Jwt edits

molSimplify/Classes/ligand.py

@@ -286,6 +286,7 @@ def ligand_breakdown(mol, BondedOct=False, silent=True, transition_metals_only=T
     # this function takes an octahedral
     # complex and returns ligands
     metal_index = mol.findMetal(transition_metals_only=transition_metals_only)[0]
+    # print(BondedOct)
     bondedatoms = mol.getBondedAtomsSmart(metal_index, oct=BondedOct)
     # print('!!!!!boundatoms', bondedatoms)
     # print('from get oct' + str(bondedatoms))

molSimplify/Classes/mol3D.py

@@ -1345,6 +1345,7 @@ def findcloseMetal(self, atom0):
         return close_metal
 
     def findMetal(self, transition_metals_only: bool = True) -> List[int]:
+#        transition_metals_only = False
         """
         Find metal(s) in a mol3D class.
 
@@ -5249,7 +5250,7 @@ def get_symmetry_denticity(self, return_eq_catoms=False, BondedOct=False):
                 eq_catoms = False
             return eqsym, maxdent, ligdents, homoleptic, ligsymmetry, eq_catoms
 
-    def is_sandwich_compound(self):
+    def is_sandwich_compound(self, transition_metals_only=True):
         """
         Evaluates whether a compound is a sandwich compound
 
@@ -5275,7 +5276,7 @@ def is_sandwich_compound(self):
 
         from molSimplify.Informatics.graph_analyze import obtain_truncation_metal
         mol_fcs = obtain_truncation_metal(self, hops=1)
-        metal_ind = mol_fcs.findMetal()[0]
+        metal_ind = mol_fcs.findMetal(transition_metals_only=transition_metals_only)[0]
         catoms = list(range(mol_fcs.natoms))
         catoms.remove(metal_ind)
         sandwich_ligands, _sl = list(), list()
@@ -5305,7 +5306,7 @@ def is_sandwich_compound(self):
                           for x in info_sandwich_lig])
         return num_sandwich_lig, info_sandwich_lig, aromatic, allconnect
 
-    def is_edge_compound(self):
+    def is_edge_compound(self, transition_metals_only=True):
         """
         Check if a structure is edge compound.
 
@@ -5322,10 +5323,10 @@ def is_edge_compound(self):
         # two connected non-metal atoms both connected to the metal.
 
         from molSimplify.Informatics.graph_analyze import obtain_truncation_metal
-        num_sandwich_lig, info_sandwich_lig, aromatic, allconnect = self.is_sandwich_compound()
+        num_sandwich_lig, info_sandwich_lig, aromatic, allconnect = self.is_sandwich_compound(transition_metals_only=transition_metals_only)
         if not num_sandwich_lig or (num_sandwich_lig and not allconnect):
             mol_fcs = obtain_truncation_metal(self, hops=1)
-            metal_ind = mol_fcs.findMetal()[0]
+            metal_ind = mol_fcs.findMetal(transition_metals_only=transition_metals_only)[0]
             catoms = list(range(mol_fcs.natoms))
             catoms.remove(metal_ind)
             edge_ligands, _el = list(), list()
@@ -5399,8 +5400,8 @@ def get_geometry_type(self, dict_check=False, angle_ref=False, num_coord=False,
         if catoms_arr is not None and len(catoms_arr) != num_coord:
             raise ValueError("num_coord and the length of catoms_arr do not match.")
 
-        num_sandwich_lig, info_sandwich_lig, aromatic, allconnect = self.is_sandwich_compound()
-        num_edge_lig, info_edge_lig = self.is_edge_compound()
+        num_sandwich_lig, info_sandwich_lig, aromatic, allconnect = self.is_sandwich_compound(transition_metals_only=transition_metals_only)
+        num_edge_lig, info_edge_lig = self.is_edge_compound(transition_metals_only=transition_metals_only)
 
         if num_coord not in [3, 4, 5, 6, 7]:
             if num_sandwich_lig:

molSimplify/Informatics/MOF/MOF_descriptors.py

@@ -246,7 +246,7 @@ def make_MOF_SBU_RACs(SBUlist, SBU_subgraph, molcif, depth, name, cell_v, anchor
                 """""""""
                 functional_atoms = []
                 for jj in range(len(temp_mol.graph)):
-                    if not jj in link_list: # linker atom is not bonded to a metal
+                    if jj not in link_list: # linker atom is not bonded to a metal
                         if not set({temp_mol.atoms[jj].sym}) & set({"C","H"}): # not a carbon nor a hydrogen. syms get symbols.
                             functional_atoms.append(jj)
                 """""""""

molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py

@@ -140,7 +140,7 @@
                 for jj in range(len(temp_mol.graph)):
                     #print(link_list)
                     #print(main)
-                    if not jj in main:
+                    if jj not in main:
                         if not set({temp_mol.atoms[jj].sym}) & set({"H"}):
                             functional_atoms.append(jj)
                 print(functional_atoms)

molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional_2.py

@@ -139,7 +139,7 @@
                     #print(main)
                     #print(link_list)
                     if jj in main:
-                        if not jj in link_list:
+                        if jj not in link_list:
                             if not set({temp_mol.atoms[jj].sym}) & set({"C","H"}):
                                 functional_atoms.append(jj)
                     else:

molSimplify/Informatics/MOF/PBC_functions.py

@@ -392,7 +392,7 @@
         cart_coord=np.dot(fcoord,cell)
         coord_list.append([cart_coord[0],cart_coord[1],cart_coord[2]])
     tmpstr=",".join([at for at in atoms])
-    if filename != None:
+    if filename is not None:
         np.savetxt(filename[:-4]+".net",molgraph,fmt="%i",delimiter=",",header=tmpstr)
     return coord_list, molgraph
 
@@ -936,7 +936,7 @@
             current_linker_list = current_linker_list-SBUlist
             checked_list.add(start_idx)
             for val in loop_over:
-                if (not val in SBUlist):
+                if val not in SBUlist:
                     current_linker_list.update(np.nonzero(adj_matrix[val])[1]) # np.nonzero(adj_matrix[val])[1] are the indices of atoms with bonds to the atom with index val
             left_to_check = current_linker_list-checked_list-SBUlist # Linker atoms whose connecting atoms still need to be checked.
             if len(left_to_check) == 0:
@@ -1042,7 +1042,7 @@
         disordered_atom_types = []
         disordered_atom_occupancies = []
 
-        if occupancy_index != False: # This means that occupancy information is available
+        if occupancy_index: # This means that occupancy information is available
             for idx, at in enumerate(atomlines): # Go through the lines of the cif with atom specific information. Atom by atom.
                 ln=at.strip().split()
 

molSimplify/Informatics/MOF/cluster_extraction.py

@@ -83,7 +83,7 @@
                 """""""""
                 functional_atoms = []
                 for jj in range(len(temp_mol.graph)):
-                    if not jj in link_list:
+                    if jj not in link_list:
                         if not set({temp_mol.atoms[jj].sym}) & set({"C","H"}):
                             functional_atoms.append(jj)
         # At this point, we look at the cycles for the graph, then add atoms if they are part of a cycle

molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py

@@ -682,15 +682,13 @@
             else:
                 # check number of times we cross PBC :
                 # TODO: we still can fail in multidentate ligands!
-                linker_cart_coords = np.array([at.coords() \
-                        for at in [molcif.getAtom(val) for val in atoms_list]])
+                linker_cart_coords = np.array([at.coords() for at in [molcif.getAtom(val) for val in atoms_list]])
                 linker_adjmat = np.array(linker_subgraphlist[ii])
                 pr_image_organic = ligand_detect(cell_v, linker_cart_coords, linker_adjmat, linkeranchors_list)
                 sbu_temp = linkeranchors_atoms.copy()
                 sbu_temp.update({val for val in initial_SBU_list[list(sbu_connect_list)[0]]})
                 sbu_temp = list(sbu_temp)
-                sbu_cart_coords = np.array([at.coords() \
-                       for at in [molcif.getAtom(val) for val in sbu_temp]])
+                sbu_cart_coords = np.array([at.coords() for at in [molcif.getAtom(val) for val in sbu_temp]])
                 sbu_adjmat = slice_mat(adj_matrix.todense(), sbu_temp)
                 pr_image_sbu = ligand_detect(cell_v, sbu_cart_coords, sbu_adjmat,set(range(len(linkeranchors_list))))
                 if not (len(np.unique(pr_image_sbu, axis=0))==1 and len(np.unique(pr_image_organic, axis=0))==1): # linker