Enabled and fixed numpy unit test

modules/mol/base/tests/CMakeLists.txt

@@ -17,7 +17,7 @@ set(OST_MOL_BASE_UNIT_TESTS
 )
 
 if (USE_NUMPY)
-   set(OST_MOST_BASE_UNIT_TESTS "${OST_MOST_BASE_UNIT_TESTS}" test_numpy.py)
+  list(APPEND OST_MOL_BASE_UNIT_TESTS test_numpy.py)
 endif (USE_NUMPY)
 
 ost_unittest(MODULE mol SOURCES "${OST_MOL_BASE_UNIT_TESTS}")

modules/mol/base/tests/test_numpy.py

@@ -5,6 +5,7 @@ if __name__== '__main__':
   sys.path.insert(0,"../../../../stage/lib/openstructure/")
   
 import ost
+from ost import geom, mol
 
 if ost.WITH_NUMPY:
   has_numpy=True
@@ -16,10 +17,10 @@ else:
   has_numpy=False
 
 def v2v(v):
-  return ost.geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
+  return geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
 
 def dd(v1,v2):
-  return ost.geom.Distance(v1,v2)<1e-8
+  return geom.Distance(v1,v2)<1e-8
 
 class TestNumpy(unittest.TestCase):
   def setUp(self):
@@ -28,46 +29,46 @@ class TestNumpy(unittest.TestCase):
   def test_(self):
     if not has_numpy:
       return
-    entity=ost.mol.CreateEntity()
+    entity=mol.CreateEntity()
     ed=entity.EditXCS()
     ch=ed.InsertChain("X")
     re=ed.AppendResidue(ch,"ALA")
-    a0=ed.InsertAtom(re,"A",ost.geom.Vec3(0,0,0))
+    a0=ed.InsertAtom(re,"A",geom.Vec3(0,0,0))
     self.assertEqual(a0.GetIndex(),0)
-    a1=ed.InsertAtom(re,"B",ost.geom.Vec3(1,0,0))
+    a1=ed.InsertAtom(re,"B",geom.Vec3(1,0,0))
     self.assertEqual(a1.GetIndex(),1)
-    a2=ed.InsertAtom(re,"C",ost.geom.Vec3(2,0,0))
+    a2=ed.InsertAtom(re,"C",geom.Vec3(2,0,0))
     self.assertEqual(a2.GetIndex(),2)
-    a3=ed.InsertAtom(re,"D",ost.geom.Vec3(3,0,0))
+    a3=ed.InsertAtom(re,"D",geom.Vec3(3,0,0))
     self.assertEqual(a3.GetIndex(),3)
 
-    self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,0,0)))
-    self.assertTrue(dd(a1.pos,ost.geom.Vec3(1,0,0)))
-    self.assertTrue(dd(a2.pos,ost.geom.Vec3(2,0,0)))
-    self.assertTrue(dd(a3.pos,ost.geom.Vec3(3,0,0)))
+    self.assertTrue(dd(a0.pos,geom.Vec3(0,0,0)))
+    self.assertTrue(dd(a1.pos,geom.Vec3(1,0,0)))
+    self.assertTrue(dd(a2.pos,geom.Vec3(2,0,0)))
+    self.assertTrue(dd(a3.pos,geom.Vec3(3,0,0)))
 
     ed.SetAtomTransformedPos(entity.GetAtomList(),
                              numpy.array([[0,1,0],[0,2,0],[0,3,0],[0,4,0]], dtype=numpy.float32))
 
-    self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,1,0)))
-    self.assertTrue(dd(a1.pos,ost.geom.Vec3(0,2,0)))
-    self.assertTrue(dd(a2.pos,ost.geom.Vec3(0,3,0)))
-    self.assertTrue(dd(a3.pos,ost.geom.Vec3(0,4,0)))
+    self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
+    self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
+    self.assertTrue(dd(a2.pos,geom.Vec3(0,3,0)))
+    self.assertTrue(dd(a3.pos,geom.Vec3(0,4,0)))
 
     na=entity.positions
 
-    self.assertTrue(dd(v2v(na[0]),ost.geom.Vec3(0,1,0)))
-    self.assertTrue(dd(v2v(na[1]),ost.geom.Vec3(0,2,0)))
-    self.assertTrue(dd(v2v(na[2]),ost.geom.Vec3(0,3,0)))
-    self.assertTrue(dd(v2v(na[3]),ost.geom.Vec3(0,4,0)))
+    self.assertTrue(dd(v2v(na[0]),geom.Vec3(0,1,0)))
+    self.assertTrue(dd(v2v(na[1]),geom.Vec3(0,2,0)))
+    self.assertTrue(dd(v2v(na[2]),geom.Vec3(0,3,0)))
+    self.assertTrue(dd(v2v(na[3]),geom.Vec3(0,4,0)))
 
     ed.SetAtomTransformedPos([3,99,2],
                              numpy.array([[0,0,-3],[-1,-1,-1],[0,0,-2]], dtype=numpy.float32))
 
-    self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,1,0)))
-    self.assertTrue(dd(a1.pos,ost.geom.Vec3(0,2,0)))
-    self.assertTrue(dd(a2.pos,ost.geom.Vec3(0,0,-2)))
-    self.assertTrue(dd(a3.pos,ost.geom.Vec3(0,0,-3)))
+    self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
+    self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
+    self.assertTrue(dd(a2.pos,geom.Vec3(0,0,-2)))
+    self.assertTrue(dd(a3.pos,geom.Vec3(0,0,-3)))
 
 if __name__== '__main__':
     unittest.main()