add sequence position

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"},

src/BioHelpers_FABER.egg-info/PKG-INFO

 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

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     ")