Author: bugman
Date: Fri Jun 3 17:57:07 2011
New Revision: 12849
URL: http://svn.gna.org/viewcvs/relax?rev=12849&view=rev
Log:
Fixes for the Scientific python parts included with relax for the module path.
Modified:
1.3/extern/scientific_python/Geometry/TensorModule.py
1.3/extern/scientific_python/Geometry/VectorModule.py
1.3/extern/scientific_python/IO/ArrayIO.py
1.3/extern/scientific_python/IO/PDB.py
1.3/extern/scientific_python/IO/PDBSpaceGroups.py
Modified: 1.3/extern/scientific_python/Geometry/TensorModule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/extern/scientific_python/Geometry/TensorModule.py?rev=12849&r1=12848&r2=12849&view=diff
==============================================================================
--- 1.3/extern/scientific_python/Geometry/TensorModule.py (original)
+++ 1.3/extern/scientific_python/Geometry/TensorModule.py Fri Jun 3 17:57:07
2011
@@ -5,7 +5,7 @@
# last revision: 2006-11-23
#
-from scientific_python import N; Numeric = N
+from extern.scientific_python import N; Numeric = N
class Tensor:
@@ -66,7 +66,7 @@
return Tensor(other.array-self.array, 1)
def __mul__(self, other):
- from scientific_python import Geometry
+ from extern.scientific_python import Geometry
if isTensor(other):
a = self.array[self.rank*(slice(None),)+(N.NewAxis,)]
b = other.array[other.rank*(slice(None),)+(N.NewAxis,)]
@@ -110,10 +110,10 @@
def asVector(self):
"""
@returns: an equivalent vector object
- @rtype: L{scientific_python.Geometry.Vector}
+ @rtype: L{extern.scientific_python.Geometry.Vector}
@raises ValueError: if rank > 1
"""
- from scientific_python import Geometry
+ from extern.scientific_python import Geometry
if self.rank == 1:
return Geometry.Vector(self.array)
else:
@@ -191,7 +191,7 @@
@raises ValueError: if rank !=2
"""
if self.rank == 2:
- from scientific_python.LA import eigenvalues
+ from extern.scientific_python.LA import eigenvalues
return eigenvalues(self.array)
else:
raise ValueError('Undefined operation')
@@ -204,7 +204,7 @@
@raises ValueError: if rank !=2
"""
if self.rank == 2:
- from scientific_python.LA import eigenvectors
+ from extern.scientific_python.LA import eigenvectors
ev, vectors = eigenvectors(self.array)
return ev, Tensor(vectors)
else:
@@ -217,7 +217,7 @@
@raises ValueError: if rank !=2
"""
if self.rank == 2:
- from scientific_python.LA import inverse
+ from extern.scientific_python.LA import inverse
return Tensor(inverse(self.array))
else:
raise ValueError('Undefined operation')
Modified: 1.3/extern/scientific_python/Geometry/VectorModule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/extern/scientific_python/Geometry/VectorModule.py?rev=12849&r1=12848&r2=12849&view=diff
==============================================================================
--- 1.3/extern/scientific_python/Geometry/VectorModule.py (original)
+++ 1.3/extern/scientific_python/Geometry/VectorModule.py Fri Jun 3 17:57:07
2011
@@ -6,7 +6,7 @@
# last revision: 2008-8-27
#
-from scientific_python import N; Numeric = N
+from extern.scientific_python import N; Numeric = N
class Vector:
@@ -82,7 +82,7 @@
return Vector(other.array-self.array)
def __mul__(self, other):
- from scientific_python import Geometry
+ from extern.scientific_python import Geometry
if isVector(other):
return Numeric.add.reduce(self.array*other.array)
elif Geometry.isTensor(other):
@@ -97,7 +97,7 @@
return Vector(Numeric.multiply(self.array, other))
def __rmul__(self, other):
- from scientific_python import Geometry
+ from extern.scientific_python import Geometry
if Geometry.isTensor(other):
product = other.dot(Geometry.Tensor(self.array))
if product.rank == 1:
@@ -183,20 +183,20 @@
def asTensor(self):
"""
@returns: an equivalent rank-1 tensor object
- @rtype: L{scientific_python.Geometry.Tensor}
- """
- from scientific_python import Geometry
+ @rtype: L{extern.scientific_python.Geometry.Tensor}
+ """
+ from extern.scientific_python import Geometry
return Geometry.Tensor(self.array, 1)
def dyadicProduct(self, other):
"""
@param other: a vector or a tensor
- @type other: L{Vector} or L{scientific_python.Geometry.Tensor}
+ @type other: L{Vector} or L{extern.scientific_python.Geometry.Tensor}
@returns: the dyadic product with other
- @rtype: L{scientific_python.Geometry.Tensor}
+ @rtype: L{extern.scientific_python.Geometry.Tensor}
@raises TypeError: if other is not a vector or a tensor
"""
- from scientific_python import Geometry
+ from extern.scientific_python import Geometry
if isVector(other):
return Geometry.Tensor(self.array[:, N.NewAxis]
* other.array[N.NewAxis, :], 1)
Modified: 1.3/extern/scientific_python/IO/ArrayIO.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/extern/scientific_python/IO/ArrayIO.py?rev=12849&r1=12848&r2=12849&view=diff
==============================================================================
--- 1.3/extern/scientific_python/IO/ArrayIO.py (original)
+++ 1.3/extern/scientific_python/IO/ArrayIO.py Fri Jun 3 17:57:07 2011
@@ -22,11 +22,11 @@
Numbers in files to be read must conform to Python/C syntax. For
reading files containing Fortran-style double-precision numbers
-(exponent prefixed by D), use the module
L{scientific_python.IO.FortranFormat}.
+(exponent prefixed by D), use the module
L{extern.scientific_python.IO.FortranFormat}.
"""
-from scientific_python.IO.TextFile import TextFile
-from scientific_python import N; Numeric = N
+from extern.scientific_python.IO.TextFile import TextFile
+from extern.scientific_python import N; Numeric = N
import string
def readArray(filename):
Modified: 1.3/extern/scientific_python/IO/PDB.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/extern/scientific_python/IO/PDB.py?rev=12849&r1=12848&r2=12849&view=diff
==============================================================================
--- 1.3/extern/scientific_python/IO/PDB.py (original)
+++ 1.3/extern/scientific_python/IO/PDB.py Fri Jun 3 17:57:07 2011
@@ -64,10 +64,10 @@
@undocumented: DummyChain
"""
-from scientific_python.IO.TextFile import TextFile
-from scientific_python.IO.FortranFormat import FortranFormat, FortranLine
-from scientific_python.Geometry import Vector, Tensor
-from scientific_python import N
+from extern.scientific_python.IO.TextFile import TextFile
+from extern.scientific_python.IO.FortranFormat import FortranFormat,
FortranLine
+from extern.scientific_python.Geometry import Vector, Tensor
+from extern.scientific_python import N
from PDBExportFilters import export_filters
import copy, string
@@ -142,7 +142,7 @@
X{PDB} file with access at the record level
The low-level file access is handled by the module
- L{scientific_python.IO.TextFile}, therefore compressed files and URLs
+ L{extern.scientific_python.IO.TextFile}, therefore compressed files and
URLs
(for reading) can be used as well.
"""
@@ -154,7 +154,7 @@
@type mode: C{str}
@param subformat: indicates a specific dialect of the PDB format.
Subformats are defined in
- L{scientific_python.IO.PDBExportFilters}; they are
used
+ L{extern.scientific_python.IO.PDBExportFilters};
they are used
only when writing.
@type subformat: C{str} or C{NoneType}
"""
@@ -407,7 +407,7 @@
@param name: the atom name
@type name: C{str}
@param position: the atom position
- @type position: L{scientific_python.Geometry.Vector}
+ @type position: L{extern.scientific_python.Geometry.Vector}
@param occupancy: the occupancy
@type occupancy: C{float}
@param temperature_factor: the temperature factor (B-factor)
@@ -529,7 +529,7 @@
@param name: the atom name
@type name: C{str}
@param position: the atom position
- @type position: L{scientific_python.Geometry.Vector}
+ @type position: L{extern.scientific_python.Geometry.Vector}
@param properties: any other atom properties as keyword parameters.
These properties are stored in the atom object
and can be accessed by indexing, as for
@@ -1378,7 +1378,7 @@
self._scale_matrix = {}
self._scale_matrix[type[-1]] = data
if type[-1] == '3': # last line read
- from scientific_python.Geometry.Transformation \
+ from extern.scientific_python.Geometry.Transformation \
import Shear, Translation
l1 = self._scale_matrix['1']
l2 = self._scale_matrix['2']
@@ -1395,7 +1395,7 @@
self._ncs_matrix = {}
self._ncs_matrix[type[-1]] = data
if type[-1] == '3': # last line read
- from scientific_python.Geometry.Transformation \
+ from extern.scientific_python.Geometry.Transformation \
import Rotation, Translation
l1 = self._ncs_matrix['1']
l2 = self._ncs_matrix['2']
@@ -1453,7 +1453,7 @@
def findSpaceGroupTransformations(self):
if self.space_group is not None and self.to_fractional is not None:
- from scientific_python.IO.PDBSpaceGroups import \
+ from extern.scientific_python.IO.PDBSpaceGroups import \
getSpaceGroupTransformations
try:
trs = getSpaceGroupTransformations(self.space_group)
Modified: 1.3/extern/scientific_python/IO/PDBSpaceGroups.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/extern/scientific_python/IO/PDBSpaceGroups.py?rev=12849&r1=12848&r2=12849&view=diff
==============================================================================
--- 1.3/extern/scientific_python/IO/PDBSpaceGroups.py (original)
+++ 1.3/extern/scientific_python/IO/PDBSpaceGroups.py Fri Jun 3 17:57:07 2011
@@ -2,9 +2,9 @@
# obtained from the Computational Crystallography Toolbox
#
-from scientific_python.Geometry import Vector, Tensor
-from scientific_python.Geometry.Transformation import Rotation, Translation
-from scientific_python import N
+from extern.scientific_python.Geometry import Vector, Tensor
+from extern.scientific_python.Geometry.Transformation import Rotation,
Translation
+from extern.scientific_python import N
class SpaceGroup(object):
r12849 - in /1.3/extern/scientific_python: Geometry/ IO/