Author: semor
Date: Thu Jan 17 23:00:51 2008
New Revision: 4848
URL: http://svn.gna.org/viewcvs/relax?rev=4848&view=rev
Log:
Converted generic_fns modules from Numeric to numpy.
As point in a post by Edward d'Auvergne (minfx-devel mailing list, see
below), the select_sim array
(which calls 'ones()') was specified as a integer array.
https://mail.gna.org/public/minfx-commits/2008-01/msg00004.html (Message-id:
<E1JF9Gs-000081-9c@xxxxxxxxxxxxxxxxxx>)
Modified:
1.3/generic_fns/angles.py
1.3/generic_fns/diffusion_tensor.py
1.3/generic_fns/grace.py
1.3/generic_fns/monte_carlo.py
1.3/generic_fns/structure.py
Modified: 1.3/generic_fns/angles.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/angles.py?rev=4848&r1=4847&r2=4848&view=diff
==============================================================================
--- 1.3/generic_fns/angles.py (original)
+++ 1.3/generic_fns/angles.py Thu Jan 17 23:00:51 2008
@@ -22,7 +22,7 @@
# Python module imports.
from math import acos, sin
-from Numeric import dot
+from numpy import dot
# relax module imports.
from data import Data as relax_data_store
Modified: 1.3/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/diffusion_tensor.py?rev=4848&r1=4847&r2=4848&view=diff
==============================================================================
--- 1.3/generic_fns/diffusion_tensor.py (original)
+++ 1.3/generic_fns/diffusion_tensor.py Thu Jan 17 23:00:51 2008
@@ -1538,7 +1538,7 @@
# Spheroid.
if cdp.diff_tensor.type == 'spheroid':
# Initialise.
- Dpar = zeros(3, Float64)
+ Dpar = zeros(3, float64)
# Trig.
sin_theta = sin(cdp.diff_tensor.theta)
@@ -1557,9 +1557,9 @@
# Ellipsoid.
if cdp.diff_tensor.type == 'ellipsoid':
# Initialise.
- Dx = zeros(3, Float64)
- Dy = zeros(3, Float64)
- Dz = zeros(3, Float64)
+ Dx = zeros(3, float64)
+ Dy = zeros(3, float64)
+ Dz = zeros(3, float64)
# Trig.
sin_alpha = sin(cdp.diff_tensor.alpha)
Modified: 1.3/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/grace.py?rev=4848&r1=4847&r2=4848&view=diff
==============================================================================
--- 1.3/generic_fns/grace.py (original)
+++ 1.3/generic_fns/grace.py Thu Jan 17 23:00:51 2008
@@ -21,7 +21,7 @@
###############################################################################
# Python module imports.
-from Numeric import array
+from numpy import array
from os import system
from re import match
Modified: 1.3/generic_fns/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/monte_carlo.py?rev=4848&r1=4847&r2=4848&view=diff
==============================================================================
--- 1.3/generic_fns/monte_carlo.py (original)
+++ 1.3/generic_fns/monte_carlo.py Thu Jan 17 23:00:51 2008
@@ -23,7 +23,7 @@
# Python module imports.
from copy import deepcopy
from math import sqrt
-from Numeric import ones
+from numpy import ones
from random import gauss
# relax module imports.
@@ -331,7 +331,7 @@
# Create the selected simulation array with all simulations selected.
if all_select_sim == None:
- select_sim = ones(number)
+ select_sim = ones(number, int)
# Loop over the instances.
for instance in xrange(num_instances):
@@ -353,7 +353,7 @@
@params all_select_sim: The selection status of the Monte Carlo
simulations. The first
dimension of this matrix corresponds to the simulation and the
second corresponds to the
instance.
- @type all_select_sim: Numeric matrix (int)
+ @type all_select_sim: numpy matrix (int)
"""
# Arguments.
Modified: 1.3/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure.py?rev=4848&r1=4847&r2=4848&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Thu Jan 17 23:00:51 2008
@@ -22,7 +22,7 @@
# Python module imports.
from math import sqrt, cos, pi, sin
-from Numeric import Float64, arccos, dot, zeros
+from numpy import arccos, dot, float64, zeros
from os import F_OK, access
from re import compile, match
import Scientific.IO.PDB
@@ -201,7 +201,7 @@
print "Calculating the centre of mass."
# Initialise the centre of mass.
- R = zeros(3, Float64)
+ R = zeros(3, float64)
# Initialise the total mass.
M = 0.0
@@ -635,7 +635,7 @@
@param res_num: The residue number.
@type res_num: int
@param R: The centre of mass.
- @type R: Numeric array (Float64)
+ @type R: numpy array (float64)
@param i: The Monte Carlo simulation index.
@type i: int
@return: None
@@ -725,7 +725,7 @@
@param res_num: The residue number.
@type res_num: int
@param R: The centre of mass.
- @type R: Numeric array (Float64)
+ @type R: numpy array (float64)
@param i: The Monte Carlo simulation index.
@type i: int
@return: None
@@ -1075,13 +1075,13 @@
raise RelaxError, "The increment value of " + `inc` + " must be
an even number."
# Generate the increment values of u.
- u = zeros(inc, Float64)
+ 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)
+ 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
@@ -1584,7 +1584,7 @@
# Initialise.
vector_array = []
- ave_vector = zeros(3, Float64)
+ ave_vector = zeros(3, float64)
# Number of structures.
num_str = len(relax_data_store.pdb[self.run].structures)
r4848 - in /1.3/generic_fns: angles.py diffusion_tensor.py grace.py monte_carlo.py structure.py