Author: bugman
Date: Wed Apr 15 11:46:03 2009
New Revision: 9008
URL: http://svn.gna.org/viewcvs/relax?rev=9008&view=rev
Log:
Completed the calculate() and calc_ave_dist() methods for the dynamically
averaged NOE analysis.
Modified:
branches/ave_noe/specific_fns/n_state_model.py
Modified: branches/ave_noe/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/specific_fns/n_state_model.py?rev=9008&r1=9007&r2=9008&view=diff
==============================================================================
--- branches/ave_noe/specific_fns/n_state_model.py (original)
+++ branches/ave_noe/specific_fns/n_state_model.py Wed Apr 15 11:46:03 2009
@@ -34,12 +34,13 @@
# relax module imports.
from float import isNaN, isInf
import generic_fns
-from generic_fns.mol_res_spin import spin_loop
+from generic_fns.mol_res_spin import return_spin, spin_loop
from generic_fns import pipes
import generic_fns.structure.geometric
from generic_fns.structure.internal import Internal
import generic_fns.structure.mass
from maths_fns.n_state_model import N_state_opt
+from maths_fns.potential import quad_pot
from maths_fns.rotation_matrix import R_2vect, R_euler_zyz
from physical_constants import dipolar_constant, g1H, pcs_constant,
return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxInfError, RelaxModelError,
RelaxNaNError, RelaxNoModelError, RelaxNoTensorError
@@ -919,7 +920,7 @@
generic_fns.align_tensor.init(tensor=id, params=[0.0, 0.0,
0.0, 0.0, 0.0])
- def calc_ave_dist(self, exp=1):
+ def calc_ave_dist(self, atom1, atom2, exp=1):
"""Calculate the average distances.
The formula used is:
@@ -930,37 +931,40 @@
\ N /__ /
i
- where i are the members of the ensemble.
-
-
+ 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 averaging.
+ r^-6 NOE averaging.
@type exp: int
- """
-
- # Loop over the NOE and non-NOEs:
- for noe in self.noes + self.non_noes:
- # Append the atom names with zero distance.
- self.ave_dist.append([noe[0], noe[1], 0.0])
-
- # Loop over each model.
- for i in xrange(NUM_MODELS):
- # Switch to the data pipe containing the model.
- pipe.switch(`i`)
-
- # Get the corresonding spins.
- spin0 = return_spin('@'+noe[0])
- spin1 = return_spin('@'+noe[1])
-
- # Distance to the minus sixth power.
- dist = norm(spin0.pos - spin1.pos)
- self.ave_dist[-1][2] = self.ave_dist[-1][2] + dist**(-EXP)
-
- # Average.
- self.ave_dist[-1][2] = self.ave_dist[-1][2] / NUM_MODELS
-
- # The exponent.
- self.ave_dist[-1][2] = self.ave_dist[-1][2]**(-1.0/EXP)
+ @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)
+ for i in range(num_models):
+ # Distance to the minus sixth power.
+ dist = norm(spin1.pos[i] - spin2.pos[i])
+ 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 calculate(self, verbosity=1):
@@ -981,9 +985,32 @@
if not hasattr(cdp, 'model'):
raise RelaxNoModelError, 'N-state'
- # Calculate the average distances, using -6 power averaging.
- self.calc_ave_dist(exp=-6)
-
+ # Init some numpy arrays.
+ num_restraints = len(cdp.noe_restraints)
+ dist = zeros(num_restraints, float64)
+ pot = zeros(num_restraints, float64)
+ lower = zeros(num_restraints, float64)
+ upper = zeros(num_restraints, float64)
+
+ # Loop over the NOEs.
+ for i in range(num_restraints):
+ # Create arrays of the NOEs.
+ lower[i] = cdp.noe_restraints[i][2]
+ 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)
+
+ # Calculate the quadratic potential.
+ quad_pot(dist, pot, lower, upper)
+
+ # Store the distance and potential information.
+ cdp.ave_dist = []
+ cdp.quad_pot = []
+ for i in range(num_restraints):
+ cdp.ave_dist.append([cdp.noe_restraints[i][0],
cdp.noe_restraints[i][1], dist[i]])
+ cdp.quad_pot.append([cdp.noe_restraints[i][0],
cdp.noe_restraints[i][1], pot[i]])
+
def CoM(self, pivot_point=None, centre=None):
"""Centre of mass analysis.
r9008 - /branches/ave_noe/specific_fns/n_state_model.py