Author: bugman
Date: Thu Aug 21 19:01:29 2008
New Revision: 7224
URL: http://svn.gna.org/viewcvs/relax?rev=7224&view=rev
Log:
Fixed the generation of the diffusion in a cone geometric object.
Modified:
1.3/generic_fns/structure/geometric.py
1.3/specific_fns/n_state_model.py
Modified: 1.3/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=7224&r1=7223&r2=7224&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Thu Aug 21 19:01:29 2008
@@ -471,25 +471,25 @@
centred and at the head of the vector, a proton is placed.
- @param structure: The structural data object.
+ @keyword structure: The structural data object.
@type structure: instance of class derived from Base_struct_API
- @param res_name: The residue name.
+ @keyword res_name: The residue name.
@type res_name: str
- @param res_num: The residue number.
+ @keyword res_num: The residue number.
@type res_num: int
- @param chain_id: The chain identifier.
+ @keyword chain_id: The chain identifier.
@type chain_id: str
- @param centre: The centre of the distribution.
+ @keyword centre: The centre of the distribution.
@type centre: numpy array, len 3
- @param R: The optional 3x3 rotation matrix.
+ @keyword R: The optional 3x3 rotation matrix.
@type R: 3x3 numpy array
- @param warp: The optional 3x3 warping matrix.
+ @keyword 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.
+ @keyword max_angle: The maximal polar angle, in rad, after which all
vectors are skipped.
@type max_angle: float
- @param scale: The scaling factor to stretch all rotated and
warped vectors by.
+ @keyword scale: The scaling factor to stretch all rotated and
warped vectors by.
@type scale: float
- @param inc: The number of increments or number of vectors
used to generate the outer
+ @keyword inc: The number of increments or number of vectors
used to generate the outer
edge of the cone.
@type inc: int
"""
@@ -549,11 +549,11 @@
# Connect across the radial arrays (to generate the latitudinal
lines).
if i != 0:
- structure.atom_connect(index1=atom_num-1,
index2=atom_num-1-j_min)
+ structure.atom_connect(index1=atom_num-1,
index2=atom_num-1-j_min-2)
# Connect the last radial array to the first (to zip up the
geometric object and close the latitudinal lines).
if i == inc-1:
- structure.atom_connect(index1=atom_num-1,
index2=origin_num-1+j)
+ structure.atom_connect(index1=atom_num-1,
index2=origin_num-1+j+2)
# Increment the atom number.
atom_num = atom_num + 1
@@ -659,48 +659,6 @@
@type inc: int
"""
- # Loop over the radial array of vectors (change in longitude).
- for i in range(inc):
- # Connect the two atoms (to stitch up the 2 objects).
- structure.atom_connect(index1=cone_start-1+i, index2=cap_start-1+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
-
- | cos(theta) * sin(phi) |
- vector = | sin(theta) * sin(phi) |.
- | cos(phi) |
-
- The vectors of this distribution generate both longitudinal and
latitudinal lines.
- """
-
- # The inc argument must be an even number.
- if inc%2:
- raise RelaxError, "The increment value of " + `inc` + " must be an
even number."
-
- # 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+2, float64)
val = 1.0 / float(inc/2)
@@ -708,6 +666,72 @@
v[i] = float(i-1) * val + val/2.0
v[-1] = 1.0
+ # Generate the distribution of spherical angles phi.
+ phi = arccos(2.0 * v - 1.0)
+
+ # Loop over the angles and find the minimum latitudinal index.
+ for j_min in xrange(len(phi)):
+ if phi[j_min] < max_angle:
+ break
+
+ print "j_min " + `j_min`
+ # Loop over the radial array of vectors (change in longitude).
+ for i in range(inc):
+ # Cap atom.
+ cap_atom = cap_start + i
+
+ # Dome edge atom.
+ dome_edge = cone_start + i + i*(j_min+1)
+
+ print "dome edge: " + `dome_edge` + ", cap atom: " + `cap_atom`
+
+ # Connect the two atoms (to stitch up the 2 objects).
+ structure.atom_connect(index1=dome_edge-1, index2=cap_atom-1)
+
+
+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
+
+ | cos(theta) * sin(phi) |
+ vector = | sin(theta) * sin(phi) |.
+ | cos(phi) |
+
+ The vectors of this distribution generate both longitudinal and
latitudinal lines.
+ """
+
+ # The inc argument must be an even number.
+ if inc%2:
+ raise RelaxError, "The increment value of " + `inc` + " must be an
even number."
+
+ # 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+2, float64)
+ val = 1.0 / float(inc/2)
+ for i in xrange(1, inc/2+1):
+ v[i] = float(i-1) * val + val/2.0
+ v[-1] = 1.0
+
# Generate the distribution of spherical angles theta.
theta = 2.0 * pi * u
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=7224&r1=7223&r2=7224&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Thu Aug 21 19:01:29 2008
@@ -249,7 +249,7 @@
print "\nGenerating the cone cap."
cone_start_atom = structure.structural_data[0].atom_num[-1]+1
generic_fns.structure.geometric.generate_vector_dist(structure=structure,
res_name='CON', res_num=3, centre=cdp.pivot_point, R=R, max_angle=angle,
scale=norm(cdp.pivot_CoM), inc=inc)
-
generic_fns.structure.geometric.stitch_cap_to_cone(structure=structure,
cone_start=cone_start_atom, cap_start=cap_start_atom, max_angle=angle,
inc=inc)
+
generic_fns.structure.geometric.stitch_cap_to_cone(structure=structure,
cone_start=cone_start_atom, cap_start=cap_start_atom+1, max_angle=angle,
inc=inc)
# Create the PDB file.
print "\nGenerating the PDB file."
r7224 - in /1.3: generic_fns/structure/geometric.py specific_fns/n_state_model.py