Author: bugman
Date: Thu Mar 11 15:54:13 2010
New Revision: 10981
URL: http://svn.gna.org/viewcvs/relax?rev=10981&view=rev
Log:
Various point distributions can now be used for the cone PDB representations.
This includes the original 'uniform' distribution and now the 'regular'
distribution.
Modified:
1.3/generic_fns/structure/geometric.py
Modified: 1.3/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=10981&r1=10980&r2=10981&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Thu Mar 11 15:54:13 2010
@@ -38,14 +38,48 @@
-def angles_uniform(inc=None):
- """Determine the spherical angles for a uniform sphere point
distribution.
+def angles_regular(inc=None):
+ """Determine the spherical angles for a regular sphere point
distribution.
@keyword inc: The number of increments in the distribution.
@type inc: int
@return: The phi angle array and the theta angle array.
@rtype: array of float, array of float
"""
+
+ # Generate the increment values of u.
+ u = zeros(inc, float64)
+ val = 1.0 / float(inc)
+ for i in xrange(inc):
+ u[i] = float(i) * val
+
+ # Generate the increment values of v.
+ v = zeros(inc/2+1, float64)
+ val = 1.0 / float(inc/2)
+ for i in range(inc/2+1):
+ v[i] = float(i) * val
+
+ # Generate the distribution of spherical angles theta.
+ theta = 2.0 * pi * u
+
+ # Generate the distribution of spherical angles phi (from bottom to top).
+ phi = zeros(len(v), float64)
+ for i in range(len(v)):
+ phi[len(v)-1-i] = pi * v[i]
+
+ # Return the angle arrays.
+ return phi, theta
+
+
+def angles_uniform(inc=None):
+ """Determine the spherical angles for a uniform sphere point
distribution.
+
+ @keyword inc: The number of increments in the distribution.
+ @type inc: int
+ @return: The phi angle array and the theta angle array.
+ @rtype: array of float, array of float
+ """
+
# Generate the increment values of u.
u = zeros(inc, float64)
val = 1.0 / float(inc)
@@ -89,7 +123,7 @@
return 1.8e-6
-def cone_edge(mol=None, cone=None, res_name='CON', res_num=None,
chain_id='', apex=None, axis=None, R=None, scale=None, inc=None, debug=False):
+def cone_edge(mol=None, cone=None, res_name='CON', res_num=None,
chain_id='', apex=None, axis=None, R=None, scale=None, inc=None,
distribution='uniform', debug=False):
"""Add a residue to the atomic data representing a cone of the given
angle.
A series of vectors totalling the number of increments and starting at
the origin are equally
@@ -117,6 +151,8 @@
@type scale: float
@keyword inc: The number of increments or number of vectors
used to generate the outer edge of the cone.
@type inc: int
+ @keyword distribution: The type of point distribution to use. This can
be 'uniform' or 'regular'.
+ @type distribution: str
"""
# The atom numbers (and indices).
@@ -127,7 +163,10 @@
origin_atom = atom_num
# Get the polar and azimuthal angles for the distribution.
- phi, theta = angles_uniform(inc)
+ if distribution == 'uniform':
+ phi, theta = angles_uniform(inc)
+ else:
+ phi, theta = angles_regular(inc)
# Initialise the rotation matrix.
if R == None:
@@ -146,7 +185,7 @@
# The index.
for j in range(len(phi)):
- if phi[j] < phi_max[i]:
+ if phi[j] <= phi_max[i]:
edge_index[i] = j
break
@@ -192,16 +231,16 @@
# Debugging.
if debug:
- print("%sj: %s; phi: %-20s; k: %s; phi: %-20s" % (" "*4, j,
phi[j], k, phi[k]))
+ print("%sj: %s; phi: %-20s; k: %s; phi: %-20s; phi_max:
%-20s" % (" "*4, j, phi[j], k, phi[k], phi_max[i]))
# No edge.
skip = True
- # Forward edge.
- index = i+1
+ # Forward edge (skip when the latitude is phi max).
+ fwd_index = i+1
if i == len(theta)-1:
- index = 0
- if j >= edge_index[i] and j < edge_index[index]:
+ fwd_index = 0
+ if j >= edge_index[i] and j < edge_index[fwd_index] and not
abs(phi_max[fwd_index] - phi[j]) < 1e-6:
# Debugging.
if debug:
print("%sForward edge." % (" "*8))
@@ -211,14 +250,17 @@
# Find the theta value for this polar angle phi.
phi_val = phi[j]
- if index == 0:
- theta_max = theta[index] + 2*pi
+ if fwd_index == 0:
+ theta_max = theta[fwd_index] + 2*pi
else:
- theta_max = theta[index]
+ theta_max = theta[fwd_index]
theta_max = cone.theta_max(phi_val, theta_min=theta[i],
theta_max=theta_max-1e-7)
- # Back edge.
- if i < len(theta)-1 and j > edge_index_rev[i] and j <=
edge_index_rev[i+1]:
+ # Back edge (skip when the latitude is phi max).
+ rev_index = i-1
+ if i == 0:
+ rev_index = len(theta)-1
+ if i < len(theta)-1 and j > edge_index_rev[i] and j <=
edge_index_rev[i+1] and not abs(phi_max[fwd_index] - phi[k]) < 1e-6:
# Debugging.
if debug:
print("%sBack edge." % (" "*8))
@@ -268,7 +310,7 @@
mol.atom_connect(index1=atom_num-2, index2=origin_atom)
-def create_cone_pdb(cone=None, apex=None, axis=None, R=None, inc=None,
scale=30.0, file=None, dir=None, force=False):
+def create_cone_pdb(cone=None, apex=None, axis=None, R=None, inc=None,
scale=30.0, distribution='regular', file=None, dir=None, force=False):
"""Create a PDB representation of the given cone object.
@keyword cone: The cone object. This should provide the
limit_check() method with determines the limits of the distribution accepting
two arguments, the polar angle phi and the azimuthal angle theta, and return
True if the point is in the limits or False if outside. It should also
provide the theta_max() method for returning the theta value for the given
phi, the phi_max() method for returning the phi value for the given theta.
@@ -283,6 +325,8 @@
@type inc: int
@keyword scale: The scaling factor to stretch the unit cone by.
@type scale: float
+ @keyword distribution: The type of point distribution to use. This can
be 'uniform' or 'regular'.
+ @type distribution: str
@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.
@@ -318,13 +362,13 @@
# Generate the cone outer edge.
print("\nGenerating the cone outer edge.")
edge_start_atom = mol.atom_num[-1]+1
- cone_edge(mol=mol, cone=cone, res_name='EDG', res_num=3, apex=apex, R=R,
scale=scale, inc=inc)
+ cone_edge(mol=mol, cone=cone, res_name='EDG', res_num=3, apex=apex, R=R,
scale=scale, inc=inc, distribution=distribution)
# 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=4, centre=apex,
R=R, limit_check=cone.limit_check, scale=scale, inc=inc)
- stitch_cone_to_edge(mol=mol, cone=cone, dome_start=cone_start_atom,
edge_start=edge_start_atom+1, scale=scale, inc=inc)
+ generate_vector_dist(mol=mol, res_name='CON', res_num=4, centre=apex,
R=R, limit_check=cone.limit_check, scale=scale, inc=inc,
distribution=distribution)
+ stitch_cone_to_edge(mol=mol, cone=cone, dome_start=cone_start_atom,
edge_start=edge_start_atom+1, scale=scale, inc=inc, distribution=distribution)
# Create the PDB file.
print("\nGenerating the PDB file.")
@@ -631,13 +675,10 @@
tensor_pdb_file.close()
-def generate_vector_dist(mol=None, res_name=None, res_num=None, chain_id='',
centre=zeros(3, float64), R=eye(3), warp=eye(3), limit_check=None, scale=1.0,
inc=20, debug=False):
+def generate_vector_dist(mol=None, res_name=None, res_num=None, chain_id='',
centre=zeros(3, float64), R=eye(3), warp=eye(3), limit_check=None, scale=1.0,
inc=20, distribution='uniform', debug=False):
"""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.
+ The vectors from the function 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.
@keyword mol: The molecule container.
@@ -658,9 +699,10 @@
@type limit_check: function
@keyword scale: The scaling factor to stretch all rotated and
warped vectors by.
@type scale: float
- @keyword inc: The number of increments or number of vectors
used to generate the outer
- edge of the cone.
+ @keyword inc: The number of increments or number of vectors
used to generate the outer edge of the cone.
@type inc: int
+ @keyword distribution: The type of point distribution to use. This can
be 'uniform' or 'regular'.
+ @type distribution: str
"""
# Initial atom number.
@@ -669,10 +711,13 @@
# Get the uniform vector distribution.
print(" Creating the uniform vector distribution.")
- vectors = uniform_vect_dist_spherical_angles(inc=inc)
+ vectors = vect_dist_spherical_angles(inc=inc, distribution=distribution)
# Get the polar and azimuthal angles for the distribution.
- phi, theta = angles_uniform(inc)
+ if distribution == 'uniform':
+ phi, theta = angles_uniform(inc)
+ else:
+ phi, theta = angles_regular(inc)
# Init the arrays for stitching together.
edge = zeros(len(theta))
@@ -775,16 +820,13 @@
@type mol: MolContainer instance
@param vector: The vector to be represented in the PDB.
@type vector: numpy array, len 3
- @param atom_name: The atom name used to label the atom
representing the head of the
- vector.
+ @param atom_name: The atom name used to label the atom
representing the head of the vector.
@type atom_name: str
@param res_name_vect: The 3 letter PDB residue code used to represent
the vector.
@type res_name_vect: str
- @param sim_vectors: The optional Monte Carlo simulation vectors to
be represented in the
- PDB.
+ @param sim_vectors: The optional Monte Carlo simulation vectors to
be represented in the PDB.
@type sim_vectors: list of numpy array, each len 3
- @param res_name_sim: The 3 letter PDB residue code used to represent
the Monte Carlo
- simulation vectors.
+ @param res_name_sim: The 3 letter PDB residue code used to represent
the Monte Carlo simulation vectors.
@type res_name_sim: str
@param chain_id: The chain identification code.
@type chain_id: str
@@ -794,11 +836,9 @@
@type origin: numpy array, len 3
@param scale: The scaling factor to stretch the vectors by.
@type scale: float
- @param label_placement: A scaling factor to multiply the pre-scaled
vector by. This is used to
- place the vector labels a little further out
from the vector itself.
+ @param label_placement: A scaling factor to multiply the pre-scaled
vector by. This is used to place the vector labels a little further out from
the vector itself.
@type label_placement: float
- @param neg: If True, then the negative vector positioned at
the origin will also be
- included.
+ @param neg: If True, then the negative vector positioned at
the origin will also be included.
@type neg: bool
@return: The new residue number.
@rtype: int
@@ -871,7 +911,7 @@
return names[i] + repr(atom_num - lims[i])
-def stitch_cone_to_edge(mol=None, cone=None, chain_id='', dome_start=None,
edge_start=None, scale=1.0, inc=None, debug=False):
+def stitch_cone_to_edge(mol=None, cone=None, chain_id='', dome_start=None,
edge_start=None, scale=1.0, inc=None, distribution='uniform', debug=False):
"""Function for stitching the cone dome to its edge, in the PDB
representations.
@keyword mol: The molecule container.
@@ -889,10 +929,15 @@
@type scale: float
@keyword inc: The number of increments or number of vectors
used to generate the outer edge of the cone.
@type inc: int
+ @keyword distribution: The type of point distribution to use. This can
be 'uniform' or 'regular'.
+ @type distribution: str
"""
# Get the polar and azimuthal angles for the distribution.
- phi, theta = angles_uniform(inc)
+ if distribution == 'uniform':
+ phi, theta = angles_uniform(inc)
+ else:
+ phi, theta = angles_regular(inc)
# Determine the maximum phi values and the indices of the point just
above the edge.
phi_max = zeros(len(theta), float64)
@@ -903,7 +948,7 @@
# The index.
for j in range(len(phi)):
- if phi[j] < phi_max[i]:
+ if phi[j] <= phi_max[i]:
edge_index[i] = j
break
@@ -924,6 +969,7 @@
# Debugging.
if debug:
print("i: %s; theta: %s" % (i, theta[i]))
+ print("%sDome atom: %s" % (" "*4, get_proton_name(dome_atom)))
print("%sStitching longitudinal line to edge - %s to %s." % ("
"*4, get_proton_name(edge_atom), get_proton_name(dome_atom)))
# Connect the two atoms (to stitch up the 2 objects).
@@ -939,16 +985,16 @@
# Debugging.
if debug:
- print("%sj: %s; phi: %-20s; k: %s; phi: %-20s" % (" "*4, j,
phi[j], k, phi[k]))
+ print("%sj: %s; phi: %-20s; k: %s; phi: %-20s; phi_max:
%-20s" % (" "*4, j, phi[j], k, phi[k], phi_max[i]))
# No edge.
skip = True
- # Forward edge.
+ # Forward edge (skip when the latitude is phi max).
fwd_index = i+1
if i == len(theta)-1:
fwd_index = 0
- if j >= edge_index[i] and j < edge_index[fwd_index]:
+ if j >= edge_index[i] and j < edge_index[fwd_index] and not
abs(phi_max[fwd_index] - phi[j]) < 1e-6:
# Debugging.
if debug:
print("%sForward edge." % (" "*8))
@@ -957,11 +1003,11 @@
skip = False
forward = True
- # Back edge.
+ # Back edge (skip when the latitude is phi max).
rev_index = i-1
if i == 0:
rev_index = len(theta)-1
- if i < len(theta)-1 and j > edge_index_rev[i] and j <=
edge_index_rev[i+1]:
+ if i < len(theta)-1 and j > edge_index_rev[i] and j <=
edge_index_rev[i+1] and not abs(phi_max[fwd_index] - phi[k]) < 1e-6:
# Debugging.
if debug:
print("%sBack edge." % (" "*8))
@@ -978,7 +1024,7 @@
if forward:
atom = dome_atom + j - edge_index[i]
else:
- atom = dome_atom + edge_index_rev[i]+1 + k -
edge_index[fwd_index]
+ atom = dome_atom + (edge_index_rev[i]+1) + k -
edge_index[fwd_index]
# Debugging.
if debug:
@@ -990,24 +1036,14 @@
# Increment the cone edge atom number.
edge_atom = edge_atom + 1
- # Update the cone dome and edge atoms.
+ # Update the cone dome atom.
dome_atom = dome_atom + (len(phi) - edge_index[i])
-def uniform_vect_dist_spherical_angles(inc=20):
- """Uniform distribution of vectors on a sphere using uniform spherical
angles.
-
- This function returns an array of unit vectors uniformly distributed
within 3D space. To create the distribution, uniform spherical angles are
used. The two spherical angles are defined as::
-
- theta = 2.pi.u,
- phi = cos^-1(2v - 1),
-
- where::
-
- u in [0, 1),
- v in [0, 1].
-
- Because theta is defined between [0, pi] and phi is defined between [0,
2pi], for a uniform distribution u is only incremented half of 'inc'. The
unit vectors are generated using the equation::
+def vect_dist_spherical_angles(inc=20, distribution='uniform'):
+ """Create a distribution of vectors on a sphere using a distribution of
spherical angles.
+
+ This function returns an array of unit vectors distributed within 3D
space. The unit vectors are generated using the equation::
| cos(theta) * sin(phi) |
vector = | sin(theta) * sin(phi) |.
@@ -1016,18 +1052,19 @@
The vectors of this distribution generate both longitudinal and
latitudinal lines.
- @keyword inc: The number of increments in the distribution.
- @type inc: int
- @return: The distribution of vectors on a sphere.
- @rtype: list of rank-1, 3D numpy arrays, array of float, array
of float
- """
-
- # The inc argument must be an even number.
- if inc%2:
- raise RelaxError("The increment value of " + repr(inc) + " must be
an even number.")
+ @keyword inc: The number of increments in the distribution.
+ @type inc: int
+ @keyword distribution: The type of point distribution to use. This can
be 'uniform' or 'regular'.
+ @type distribution: str
+ @return: The distribution of vectors on a sphere.
+ @rtype: list of rank-1, 3D numpy arrays, array of float,
array of float
+ """
# Get the polar and azimuthal angles for the distribution.
- phi, theta = angles_uniform(inc)
+ if distribution == 'uniform':
+ phi, theta = angles_uniform(inc)
+ else:
+ phi, theta = angles_regular(inc)
# Initialise array of the distribution of vectors.
vectors = []
r10981 - /1.3/generic_fns/structure/geometric.py