comments

src/BioHelpers_FABER/rmsd.py

@@ -102,7 +102,7 @@ def rmsd_from_rot_tran(
     """Calculate an RMSD like value for a given set of vectors x and y with a given rotation matrix and translation vector
     Mathematical formula:
 
-    .. math:: \tilde{\mathrm{RMSD}} = \\frac{1}{M} \sum_{k=1..M} |\mathscr{U}\mathbf{x}^k + \mathbf{r} - \mathbf{y}^k|^2
+    .. math:: \mathrm{E} = \\frac{1}{M} \sum_{k=1..M} |\mathscr{U}\mathbf{x}^k + \mathbf{r} - \mathbf{y}^k|^2
 
     **Important Note:** The translation vector differs from Kabsch algorithm, there you translate befor rotating. In Coutsias paper it is the otherway round.
 
@@ -114,9 +114,12 @@ def rmsd_from_rot_tran(
     :type rot: np.ndarray
     :param trans: Translation vector r, see note above
     :type trans: np.ndarray
-    :return: RMSD like value
+    :return: RMSD like value (:math:`\sqrt{E}`)
     :rtype: float
     """
+    print(trans.shape)
+    print(np.matmul(rot, x).shape, y.shape)
+
     return 0.0
 
 
@@ -217,6 +220,7 @@ def rmsd_per_residue(file1: str, file2: str) -> list[float]:
             res2_AA = [list(a.get_vector()) for a in res2.get_atoms()]
             res1_AA = np.transpose(np.array(res1_AA))
             res2_AA = np.transpose(np.array(res2_AA))
+            rmsd_from_rot_tran(res1_AA, res2_AA, rot, trans)
 
     return [0.0]