From bf7e672fdab89f9f4f99e18c304629b9e7745035 Mon Sep 17 00:00:00 2001
From: "c.faber" <c.faber@fz-juelich.de>
Date: Tue, 22 Oct 2024 10:54:10 +0200
Subject: [PATCH] fix rmsd function
---
setup.py | 2 +-
src/BioHelpers_FABER/rmsd.py | 12 ++++++++++--
2 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/setup.py b/setup.py
index a04d15b..d0296a1 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@ with open("README.md", "r") as f:
setup(
name="BioHelpers_FABER",
- version="0.2.9",
+ version="0.2.10",
description="Small collection of useful scripts for the computational work with RNA Data.",
url="https://gitlab.jsc.fz-juelich.de/faber1/biohelpers",
package_dir={"": "src"},
diff --git a/src/BioHelpers_FABER/rmsd.py b/src/BioHelpers_FABER/rmsd.py
index c20ad6d..84ed055 100644
--- a/src/BioHelpers_FABER/rmsd.py
+++ b/src/BioHelpers_FABER/rmsd.py
@@ -194,8 +194,16 @@ def rmsd_pdb(file1: str, file2: str, exclude_residues: Optional[list] = None) ->
p2.detach_child((" ", i, " "))
# p1_AA = [list(a.get_vector()) for a in p1.get_atoms()]
# p2_AA = [list(a.get_vector()) for a in p2.get_atoms()]
- p1_AA = [list(a.get_vector()) for a in p1.get_atoms() if a.id != "OP3"]
- p2_AA = [list(a.get_vector()) for a in p2.get_atoms() if a.id != "OP3"]
+ p1_AA = [
+ list(a.get_vector())
+ for a in p1.get_atoms()
+ if a.id != "OP3" and a.element != "H"
+ ]
+ p2_AA = [
+ list(a.get_vector())
+ for a in p2.get_atoms()
+ if a.id != "OP3" and a.element != "H"
+ ]
p1_AA = np.transpose(np.array(p1_AA))
p2_AA = np.transpose(np.array(p2_AA))
return rmsd(p1_AA, p2_AA)
--
GitLab