Handling old numpy versions

MMTK/Collections.py

@@ -321,7 +321,7 @@ class GroupOfAtoms(object):
         :rtype: Scientific.Geometry.Transformation.RigidBodyTransformation
         """
         cm, inertia = self.centerAndMomentOfInertia()
-        ev, diag = numpy.linalg.eig(inertia)
+        ev, diag = numpy.linalg.eig(inertia.array)
         diag = numpy.transpose(diag)
         if numpy.linalg.det(diag) < 0:
             diag[0] = -diag[0]

MMTK/InternalCoordinates.py

@@ -203,11 +203,11 @@ class BondAngle(InternalCoordinate):
         cm1, th1 = self.fragment1.centerAndMomentOfInertia()
         r1 = self.universe.distanceVector(self.atoms[1], cm1)
         th1 -= self.fragment1.mass()*((r1*r1)*delta-r1.dyadicProduct(r1))
-        i1 = numpy.dot(axis, numpy.dot(th1, axis))
+        i1 = numpy.dot(axis.array, numpy.dot(th1.array, axis.array))
         cm2, th2 = self.fragment2.centerAndMomentOfInertia()
         r2 = self.universe.distanceVector(self.atoms[1], cm2)
         th2 -= self.fragment2.mass()*((r2*r2)*delta-r2.dyadicProduct(r2))
-        i2 = numpy.dot(axis, numpy.dot(th2, axis))
+        i2 = numpy.dot(axis.array, numpy.dot(th2.array, axis.array))
         d1 = i2*d/(i1+i2)
         d2 = d1-d
         self.fragment1.rotateAroundAxis(self.atoms[1].position(),
@@ -284,11 +284,11 @@ class DihedralAngle(InternalCoordinate):
         cm1, th1 = self.fragment1.centerAndMomentOfInertia()
         r1 = self.universe.distanceVector(self.atoms[1], cm1)
         th1 -= self.fragment1.mass()*((r1*r1)*delta-r1.dyadicProduct(r1))
-        i1 = numpy.dot(axis, numpy.dot(th1, axis))
+        i1 = numpy.dot(axis.array, numpy.dot(th1.array, axis.array))
         cm2, th2 = self.fragment2.centerAndMomentOfInertia()
         r2 = self.universe.distanceVector(self.atoms[2], cm2)
         th2 -= self.fragment2.mass()*((r2*r2)*delta-r2.dyadicProduct(r2))
-        i2 = numpy.dot(axis, numpy.dot(th2, axis))
+        i2 = numpy.dot(axis.array, numpy.dot(th2.array, axis.array))
         d1 = i2*d/(i1+i2)
         d2 = d1-d
         self.fragment1.rotateAroundAxis(self.atoms[1].position(),