Fix error in prefilter_cif

lcmd-epfl · Nov 17, 2024 · be3bcf5 · be3bcf5
1 parent ab3d1b7
commit be3bcf5
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Showing 2 changed files with 18 additions and 13 deletions.
diff --git a/cell2mol/final_c2m_driver.py b/cell2mol/final_c2m_driver.py
@@ -4,7 +4,7 @@
 from cell2mol.refcell import process_refcell
 from cell2mol.unitcell import process_unitcell
 from cell2mol.xyz_molecule import get_molecule
-from cell2mol.read_write import prefiter_cif
+from cell2mol.read_write import prefilter_cif, exit_with_error
 
 def main():
     input, system_type, cell_para, debug_mode = parsing_arguments()
@@ -17,7 +17,7 @@ def main():
     if not os.path.exists(input_path):
         exit_with_error(f"Input file not found: {input_path}")
     if extension == ".cif":
-        if prefiter_cif(input_path):
+        if prefilter_cif(input_path):
             handle_cif_file(input_path, system_type, name, current_dir, debug_mode)
         else:
             exit_with_error("CIF file is not suitable for processing")
@@ -51,12 +51,6 @@ def handle_xyz_file(input_path, system_type, name, cell_para, current_dir, debug
     else:
         exit_with_error("Invalid system type for .xyz file", {"system_type": system_type})
 
-def exit_with_error(message):
-    """Logs the error message to a file and exits the program."""
-    error_log_path = os.path.join(os.getcwd(), "error_input.out")
-    with open(error_log_path, "w") as error_log:
-        error_log.write(f"Error: {message}\n")
-    sys.exit(message)
 
 if __name__ == "__main__" or __name__ == "cell2mol.final_c2m_driver":
     main()
diff --git a/cell2mol/read_write.py b/cell2mol/read_write.py
@@ -5,6 +5,7 @@
 import sys
 import re
 from collections import defaultdict
+import os
 
 #######################
 def get_wyckoff_positions(file_path):
@@ -53,25 +54,35 @@ def get_wyckoff_positions(file_path):
     return ref_labels, ref_fracs
 
 #######################
-def prefiter_cif(input_path):
+def exit_with_error(message):
+    """Logs the error message to a file and exits the program."""
+    error_log_path = os.path.join(os.getcwd(), "error_input.out")
+    with open(error_log_path, "w") as error_log:
+        error_log.write(f"Error: {message}\n")
+    sys.exit(message)
+
+#######################
+def prefilter_cif(input_path):
 
     with open(input_path, 'r') as ciffile:
         file_content = ciffile.read()
         if 'radical' in file_content:
-            print("Radical found in cif file. STOPPING")                   
+            exit_with_error("Radical found in cif file. STOPPING")                   
             return False
         elif '_atom_site_fract_x' not in file_content:
-            print("No fractional coordinates found in cif file. STOPPING")  
+            exit_with_error("No fractional coordinates found in cif file. STOPPING")  
             return False
         elif '?' in file_content:
             if "_diffrn_ambient_temperature ?" not in file_content and "_chemical_melting_point ?" not in file_content:
-                print("Disorder found in cif file. STOPPING")
+                exit_with_error("Disorder found in cif file. STOPPING")
                 return False
             else:
                 num_greps = file_content.count('?')
                 if num_greps > 1:
-                    print("Disorder found in cif file. STOPPING")                      
+                    exit_with_error("Disorder found in cif file. STOPPING")                      
                     return False
+                else:
+                    return True
         else:
             print("Cif file is ready for processing")
             return True