Merge pull request #147 from hjkgrp/MOF_descriptors_update

changes to two functions (mol3D, and Informatics/MOF)

molSimplify/Classes/mol3D.py

@@ -702,9 +702,13 @@ def convert2OBMol2(self, force_clean=False, ignoreX=False):
             #####
             obConversion.SetOutFormat('mol2')
             ss = obConversion.WriteString(OBMol)
-            # Update atom types from OBMol
-            lines = ss.split('ATOM\n')[1].split(
-                '@<TRIPOS>BOND')[0].split('\n')[:-1]
+            # Update atom types from OBMol.
+            if "UNITY_ATOM_ATTR" in ss: # If this section is present, it will be before the @<TRIPOS>BOND section.
+                lines = ss.split('ATOM\n')[1].split(
+                    '@<TRIPOS>UNITY_ATOM_ATTR')[0].split('\n')[:-1]
+            else:
+                lines = ss.split('ATOM\n')[1].split(
+                    '@<TRIPOS>BOND')[0].split('\n')[:-1]  
             for i, line in enumerate(lines):
                 if '.' in line.split()[5]:
                     self.atoms[i].name = line.split()[5].split('.')[1]

molSimplify/Informatics/MOF/MOF_descriptors.py

@@ -800,16 +800,17 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F
         # except:
         #     full_names = [0]
         #     full_descriptors = [0]
-    elif len(linker_subgraphlist) == 1: # this never happens, right?
+    elif len(linker_subgraphlist) == 1: # Only one linker identified.
         print('Suspicious featurization')
         full_names = [1]
         full_descriptors = [1]
-    else:
-        print('Failed to featurize this MOF.')
+    else: # Means len(linker_subgraphlist) is zero.
+        print('Failed to featurize this MOF; no linkers were identified.')
         full_names = [0]
         full_descriptors = [0]
     if (len(full_names) <= 1) and (len(full_descriptors) <= 1):
-        tmpstr = "Failed to featurize %s\n"%(name)
+        print(f'full_names is {full_names} and full_descriptors is {full_descriptors}')
+        tmpstr = "Failed to featurize %s: Only zero or one total linkers identified.\n"%(name)
         write2file(path,"/FailedStructures.log",tmpstr)
     return full_names, full_descriptors