Adding Solvent Workflow

.gitignore

@@ -8,4 +8,6 @@
 *.traj
 *__pycache__*
 **/.vscode/
-meta_production_sample.pkl
+meta_production_sample.pkl
+development/**/*.csv
+development/**/*.mol2

architector/complex_construction.py

@@ -487,7 +487,7 @@ def complex_driver(inputDict1):
                 ligandDict = newligDict
             else: # Generate from scratch
                 ligandDict = {} #
-            
+
             coreCoordList = core_geo_class.geometry_dict[coreType]
 
             # Assign con atoms based on all ligands
@@ -540,7 +540,7 @@ def complex_driver(inputDict1):
                             out_energies.append(complexClass.calculator.energy)
                             if inputDict['parameters']['return_only_1']:
                                 break
-                if not isinstance(complexClass, bool): # Catch cases where no conformation generated.
+                if not isinstance(complexClass, bool):  # Catch cases where no conformation generated.
                     order = np.argsort(out_energies)
                     for ind, j in enumerate(order[0:inputDict[
                        'parameters']['n_conformers']]):
@@ -585,7 +585,7 @@ def complex_driver(inputDict1):
         return conf_dict,inputDict,core_preprocess_time,symmetry_preprocess_time,int_time1
     else:
         return {},inputDict,0,0,0
-    
+
 def build_complex_driver(inputDict1): 
     """build_complex_driver overall driver building of the complex
 
@@ -787,12 +787,13 @@ def build_complex(inputDict):
             keys.append(key)
             vals.append(val)
         order = np.argsort(xtb_energies)
-        for j,i in enumerate(order):
+        for j, i in enumerate(order):
             if tmp_inputDict['parameters']['add_secondary_shell_species'] and \
                   (j < tmp_inputDict['parameters'][
                       'secondary_shell_n_conformers']):
                 if tmp_inputDict['parameters']['debug']:
-                    print('Starting secondary shell addition on {} of {}!'.format(j+1,len(order)))
+                    print('Starting secondary shell addition on {} of {}!'.format(j+1,
+                                                                                  len(order)))
                     print('Normally adds a chunk of time to generation.')
                 # Use the docking function to add species specified in inputDict/parameters
                 mol_plus_species, species_list = \

architector/io_process_input.py

@@ -1094,12 +1094,13 @@ def inparse(inputDict):
             if metal in io_ptable.metal_charge_dict:
                 outparams['metal_ox'] = io_ptable.metal_charge_dict[metal]
             else: # Pull lowest positive "main" oxidation state from mendeleev
-                elem = mendeleev.__dict__[newinpDict['core']['metal']]
+                elem = mendeleev.element(newinpDict['core']['metal'])
                 outparams['metal_ox'] = [x.oxidation_state for x in elem._oxidation_states if (x.category == 'main') and (x.oxidation_state > 0)][0]
         if outparams['metal_spin'] is None:
             if outparams['metal_ox'] != io_ptable.metal_charge_dict.get(metal,100):
                 # Calculate from mendeleev reference - Generally aufbau.
-                outparams['metal_spin'] = mendeleev.__dict__[newinpDict['core']['metal']].ec.ionize(outparams['metal_ox']).unpaired_electrons()
+                outparams['metal_spin'] = mendeleev.element(
+                    newinpDict['core']['metal']).ec.ionize(outparams['metal_ox']).unpaired_electrons()
             else: # Otherwise use refdict.
                 outparams['metal_spin'] = io_ptable.metal_spin_dict[metal]
 
@@ -1434,12 +1435,13 @@ def inparse_2D(inputDict):
             if metal in io_ptable.metal_charge_dict:
                 outparams['metal_ox'] = io_ptable.metal_charge_dict[metal]
             else: # Pull lowest positive "main" oxidation state from mendeleev
-                elem = mendeleev.__dict__[newinpDict['core']['metal']]
+                elem = mendeleev.element(newinpDict['core']['metal'])
                 outparams['metal_ox'] = [x.oxidation_state for x in elem._oxidation_states if (x.category == 'main') and (x.oxidation_state > 0)][0]
         if outparams['metal_spin'] is None:
             if outparams['metal_ox'] != io_ptable.metal_charge_dict.get(metal,100):
                 # Calculate from mendeleev reference - Generally aufbau.
-                outparams['metal_spin'] = mendeleev.__dict__[newinpDict['core']['metal']].ec.ionize(outparams['metal_ox']).unpaired_electrons()
+                outparams['metal_spin'] = mendeleev.element(
+                    newinpDict['core']['metal']).ec.ionize(outparams['metal_ox']).unpaired_electrons()
             else: # Otherwise use refdict.
                 outparams['metal_spin'] = io_ptable.metal_spin_dict[metal]