convenience function to directly get RMSD of two matrices

hng · Mar 16, 2015 · a02923f · a02923f
1 parent 0780112
commit a02923f
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Showing 2 changed files with 10 additions and 7 deletions.
diff --git a/src/KABSCH/kabsch.jl b/src/KABSCH/kabsch.jl
@@ -1,5 +1,5 @@
 module Kabsch
-export calc_centroid, kabsch, rotate, rmsd, translate_points
+export calc_centroid, kabsch, rotate, rmsd, translate_points, kabsch_rmsd
 	# Calculate root mean square deviation of two matrices A, B
 	# http://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions
 	function rmsd(A, B)
@@ -48,7 +48,7 @@ export calc_centroid, kabsch, rotate, rmsd, translate_points
 		A = *(P', Q)		
 
 		# calculate SVD (singular value decomposition) of covariance matrix
-		# http://de.wikipedia.org/wiki/Singul%C3%A4rwertzerlegung
+		# http://de.wikipedia.org/wiki/Singul%C3%A4rwertzerlegunggo
 		V, S, W = svd(A)
 
 		# decide if rotation matrix needs correction (ensures right-handed coordinate system)
@@ -69,4 +69,11 @@ export calc_centroid, kabsch, rotate, rmsd, translate_points
 		U, P = kabsch(P,Q)
 		return *(P, U)
 	end
+
+	# directly return RMSD for matrices P, Q for convenience
+	function kabsch_rmsd(P, Q)
+		P_1, Q_1 = translate_points(P, Q)
+		P = rotate(P, Q)
+		return rmsd(P, Q_1)
+	end
 end
diff --git a/src/KABSCH/runtests.jl b/src/KABSCH/runtests.jl
@@ -20,8 +20,4 @@ Q = [9 8 7; 6 5 4; 3 2 1]
 
 @test_approx_eq_eps rmsd(P,Q) 8.94427191 1e-4
 
-# Q needs to be translated to the origin of the coordinate system, otherwise the comparison makes no sense
-P_1, Q_1 = translate_points(P,Q)
-P = rotate(P, Q)
-
-@test_approx_eq_eps rmsd(P,Q_1) 2.4323767778e-15 1e-6
+@test_approx_eq_eps kabsch_rmsd(P,Q) 2.4323767778e-15 1e-6