adding boilerplate text at top of scripts missing it NO_JIRA

Author: IsaacSugden

scripts/multi_component_hydrogen_bond_propensity/mol2smiles.py

@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+
+from ccdc.io import MoleculeReader
+import os
+import csv
+import argparse
+from utilities import file_list, string_scrubber, read_experimental_csv
+
+
+def read_mol_file(directory, file):
+    '''Returns: identifier, smiles'''
+    mol_reader = MoleculeReader(os.path.join(directory, file))
+    mol = mol_reader[0]
+    
+    return mol.identifier, mol.heaviest_component.smiles
+
+
+def main():
+    parser = argparse.ArgumentParser(__doc__)
+    parser.add_argument(
+        "--input_dir",
+        type=str,
+        required=True,
+        help="Directory containing API folders."
+    )
+    parser.add_argument(
+        "--output_filename",
+        type=str,
+        required=True,
+        help="Filename of formatted .csv file containing SMILES."
+    )
+    parser.add_argument(
+        "--experimental_csv",
+        type=str,
+        required=False,
+        help="Filename of formatted .csv file containing identifier names and experimental bool."
+    )
+    parser.add_argument(
+        '--clean_id',
+        action='store_true',
+        help='Removes special characters from ids that may be problematic.'
+    )
+    
+    args = parser.parse_args()
+
+    output_path = os.path.join(args.input_dir, args.output_filename)
+    with open(output_path, 'w', newline='', encoding="utf-8") as output_file:
+        csvwriter = csv.writer(output_file, delimiter=',', quotechar='|')
+        csvwriter.writerow(['identifier', 'n_components',
+                           'component_a', 'component_b', 'neutral_a', 'neutral_b'])
+    
+    if args.experimental_csv:
+        experimental_dict = read_experimental_csv(args.experimental_csv)
+
+    # API group directories contain one or more API files and a directory of coformers
+    API_groups = [name for name in os.listdir(
+        args.input_dir) if os.path.isdir(os.path.join(args.input_dir, name))]
+    
+    exp_replaced = combo_count = 0
+    
+    with open(output_path, 'a+', newline='', encoding="utf-8") as output_file:
+        
+        for API_group in API_groups:
+            csvwriter = csv.writer(output_file, delimiter=',', quotechar='|')
+            API_group_path = os.path.join(args.input_dir, API_group)
+            
+            for API_file in file_list(API_group_path):
+                api_id, api_smiles = read_mol_file(
+                    API_group_path, API_file)
+                print(api_id)
+                coformer_dir_path = os.path.join(API_group_path, 'coformers')
+                
+                for coformer_file in file_list(coformer_dir_path):
+                    coformer_id, coformer_smiles = read_mol_file(
+                        coformer_dir_path, coformer_file)
+                    
+                    combo_count += 1
+                    exp_bool = "?"
+                    # Try to look up the experimental boolean in dictionary, if provided
+                    if args.experimental_csv:
+                        for (x, y) in [(api_id, coformer_id), (coformer_id, api_id)]:
+                            if (x, y) in list(experimental_dict.keys()):
+                                exp_bool = experimental_dict[(x, y)]
+                                exp_replaced += 1
+                    
+                    # Clean the ids if the option is turned on
+                    if args.clean_id:
+                        api_id = string_scrubber(api_id)
+                        coformer_id = string_scrubber(coformer_id)
+                    
+                    n_components = 2
+                    if api_smiles == coformer_smiles:
+                        n_components = 1
+                    
+                    combo_id = ".".join([api_id, coformer_id, str(exp_bool)])
+                    csvwriter.writerow([f'"{combo_id}"', n_components, api_smiles, coformer_smiles, "", ""])
+    
+    if args.experimental_csv:
+        print(f"Found experimental labels for {exp_replaced} out of {combo_count} combinations")
+
+
+if __name__ == '__main__':
+    main()

scripts/november_2023_morphology_webinar/morphology_plot.py

@@ -1,3 +1,11 @@
+#!/usr/bin/env python
+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
 import matplotlib
 # matplotlib.use('Agg')
 import matplotlib.pyplot as plt

scripts/particle_rugosity/particle_rugosity.py

@@ -1,3 +1,12 @@
+#!/usr/bin/env python
+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+
 # script for calculating the particle rugosity for a given crystal structure (.cif in local working directory, or refcode of a CSD entry)
 # requires a CCDC license, and loading of the CSD-python miniconda environment if run from Linux command line
 

scripts/refcodes_with_properties/test_entry_property_calculator.py

@@ -1,3 +1,12 @@
+#!/usr/bin/env python
+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+
 import unittest
 
 from ccdc.io import EntryReader