Author: bugman
Date: Fri Jun 14 13:54:21 2013
New Revision: 20118
URL: http://svn.gna.org/viewcvs/relax?rev=20118&view=rev
Log:
Shifted another method from the N_state_model class to the
specific_analyses.n_state_model.data module.
Modified:
trunk/specific_analyses/n_state_model/__init__.py
trunk/specific_analyses/n_state_model/data.py
Modified: trunk/specific_analyses/n_state_model/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/__init__.py?rev=20118&r1=20117&r2=20118&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/__init__.py (original)
+++ trunk/specific_analyses/n_state_model/__init__.py Fri Jun 14 13:54:21 2013
@@ -56,7 +56,7 @@
from pipe_control.structure.mass import centre_of_mass
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
-from specific_analyses.n_state_model.data import base_data_types,
check_rdcs, num_data_points, opt_tensor, opt_uses_align_data, tensor_loop
+from specific_analyses.n_state_model.data import base_data_types,
calc_ave_dist, check_rdcs, num_data_points, opt_tensor, opt_uses_align_data,
tensor_loop
from specific_analyses.n_state_model.parameters import
assemble_param_vector, assemble_scaling_matrix, disassemble_param_vector,
linear_constraints, param_model_index, param_num, update_model
from target_functions.n_state_model import N_state_opt
from target_functions.potential import quad_pot
@@ -86,54 +86,6 @@
# Add the minimisation data.
self.PARAMS.add_min_data(min_stats_global=False, min_stats_spin=True)
-
-
- def _calc_ave_dist(self, atom1, atom2, exp=1):
- """Calculate the average distances.
-
- The formula used is::
-
- _N_
- / 1 \ \ 1/exp
- <r> = | - > |p1i - p2i|^exp |
- \ N /__ /
- i
-
- where i are the members of the ensemble, N is the total number of
structural models, and p1
- and p2 at the two atom positions.
-
-
- @param atom1: The atom identification string of the first atom.
- @type atom1: str
- @param atom2: The atom identification string of the second atom.
- @type atom2: str
- @keyword exp: The exponent used for the averaging, e.g. 1 for
linear averaging and -6 for
- r^-6 NOE averaging.
- @type exp: int
- @return: The average distance between the two atoms.
- @rtype: float
- """
-
- # Get the spin containers.
- spin1 = return_spin(atom1)
- spin2 = return_spin(atom2)
-
- # Loop over each model.
- num_models = len(spin1.pos)
- ave_dist = 0.0
- for i in range(num_models):
- # Distance to the minus sixth power.
- dist = norm(spin1.pos[i] - spin2.pos[i])
- ave_dist = ave_dist + dist**(exp)
-
- # Average.
- ave_dist = ave_dist / num_models
-
- # The exponent.
- ave_dist = ave_dist**(1.0/exp)
-
- # Return the average distance.
- return ave_dist
def _CoM(self, pivot_point=None, centre=None):
@@ -1004,7 +956,7 @@
upper[i] = cdp.noe_restraints[i][3]
# Calculate the average distances, using -6 power averaging.
- dist[i] = self._calc_ave_dist(cdp.noe_restraints[i][0],
cdp.noe_restraints[i][1], exp=-6)
+ dist[i] = calc_ave_dist(cdp.noe_restraints[i][0],
cdp.noe_restraints[i][1], exp=-6)
# Calculate the quadratic potential.
quad_pot(dist, pot, lower, upper)
Modified: trunk/specific_analyses/n_state_model/data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/data.py?rev=20118&r1=20117&r2=20118&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/data.py (original)
+++ trunk/specific_analyses/n_state_model/data.py Fri Jun 14 13:54:21 2013
@@ -23,6 +23,7 @@
"""Module for handling base data of the N-state model or structural ensemble
analysis."""
# Python module imports.
+from numpy.linalg import norm
from warnings import warn
# relax module imports.
@@ -30,7 +31,7 @@
from lib.warnings import RelaxWarning
from pipe_control import align_tensor
from pipe_control.interatomic import interatomic_loop
-from pipe_control.mol_res_spin import spin_loop
+from pipe_control.mol_res_spin import return_spin, spin_loop
def base_data_types():
@@ -75,6 +76,54 @@
# Return the list.
return list
+
+
+def calc_ave_dist(atom1, atom2, exp=1):
+ """Calculate the average distances.
+
+ The formula used is::
+
+ _N_
+ / 1 \ \ 1/exp
+ <r> = | - > |p1i - p2i|^exp |
+ \ N /__ /
+ i
+
+ where i are the members of the ensemble, N is the total number of
structural models, and p1
+ and p2 at the two atom positions.
+
+
+ @param atom1: The atom identification string of the first atom.
+ @type atom1: str
+ @param atom2: The atom identification string of the second atom.
+ @type atom2: str
+ @keyword exp: The exponent used for the averaging, e.g. 1 for linear
averaging and -6 for
+ r^-6 NOE averaging.
+ @type exp: int
+ @return: The average distance between the two atoms.
+ @rtype: float
+ """
+
+ # Get the spin containers.
+ spin1 = return_spin(atom1)
+ spin2 = return_spin(atom2)
+
+ # Loop over each model.
+ num_models = len(spin1.pos)
+ ave_dist = 0.0
+ for i in range(num_models):
+ # Distance to the minus sixth power.
+ dist = norm(spin1.pos[i] - spin2.pos[i])
+ ave_dist = ave_dist + dist**(exp)
+
+ # Average.
+ ave_dist = ave_dist / num_models
+
+ # The exponent.
+ ave_dist = ave_dist**(1.0/exp)
+
+ # Return the average distance.
+ return ave_dist
def check_rdcs(interatom, spin1, spin2):
r20118 - in /trunk/specific_analyses/n_state_model: __init__.py data.py