removed Scientific.LA deps

Updated code accordingly (eigen vectors tranpose)

MMTK/Collections.py

@@ -320,10 +320,10 @@ class GroupOfAtoms(object):
         :returns: the normalizing transformation
         :rtype: Scientific.Geometry.Transformation.RigidBodyTransformation
         """
-        from Scientific.LA import determinant
+        from numpy.linalg.linalg import det
         cm, inertia = self.centerAndMomentOfInertia()
         ev, diag = inertia.diagonalization()
-        if determinant(diag.array) < 0:
+        if det(diag.array) < 0:
             diag.array[0] = -diag.array[0]
         if repr != None:
             seq = numpy.argsort(ev)

MMTK/NormalModes/Core.py

@@ -42,7 +42,7 @@ if dgesdd is None:
         from lapack_dge import dgesdd
     except ImportError: pass
 if dsyevd is None:
-    from Scientific.LA import Heigenvectors
+    from numpy.linalg import eigh
 if dsyevd:
     n = 1
     array = numpy.zeros((n, n), numpy.float)
@@ -259,7 +259,7 @@ class NormalModes(object):
             ev, modes = Heigenvectors(self.array)
             ev = ev.real
             modes = modes.real
-            self.array = modes
+            self.array = modes.T
         else:
             ev = numpy.zeros((self.nmodes,), numpy.float)
             work = numpy.zeros((1,), numpy.float)

MMTK/Trajectory.py

@@ -935,9 +935,10 @@ class RigidBodyTrajectory(object):
 
         quaternions = numpy.zeros((steps, 4), numpy.float)
         fit = numpy.zeros((steps,), numpy.float)
-        from Scientific.LA import eigenvectors
+        from numpy.linalg import eig
         for i in range(steps):
-            e, v = eigenvectors(k[i])
+            e, v = eig(k[i])
+            v = v.T
             j = numpy.argmin(e)
             if e[j] < 0.:
                 fit[i] = 0.