From 28866848dab222c0aa1552be0e36fd20a10edc89 Mon Sep 17 00:00:00 2001
From: "c.faber" <c.faber@fz-juelich.de>
Date: Tue, 3 Sep 2024 10:31:46 +0200
Subject: [PATCH] add sequence position
---
setup.py | 2 +-
src/BioHelpers_FABER.egg-info/PKG-INFO | 2 +-
src/BioHelpers_FABER/bio_mod.py | 26 ++++++++++++++++++++++++++
3 files changed, 28 insertions(+), 2 deletions(-)
diff --git a/setup.py b/setup.py
index 4f926fb..0a6b022 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@ with open("README.md", "r") as f:
setup(
name="BioHelpers_FABER",
- version="0.1.13",
+ version="0.1.14",
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.egg-info/PKG-INFO b/src/BioHelpers_FABER.egg-info/PKG-INFO
index a691826..e0314b7 100644
--- a/src/BioHelpers_FABER.egg-info/PKG-INFO
+++ b/src/BioHelpers_FABER.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: BioHelpers-FABER
-Version: 0.1.12
+Version: 0.1.13
Summary: Small collection of useful scripts for the computational work with RNA Data.
Home-page: https://gitlab.jsc.fz-juelich.de/faber1/biohelpers
Author: Christian Faber
diff --git a/src/BioHelpers_FABER/bio_mod.py b/src/BioHelpers_FABER/bio_mod.py
index f57e88e..9651f73 100644
--- a/src/BioHelpers_FABER/bio_mod.py
+++ b/src/BioHelpers_FABER/bio_mod.py
@@ -491,6 +491,32 @@ def numberOfResidues(file: str) -> int:
return int(len(res))
+def get_sequence_position(filename: str) -> tuple:
+ """Show all the non-het Residues in a given pdb file and the associated position in the native molecule.
+
+ :param filename: Filename of PDB
+ :type filename: str
+ :return: Tuple of list with positions and sequence as string
+ :rtype: tuple
+ """
+ chain = pdb.PDBParser().get_structure("id", filename)[0].get_chains()
+ chain = next(chain)
+ residues = chain.get_residues()
+ r1 = next(residues)
+ r2 = next(residues)
+ numb = [r1.id[1], r2.id[1]]
+ sequ = [r1.get_resname(), r2.get_resname()]
+ for r in residues:
+ if r.id[0] == " ":
+ sequ.append(r.get_resname())
+ if abs(numb[-1] - r.id[1]) > 1:
+ numb.append(r.id[1])
+ numb.append(r.id[1])
+ else:
+ numb[-1] = r.id[1]
+ return (numb, "".join(sequ))
+
+
if __name__ == "__main__":
print("------------------")
print(" gmap 1.0 - sub module ")
--
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