Author: bugman
Date: Wed Jul 21 11:24:16 2010
New Revision: 11324
URL: http://svn.gna.org/viewcvs/relax?rev=11324&view=rev
Log:
Added support for the pseudo-elliptic cone model in the frame order user
function and specific code.
Modified:
1.3/prompt/frame_order.py
1.3/specific_fns/frame_order.py
Modified: 1.3/prompt/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/frame_order.py?rev=11324&r1=11323&r2=11324&view=diff
==============================================================================
--- 1.3/prompt/frame_order.py (original)
+++ 1.3/prompt/frame_order.py Wed Jul 21 11:24:16 2010
@@ -181,7 +181,12 @@
Prior to optimisation, the Frame Order model should be selected.
The list of available
models are:
- 'iso cone' - The isotropic cone model.
+ 'iso cone' - The isotropic cone model. The cone is defined by a
single opening angle
+ theta. The torsion angle sigma is unrestricted.
+
+ 'pseudo-ellipse' - The pseudo-elliptic cone model. The cone is
defined by two opening
+ angles, theta_x and theta_y. In the tilt-torsion angle system
these define the
+ allowable tilt. The torsion angle sigma is restricted.
Examples
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=11324&r1=11323&r2=11324&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Wed Jul 21 11:24:16 2010
@@ -76,6 +76,10 @@
elif cdp.model == 'iso cone':
return array([cdp.beta, cdp.gamma, cdp.theta_axis, cdp.phi_axis,
cdp.s1], float64)
+ # The pseudo-elliptic cone model initial parameter vector (the
average position rotation, eigenframe and cone parameters).
+ elif cdp.model == 'iso cone':
+ return array([cdp.alpha, cdp.beta, cdp.gamma, cdp.eigen_alpha,
cdp.eigen_beta, cdp.eigen_gamma, cdp.cone_theta_x, cdp.cone_theta_y,
cdp.cone_sigma_max], float64)
+
def _back_calc(self):
"""Back-calculation of the reduced alignment tensor.
@@ -204,7 +208,7 @@
pdb_file.close()
- def _grid_row(self, incs, lower, upper, dist_type=None):
+ def _grid_row(self, incs, lower, upper, dist_type=None, end_point=True):
"""Set up a row of the grid search for a given parameter.
@param incs: The number of increments.
@@ -213,10 +217,10 @@
@type lower: float
@param upper: The upper bounds.
@type upper: float
- @keyword dist_type: The spacing or distribution type between grid
nodes. If None, then a
- linear grid row is returned. If 'acos', then an
inverse cos
- distribution of points is returned (e.g. for
uniform sampling in angular space).
+ @keyword dist_type: The spacing or distribution type between grid
nodes. If None, then a linear grid row is returned. If 'acos', then an
inverse cos distribution of points is returned (e.g. for uniform sampling in
angular space).
@type dist_type: None or str
+ @keyword end_point: A flag which if False will cause the end point
to be removed.
+ @type end_point: bool
@return: The row of the grid.
@rtype: list of float
"""
@@ -241,6 +245,10 @@
# Generate the distribution.
row = arccos(v)
+
+ # Remove the last point.
+ if not end_point:
+ row = row[:-1]
# Return the row (as a list).
return list(row)
@@ -370,7 +378,7 @@
def _select_model(self, model=None):
"""Select the Frame Order model.
- @param model: The Frame Order model. As of yet, this can only be
'iso cone'.
+ @param model: The Frame Order model. This can be one of 'rigid',
'iso cone', or 'pseudo-ellipse'.
@type model: str
"""
@@ -382,7 +390,7 @@
raise RelaxModelError('Frame Order')
# Test if the model name exists.
- if not model in ['rigid', 'iso cone']:
+ if not model in ['rigid', 'iso cone', 'pseudo-ellipse']:
raise RelaxError("The model name " + repr(model) + " is
invalid.")
# Set the model
@@ -469,6 +477,31 @@
if not hasattr(cdp, 's1'):
cdp.s1 = 0.0
+ # Pseudo-elliptic cone model.
+ elif cdp.model == 'pseudo-ellipse':
+ # Set up the parameter arrays.
+ if init:
+ cdp.params.append('eigen_alpha')
+ cdp.params.append('eigen_beta')
+ cdp.params.append('eigen_gamma')
+ cdp.params.append('cone_theta_x')
+ cdp.params.append('cone_theta_y')
+ cdp.params.append('cone_sigma_max')
+
+ # Initialise the cone axis angles and order parameter values.
+ if not hasattr(cdp, 'eigen_alpha'):
+ cdp.eigen_alpha = 0.0
+ if not hasattr(cdp, 'eigen_beta'):
+ cdp.eigen_beta = 0.0
+ if not hasattr(cdp, 'eigen_gamma'):
+ cdp.eigen_gamma = 0.0
+ if not hasattr(cdp, 'cone_theta_x'):
+ cdp.cone_theta_x = 0.0
+ if not hasattr(cdp, 'cone_theta_y'):
+ cdp.cone_theta_y = 0.0
+ if not hasattr(cdp, 'cone_sigma_max'):
+ cdp.cone_sigma_max = 0.0
+
def _unpack_opt_results(self, results, sim_index=None):
"""Unpack and store the Frame Order optimisation results.
@@ -526,6 +559,31 @@
cdp.theta_axis = theta_axis
cdp.phi_axis = phi_axis
cdp.s1 = s1
+
+ # Pseudo-ellipse cone model.
+ elif cdp.model == 'pseudo-ellipse':
+ # Disassemble the parameter vector.
+ alpha, beta, gamma, eigen_alpha, eigen_beta, eigen_gamma,
cone_theta_x, cone_theta_y, cone_sigma_max = param_vector
+
+ # Monte Carlo simulation data structures.
+ if sim_index != None:
+ # Model parameters.
+ cdp.eigen_alpha[sim_index] = wrap_angles(eigen_alpha, 0.0,
2.0*pi)
+ cdp.eigen_beta[sim_index] = wrap_angles(eigen_beta, 0.0,
2.0*pi)
+ cdp.eigen_gamma[sim_index] = wrap_angles(eigen_gamma, 0.0,
2.0*pi)
+ cdp.cone_theta_x[sim_index] = cone_theta_x
+ cdp.cone_theta_y[sim_index] = cone_theta_y
+ cdp.cone_sigma_max[sim_index] = cone_sigma_max
+
+ # Normal data structures.
+ else:
+ # Model parameters.
+ cdp.eigen_alpha = wrap_angles(eigen_alpha, 0.0, 2.0*pi)
+ cdp.eigen_beta = wrap_angles(eigen_beta, 0.0, 2.0*pi)
+ cdp.eigen_gamma = wrap_angles(eigen_gamma, 0.0, 2.0*pi)
+ cdp.cone_theta_x = cone_theta_x
+ cdp.cone_theta_y = cone_theta_y
+ cdp.cone_sigma_max = cone_sigma_max
# Wrap the Euler angles.
alpha = wrap_angles(alpha, 0.0, 2.0*pi)
@@ -662,24 +720,44 @@
if set == 'all' or set == 'generic':
names.append('params')
+ # The parameter suffix.
+ if error_names:
+ suffix = '_err'
+ elif sim_names:
+ suffix = '_sim'
+ else:
+ suffix = ''
+
# Parameters.
if set == 'all' or set == 'params':
# The isotropic cone model.
if hasattr(cdp, 'model') and cdp.model == 'iso cone':
# Euler angles.
- names.append('beta')
- names.append('gamma')
+ names.append('beta%s' % suffix)
+ names.append('gamma%s' % suffix)
# Angular cone parameters.
- names.append('theta_axis')
- names.append('phi_axis')
- names.append('s1')
+ names.append('theta_axis%s' % suffix)
+ names.append('phi_axis%s' % suffix)
+ names.append('s1%s' % suffix)
# All other models.
else:
- names.append('alpha')
- names.append('beta')
- names.append('gamma')
+ names.append('alpha%s' % suffix)
+ names.append('beta%s' % suffix)
+ names.append('gamma%s' % suffix)
+
+ # The pseudo-elliptic cone model.
+ if hasattr(cdp, 'model') and cdp.model == 'pseudo-ellipse':
+ # Eigenframe
+ names.append('eigen_alpha%s' % suffix)
+ names.append('eigen_beta%s' % suffix)
+ names.append('eigen_gamma%s' % suffix)
+
+ # Cone parameters.
+ names.append('cone_theta_x%s' % suffix)
+ names.append('cone_theta_y%s' % suffix)
+ names.append('cone_sigma_max%s' % suffix)
# Minimisation statistics.
if set == 'all' or set == 'min':
@@ -689,44 +767,6 @@
names.append('g_count')
names.append('h_count')
names.append('warning')
-
- # Parameter errors.
- if error_names and (set == 'all' or set == 'params'):
- # The isotropic cone model.
- if hasattr(cdp, 'model') and cdp.model == 'iso cone':
- # Euler angles.
- names.append('beta_err')
- names.append('gamma_err')
-
- # Angular cone parameters.
- names.append('theta_axis_err')
- names.append('phi_axis_err')
- names.append('s1_err')
-
- # All other models.
- else:
- names.append('alpha_err')
- names.append('beta_err')
- names.append('gamma_err')
-
- # Parameter simulation values.
- if sim_names and (set == 'all' or set == 'params'):
- # The isotropic cone model.
- if hasattr(cdp, 'model') and cdp.model == 'iso cone':
- # Euler angles.
- names.append('beta_sim')
- names.append('gamma_sim')
-
- # Angular cone parameters.
- names.append('theta_axis_sim')
- names.append('phi_axis_sim')
- names.append('s1_sim')
-
- # All other models.
- else:
- names.append('alpha_sim')
- names.append('beta_sim')
- names.append('gamma_sim')
# Return the names.
return names
@@ -769,28 +809,22 @@
incs = inc
# Initialise the grid increments structures.
- default_bounds = False
- if not lower:
- lower = []
- default_bounds = True
- if not upper:
- upper = []
+ lower_list = lower
+ upper_list = upper
grid = []
"""This structure is a list of lists. The first dimension
corresponds to the model
parameter. The second dimension are the grid node positions."""
# Generate the grid.
for i in range(n):
- # Reset the distribution type and row.
+ # Reset.
dist_type = None
- row = None
+ end_point = True
# Alpha Euler angle.
if cdp.params[i] == 'alpha':
- # Set the default bounds.
- if default_bounds:
- lower.append(0.0)
- upper.append(2*pi * (1.0 - 1.0/incs[i]))
+ lower = 0.0
+ upper = 2*pi * (1.0 - 1.0/incs[i])
# Beta Euler angle.
if cdp.params[i] == 'beta':
@@ -798,26 +832,42 @@
if not isinstance(inc, list):
incs[i] = incs[i] / 2 + 1
- # The distribution type.
+ # The distribution type and end point.
dist_type = 'acos'
+ end_point = False
# Set the default bounds.
- if default_bounds:
- lower.append(0.0)
- upper.append(pi)
-
- # Get the grid row.
- row = self._grid_row(incs[i], lower[i], upper[i],
dist_type=dist_type)
-
- # Remove the end point.
- row = row[:-1]
+ lower = 0.0
+ upper = pi
# Gamma Euler angle.
if cdp.params[i] == 'gamma':
+ lower = 0.0
+ upper = 2*pi * (1.0 - 1.0/incs[i])
+
+ # The eigenframe alpha Euler angle.
+ if cdp.params[i] == 'eigen_alpha':
+ lower = 0.0
+ upper = 2*pi * (1.0 - 1.0/incs[i])
+
+ # The eigenframe beta Euler angle.
+ if cdp.params[i] == 'eigen_beta':
+ # Change the default increment numbers.
+ if not isinstance(inc, list):
+ incs[i] = incs[i] / 2 + 1
+
+ # The distribution type and end point.
+ dist_type = 'acos'
+ end_point = False
+
# Set the default bounds.
- if default_bounds:
- lower.append(0.0)
- upper.append(2*pi * (1.0 - 1.0/incs[i]))
+ lower = 0.0
+ upper = pi
+
+ # The eigenframe gamma Euler angle.
+ if cdp.params[i] == 'eigen_gamma':
+ lower = 0.0
+ upper = 2*pi * (1.0 - 1.0/incs[i])
# The isotropic cone model.
if cdp.model == 'iso cone':
@@ -829,31 +879,42 @@
# The distribution type.
dist_type = 'acos'
+ end_point = False
# Set the default bounds.
- if default_bounds:
- lower.append(0.0)
- upper.append(pi)
+ lower = 0.0
+ upper = pi
# Cone axis azimuthal angle.
if cdp.params[i] == 'phi_axis':
- # Set the default bounds.
- if default_bounds:
- lower.append(0.0)
- upper.append(2*pi * (1.0 - 1.0/incs[i]))
+ lower = 0.0
+ upper = 2*pi * (1.0 - 1.0/incs[i])
# The cone order parameter.
if cdp.params[i] == 's1':
- # Set the default bounds.
- if default_bounds:
- lower.append(-0.5)
- upper.append(1.0)
-
- # Get the grid row.
- if not row:
- row = self._grid_row(incs[i], lower[i], upper[i],
dist_type=dist_type)
+ lower = -0.5
+ upper = 1.0
+
+ # The pseudo-elliptic cone model parameters.
+ if cdp.model == 'pseudo-ellipse':
+ # Cone opening angles.
+ if cdp.params[i] in ['theta_x', 'theta_y']:
+ lower = 0.0
+ upper = pi
+
+ # Torsion angle restriction.
+ if cdp.params[i] == 'sigma_max':
+ lower = 0.0
+ upper = pi
+
+ # Over-ride the bounds.
+ if lower_list:
+ lower = lower_list[i]
+ if upper_list:
+ upper = upper_list[i]
# Append the grid row.
+ row = self._grid_row(incs[i], lower, upper, dist_type=dist_type,
end_point=end_point)
grid.append(row)
# Minimisation.
r11324 - in /1.3: prompt/frame_order.py specific_fns/frame_order.py