From e080a99087dd18d84a2d26119546197ba0e9e9a6 Mon Sep 17 00:00:00 2001
From: Christian Faber <chris-faber@gmx.de>
Date: Mon, 21 Oct 2024 09:47:05 +0200
Subject: [PATCH] added rmsd per residue
---
src/BioHelpers_FABER/rmsd.py | 12 ++++++------
test_rmsd.py | 1 -
2 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/src/BioHelpers_FABER/rmsd.py b/src/BioHelpers_FABER/rmsd.py
index 2a066e3..5f4281d 100644
--- a/src/BioHelpers_FABER/rmsd.py
+++ b/src/BioHelpers_FABER/rmsd.py
@@ -117,10 +117,10 @@ def rmsd_from_rot_tran(
:return: RMSD like value (:math:`\sqrt{E}`)
:rtype: float
"""
- print(trans.shape)
- print(np.matmul(rot, x).shape, y.shape)
-
- return 0.0
+ num_vec = x.shape[1]
+ intermediate = np.matmul(rot, x) + trans[:, np.newaxis] + y
+ squared = np.trace(np.matmul(np.transpose(intermediate), intermediate)) / num_vec
+ return np.sqrt(squared)
def rmsd(x: np.ndarray, y: np.ndarray) -> float:
@@ -220,9 +220,9 @@ 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)
+ values.append(rmsd_from_rot_tran(res1_AA, res2_AA, rot, trans))
- return [0.0]
+ return values
if __name__ == "__main__":
diff --git a/test_rmsd.py b/test_rmsd.py
index d42a0a5..32a194c 100644
--- a/test_rmsd.py
+++ b/test_rmsd.py
@@ -32,7 +32,6 @@ def main():
rot, tran = sup.get_rotran()
# rmsd per residue
print(rmsd.rmsd_per_residue(file1, file2))
- print("Hallo Welt", val, val2)
if __name__ == "__main__":
--
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