Replace Pathlib with os to fix write issues

examples/evaluation.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+import os
 import math
 
 from Bio.PDB import PDBIO
@@ -38,7 +38,7 @@
 
 def build_linear_model(pdb_filename):
     parser = PDBParser()
-    structure = parser.get_structure("sample", Path(PDBdir, pdb_filename))
+    structure = parser.get_structure("sample", os.path.join(PDBdir, pdb_filename))
     model = structure[0]
     chain = model["A"]
     model_structure_geo = []
@@ -58,13 +58,13 @@ def build_linear_model(pdb_filename):
 def make_pdb_file(struct, file_nom):
     outfile = PDBIO()
     outfile.set_structure(struct)
-    outfile.save(Path(PDBdir, file_nom))
+    outfile.save(os.path.join(PDBdir, file_nom))
     return file_nom
 
 
 def build_backbone_model(pdb_filename):
     parser = PDBParser()
-    structure = parser.get_structure("sample", Path(PDBdir, pdb_filename))
+    structure = parser.get_structure("sample", os.path.join(PDBdir, pdb_filename))
     model = structure[0]
     chain = model["A"]
     model_structure_geo = []
@@ -134,7 +134,7 @@ def build_backbone_model(pdb_filename):
 
 def build_all_angles_model(pdb_filename):
     parser = PDBParser()
-    structure = parser.get_structure("sample", Path(PDBdir, pdb_filename))
+    structure = parser.get_structure("sample", os.path.join(PDBdir, pdb_filename))
     model = structure[0]
     chain = model["A"]
     model_structure_geo = []
@@ -192,7 +192,7 @@ def build_all_angles_model(pdb_filename):
 
 def build_phi_psi_model(pdb_filename):
     parser = PDBParser()
-    structure = parser.get_structure("sample", Path(PDBdir, pdb_filename))
+    structure = parser.get_structure("sample", os.path.join(PDBdir, pdb_filename))
     model = structure[0]
     chain = model["A"]
     seq = ""
@@ -244,8 +244,8 @@ def build_phi_psi_model(pdb_filename):
 def compare_structure(reference, alternate):
     parser = PDBParser()
 
-    ref_struct = parser.get_structure("Reference", Path(PDBdir, reference))
-    alt_struct = parser.get_structure("Alternate", Path(PDBdir, alternate))
+    ref_struct = parser.get_structure("Reference", os.path.join(PDBdir, reference))
+    alt_struct = parser.get_structure("Alternate", os.path.join(PDBdir, alternate))
 
     ref_model = ref_struct[0]
     ref_chain = ref_model["A"]