atoms on a warped
sphere.
+
+ The vectors from the function uniform_vect_dist_spherical_angles() are
used to generate the
+ distribution. These vectors are rotated to the desired frame using the
rotation matrix 'R',
+ then each compressed or stretched by the dot product with the 'warp'
matrix. Each vector is
+ centred and at the head of the vector, a proton is placed.
+
+
+ @param atomic_data: The dictionary to place the atomic data into.
+ @type atomic_data: dict
+ @param res_name: The residue name.
+ @type res_name: str
+ @param res_num: The residue number.
+ @type res_num: int
+ @param centre: The centre of the distribution.
+ @type centre: numpy array, len 3
+ @param R: The optional 3x3 rotation matrix.
+ @type R: 3x3 numpy array
+ @param warp: The optional 3x3 warping matrix.
+ @type warp: 3x3 numpy array
+ @param max_angle: The maximal polar angle, in rad, after which all
vectors are skipped.
+ @type max_angle: float
+ @param scale: The scaling factor to all rotated and warped
vectors by.
+ @type scale: float
+ @param inc: The number of increments or number of vectors
used to generate the outer
+ edge of the cone.
+ @type inc: int
+ """
+
+ # Initial atom number.
+ atom_num = 1
+
+ # Get the uniform vector distribution.
+ print " Creating the uniform vector distribution."
+ vectors = uniform_vect_dist_spherical_angles(inc=inc)
+
+ # 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` + atom_id_ext
+
+ # Rotate the vector into the diffusion frame.
+ vector = dot(R, vectors[index])
+
+ # Set the length of the vector to its diffusion rate within the
diffusion tensor geometric object.
+ vector = dot(warp, 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.
+ atom_add(atomic_data=atomic_data, atom_id=atom_id,
record_name='HETATM', atom_name='H'+`atom_num`, res_name=res_name,
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` + atom_id_ext
+ atom_connect(atomic_data=atomic_data, 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` + atom_id_ext
+ atom_connect(atomic_data=atomic_data, 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` + atom_id_ext
+ atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=neighbour_id)
+
+ # Increment the atom number.
+ atom_num = atom_num + 1
def generate_vector_residues(atomic_data=None, vector=None, atom_name=None,
res_name_vect='AXS', sim_vectors=None, res_name_sim='SIM', chain_id='',
res_num=None, origin=None, scale=1.0, label_placement=1.1, neg=False):
r5105 - /1.3/generic_fns/structure.py