Relocate PCD .cif files that have no atomic site/label while preprocessing each .cif file

news/format-PCD.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Relocate PCD .cif files that have no atomic site/label while preprocessing each .cif file.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/cifkit/models/cif_ensemble.py

@@ -64,7 +64,7 @@ def __init__(
             self._log_info(CifEnsembleLog.PREPROCESSING.value)
             for file_path in file_paths:
                 edit_cif_file_based_on_db(file_path)
-            # Move ill-formatted files after processing
+            # Move ill-formatted files after pre-processing
             move_files_based_on_errors(cif_dir_path, file_paths)
 
         # Initialize new files after ill-formatted files are moved

src/cifkit/preprocessors/error.py

@@ -2,30 +2,25 @@
 from pathlib import Path
 
 from cifkit.models.cif import Cif
+from cifkit.preprocessors.format import preprocess_label_element_loop_values
 from cifkit.utils.cif_parser import check_unique_atom_site_labels
 
 
-def make_directory_and_move(file_path, dir_path, new_file_path):
-    """Create directory if it doesn't exist and move the file."""
-    os.makedirs(dir_path, exist_ok=True)
-    new_file_path = os.path.join(dir_path, new_file_path)
-    os.rename(file_path, new_file_path)
-
-
-def move_files_based_on_errors(dir_path, file_paths):
-    print(f"\nCIF Preprocessing in {dir_path} begun...\n")
+def move_files_based_on_errors(cif_dir_path, file_paths):
+    print(f"\nCIF Preprocessing in {cif_dir_path} begun...\n")
 
     # Ensure dir_path is a Path object
-    dir_path = Path(dir_path)
+    cif_dir_path = Path(cif_dir_path)
 
     # Dictionary to hold directory paths for each error type
     error_directories = {
-        "error_operations": dir_path / "error_operations",
-        "error_duplicate_labels": dir_path / "error_duplicate_labels",
-        "error_wrong_loop_value": dir_path / "error_wrong_loop_value",
-        "error_coords": dir_path / "error_coords",
-        "error_invalid_label": dir_path / "error_invalid_label",
-        "error_others": dir_path / "error_others",
+        "error_no_labels": cif_dir_path / "error_no_labels",
+        "error_operations": cif_dir_path / "error_operations",
+        "error_duplicate_labels": cif_dir_path / "error_duplicate_labels",
+        "error_wrong_loop_value": cif_dir_path / "error_wrong_loop_value",
+        "error_coords": cif_dir_path / "error_coords",
+        "error_invalid_label": cif_dir_path / "error_invalid_label",
+        "error_others": cif_dir_path / "error_others",
     }
 
     # Ensure all direct
@@ -35,15 +30,23 @@ def move_files_based_on_errors(dir_path, file_paths):
         filename = os.path.basename(file_path)
         print(f"Preprocessing {file_path} ({i}/{len(file_paths)})")
         try:
-            # Check the label before instantiating the Cif object to save time
+            # Attempt to initialize a Cif object and if it is PCD source,
+            # preprocess the CIF file and identify the error type
+            cif = Cif(file_path, is_formatted=True)
+            db_source = cif.db_source
+            if db_source == "PCD":
+                # Preprocess the CIF file
+                preprocess_label_element_loop_values(file_path)
+            # Check site element can be parsed from site label
             check_unique_atom_site_labels(file_path)
-            # Instantiate the Cif object fully
-            Cif(file_path, is_formatted=True)
+
         except Exception as e:
             error_message = str(e)
             # Example of handling specific errors, adjust as needed
             if "symmetry operation" in error_message:
                 error_type = "error_operations"
+            elif "no atomic label and type" in error_message:
+                error_type = "error_no_labels"
             elif "contains duplicate atom site labels" in error_message:
                 error_type = "error_duplicate_labels"
             elif "Wrong number of values in loop" in error_message:
@@ -55,7 +58,7 @@ def move_files_based_on_errors(dir_path, file_paths):
             else:
                 error_type = "error_others"
 
-            make_directory_and_move(file_path, error_directories[error_type], filename)
+            _make_directory_and_move(file_path, error_directories[error_type], filename)
             num_files_moved[error_type] += 1
             print(f"File {filename} moved to '{error_type}' due to: {error_message}")
 
@@ -64,3 +67,10 @@ def move_files_based_on_errors(dir_path, file_paths):
     for error_type, count in num_files_moved.items():
         print(f"# of files moved to '{error_type}' folder: {count}")
     print()
+
+
+def _make_directory_and_move(file_path, dir_path, new_file_path):
+    """Create directory if it doesn't exist and move the file."""
+    os.makedirs(dir_path, exist_ok=True)
+    new_file_path = os.path.join(dir_path, new_file_path)
+    os.rename(file_path, new_file_path)

src/cifkit/preprocessors/format.py

@@ -18,12 +18,14 @@ def preprocess_label_element_loop_values(file_path: str) -> None:
     content_lines = cif_parser.get_line_content_from_tag(
         file_path, "_atom_site_occupancy"
     )
-
+    # Check whether the content line is empty, then throw an error
     for line in content_lines:
         line = line.strip()
-        site_label, atom_type_symbol = line.split()[:2]
+        try:
+            site_label, atom_type_symbol = line.split()[:2]
+        except ValueError:
+            raise ValueError("The file contains no atomic label and type.")
         atom_type_from_label = string_parser.get_atom_type_from_label(site_label)
-
         unique_elements = cif_parser.get_unique_elements_from_loop(loop_values)
         """Type 8. Ex) 1817279.cif.
 

src/cifkit/utils/cif_editor.py

@@ -63,6 +63,7 @@ def edit_cif_file_based_on_db(file_path: str):
         add_hashtag_in_first_line(file_path)
     elif db_source == "PCD":
         remove_author_loop(file_path)
+        # Preprocessing the label is only tested on PCD files
         preprocess_label_element_loop_values(file_path)
 
     check_unique_atom_site_labels(file_path)

tests/core/models/test_cif.py

@@ -566,7 +566,7 @@ def test_init_error_coord_missing():
     with pytest.raises(ValueError) as e:
         Cif(file_path)
 
-    assert "not enough values to unpack (expected 2, got 1)" in str(e.value)
+    assert "contains no atomic label and type." in str(e.value)
 
 
 """

tests/data/cif/error/combined/260486.cif

@@ -0,0 +1,118 @@
+##############################################################################
+#                                                                            #
+# Au-In            # Au9In4 ht                                     #  260486 #
+#                                                                            #
+##############################################################################
+#                                                                            #
+#                           Pearson's Crystal Data                           #
+#      Crystal Structure Database for Inorganic Compounds (on DVD)           #
+#                              Release 2024/25                               #
+#      Editors: Pierre Villars, Karin Cenzual, and Vitaliy Dubenskyy         #
+#                                                                            #
+#   Copyright (c) ASM International & Material Phases Data System (MPDS),    #
+# Switzerland & National Institute for Materials Science (NIMS), Japan, 2024 #
+#                   All rights reserved. Version 2024.07                     #
+#                                                                            #
+#   This copy of Pearson's Crystal Data is licensed to:                      #
+#   Hunter College - City University of New York                             #
+#                                                                            #
+##############################################################################
+
+data_260486
+_audit_creation_date                     2024-09-17
+_audit_creation_method
+;
+Pearson's Crystal Data browser
+;
+#_database_code_PCD                      260486
+_database_code_PDF                       ?
+
+# Entry summary
+
+_chemical_formula_structural             'Au~9~ In~4~'
+_chemical_formula_sum                    'Au9 In4'
+_chemical_name_mineral                   ?
+_chemical_compound_source                ?
+_chemical_name_structure_type            Au~6~(Au~0.5~In~0.5~)~6~In,cP76,215
+_chemical_formula_weight                 2232.0
+
+# Bibliographic data
+
+_publ_section_title
+'The gold-indium thin film system: A high resolution electron microscopy study'
+_journal_coden_ASTM                      JCOMAH
+_journal_name_full                       'J. Less-Common Met.'
+_journal_year                            1986
+_journal_volume                          116
+_journal_page_first                      63
+_journal_page_last                       72
+_journal_language                        English
+loop_
+ _publ_author_name
+ _publ_author_address
+''
+;
+;
+
+# Standardized crystallographic data
+
+_cell_length_a                           9.84
+_cell_length_b                           9.84
+_cell_length_c                           9.84
+_cell_angle_alpha                        90
+_cell_angle_beta                         90
+_cell_angle_gamma                        90
+_cell_volume                             952.76
+_cell_formula_units_Z                    4
+_space_group_IT_number                   215
+_space_group_name_H-M_alt                'P -4 3 m'
+loop_
+ _space_group_symop_id
+ _space_group_symop_operation_xyz
+ 1 'x, y, z'
+ 2 '-x, -y, z'
+ 3 '-x, -z, y'
+ 4 '-x, y, -z'
+ 5 '-x, z, -y'
+ 6 '-y, -x, z'
+ 7 '-y, -z, x'
+ 8 '-y, x, -z'
+ 9 '-y, z, -x'
+ 10 '-z, -x, y'
+ 11 '-z, -y, x'
+ 12 '-z, x, -y'
+ 13 '-z, y, -x'
+ 14 'x, -y, -z'
+ 15 'x, -z, -y'
+ 16 'x, z, y'
+ 17 'y, -x, -z'
+ 18 'y, -z, -x'
+ 19 'y, x, z'
+ 20 'y, z, x'
+ 21 'z, -x, -y'
+ 22 'z, -y, -x'
+ 23 'z, x, y'
+ 24 'z, y, x'
+
+
+_exptl_crystal_colour                    ?
+_exptl_crystal_density_meas              ?
+_exptl_crystal_density_diffrn            15.56
+_cell_measurement_temperature            ?
+_cell_measurement_radiation              electrons
+_cell_measurement_reflns_used            ?
+_diffrn_ambient_temperature              ?
+_diffrn_measurement_device               ?
+_diffrn_measurement_device_type          ?
+_diffrn_radiation_type                   ?
+_diffrn_reflns_number                    ?
+_exptl_absorpt_coefficient_mu            ?
+_exptl_absorpt_correction_type           ?
+_computing_structure_solution            ?
+_refine_ls_number_parameters             ?
+_refine_ls_number_reflns                 ?
+_refine_ls_R_factor_gt                   ?
+_refine_ls_wR_factor_gt                  ?
+
+# End of data set 260486
+