Sped up minimizeRMSD when no weight is used

coords.py

@@ -48,17 +48,23 @@ def _minimizeRmsd(coordsB, coordsA, weights=None):
     shapeA,shapeB = [np.shape(X) for X in (A,B)]
     assert( shapeA == shapeB )
     for X,s in zip((A,B),(shapeA,shapeB)):
-        assert( s[1] == 3 and s[0] >= s[1] )    
+        assert( s[1] == 3 and s[0] >= s[1] )
     
-    if weights is None: weights = np.ones(len(A))
-    assert( len(weights[:]) == len(B) )
-    W = np.diag(weights)
+    # if weights is None: weights = np.ones(len(A))
+    if weights is None:
+        comA,comB = [np.mean( X, axis=0 ) for X in (A,B)]
+    else:
+        assert( len(weights[:]) == len(B) )
+        W = np.diag(weights)
+        comA,comB = [np.sum( W.dot(X), axis=0 ) / np.sum(W) for X in (A,B)]
 
-    comA,comB = [np.sum( W.dot(X), axis=0 ) / np.sum(W) for X in (A,B)]
     A = np.array( A-comA )
     B = np.array( B-comB )
-    
-    s = A.T.dot(W.dot(B))
+
+    if weights is None:
+        s = A.T.dot(B)
+    else:
+        s = A.T.dot(W.dot(B))
     
     sxx,sxy,sxz = s[0,:]
     syx,syy,syz = s[1,:]