PR to verify disorders

scripts/multi_component_hydrogen_bond_propensity/ReadMe.md

@@ -47,6 +47,8 @@ optional arguments:
                         the directory of the desired coformer library
   -f FAILURE_DIRECTORY, --failure_directory FAILURE_DIRECTORY
                         The location where the failures file should be generated
+  --force_run_disordered
+                        Forces running the script on disordered entries. (NOT RECOMMENDED)
 ```
 
 The default coformer library is the one supplied with your Mercury install

scripts/multi_component_hydrogen_bond_propensity/multi_component_hydrogen_bond_propensity_report.py

@@ -21,6 +21,7 @@
 import tempfile
 import subprocess
 import json
+import warnings
 
 import matplotlib
 
@@ -32,8 +33,6 @@
 from ccdc.descriptors import CrystalDescriptors
 
 try:
-    import warnings
-
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", category=DeprecationWarning)
         import docxtpl
@@ -314,14 +313,18 @@ def make_mc_report(identifier, results, directory, diagram_file, chart_file):
     launch_word_processor(output_file)
 
 
-def main(structure, work_directory, failure_directory, library, csdrefcode):
+def main(structure, work_directory, failure_directory, library, csdrefcode, force_run):
     # This loads up the CSD if a refcode is requested, otherwise loads the structural file supplied
     if csdrefcode:
         try:
             crystal = io.CrystalReader('CSD').crystal(structure)
         except RuntimeError:
             print('Error! %s is not in the database!' % structure)
             quit()
+        if io.CrystalReader('CSD').entry(structure).has_disorder and not force_run:
+            raise RuntimeError("Disorder can cause undefined behaviour. It is not advisable to run this "
+                               "script on disordered entries.\n To force this script to run on disordered entries"
+                               " use the flag --force_run_disordered.")
     else:
         crystal = io.CrystalReader(structure)[0]
 
@@ -340,6 +343,11 @@ def main(structure, work_directory, failure_directory, library, csdrefcode):
     # for each coformer in the library, make a pair file for the api/coformer and run a HBP calculation
     for i, f in enumerate(coformer_files):
         molecule_file, coformer_name = make_pair_file(api_molecule, tempdir, f, i + 1)
+        if not io.CrystalReader(f)[0].molecule.is_3d:
+            failure_warning = f"Could not run for {coformer_name} no 3d coordinates present."
+            failures.append(failure_warning)
+            warnings.warn(failure_warning)
+            continue
         print(coformer_name)
         crystal_reader = io.CrystalReader(molecule_file)
         crystal = crystal_reader[0]
@@ -358,10 +366,11 @@ def main(structure, work_directory, failure_directory, library, csdrefcode):
                     tdata = get_mc_scores(propensities, crystal.identifier)
                     json.dump(tdata, file)
                 mc_dictionary[coformer_name] = get_mc_scores(propensities, crystal.identifier)
-            except RuntimeError:
+            except RuntimeError as error_message:
                 print("Propensity calculation failure for %s!" % coformer_name)
+                print(error_message)
                 mc_dictionary[coformer_name] = ["N/A", "N/A", "N/A", "N/A", "N/A", crystal.identifier]
-                failures.append(coformer_name)
+                failures.append(f"{coformer_name}: {error_message}")
 
     # Make sense of the outputs of all the calculations
     mc_hbp_screen = sorted(mc_dictionary.items(), key=lambda e: 0 if e[1][0] == 'N/A' else e[1][0], reverse=True)
@@ -411,6 +420,9 @@ def main(structure, work_directory, failure_directory, library, csdrefcode):
     parser.add_argument('-f', '--failure_directory', type=str,
                         help='The location where the failures file should be generated')
 
+    parser.add_argument('--force_run_disordered', action="store_true",
+                        help='Forces running the script on disordered entries. (NOT RECOMMENDED)', default=False)
+
     args = parser.parse_args()
     refcode = False
     args.directory = os.path.abspath(args.directory)
@@ -424,4 +436,5 @@ def main(structure, work_directory, failure_directory, library, csdrefcode):
     if not os.path.isdir(args.coformer_library):
         parser.error('%s - library not found.' % args.coformer_library)
 
-    main(args.input_structure, args.directory, args.failure_directory, args.coformer_library, refcode)
+    main(args.input_structure, args.directory, args.failure_directory, args.coformer_library, refcode,
+         args.force_run_disordered)