Add symmetry fixing prototyping.

architector/complex_construction.py

@@ -26,8 +26,10 @@
 class Ligand:
     """Class to contain all information about a ligand including conformers."""
 
-    def __init__(self, smiles, ligcoordList, corecoordList, core, ligGeo, ligcharge, ca_metal_dist_constraints,
-                covrad_metal=None, vdwrad_metal=None, debug=False):
+    def __init__(self, smiles, ligcoordList, corecoordList, core,
+                 ligGeo, ligcharge, ca_metal_dist_constraints,
+                 covrad_metal=None, vdwrad_metal=None, enforce_symmetry=False,
+                 debug=False):
         """Set up initial variables for ligand and run conformer generation routines.
 
         Parameters
@@ -50,6 +52,8 @@ def __init__(self, smiles, ligcoordList, corecoordList, core, ligGeo, ligcharge,
             Covalent radii of the metal, default values from io_ptable.rcov1
         vdwrad_metal : float, optional
             VDW radii of the metal, default values from io_ptable.rvdw
+        enforce_symmetry : bool, optional
+            Enforce the ligand symmetry elements during conformer generation?
         debug: bool, optional
             debug turns on/off output text/comments.
         """
@@ -59,32 +63,35 @@ def __init__(self, smiles, ligcoordList, corecoordList, core, ligGeo, ligcharge,
         self.corecoordList = corecoordList
         self.metal = core
         self.ca_metal_dist_constraints = ca_metal_dist_constraints
-        self.geo = ligGeo 
+        self.geo = ligGeo
         self.BO_dict = None
         self.atom_types = None
         self.out_ligcoordLists = None
         self.charge = ligcharge
+        self.enforce_symmetry = enforce_symmetry
         self.liggen_start_time = time.time()
         # Generate conformations
         if debug:
             print("GENERATING CONFORMATIONS for {}".format(smiles))
-        conformers, rotscores, tligcoordList, relax, bo_dict, atypes, rotlist = io_lig.find_conformers(self.smiles, 
-                                                        self.ligcoordList, 
-                                                        self.corecoordList, 
-                                                        metal=self.metal,
-                                                        ligtype=self.geo,
-                                                        ca_metal_dist_constraints=self.ca_metal_dist_constraints,
-                                                        covrad_metal=covrad_metal,
-                                                        vdwrad_metal=vdwrad_metal,
-                                                        debug=debug
-                                                        )
+        conformers, rotscores, tligcoordList, relax, bo_dict, atypes, rotlist = io_lig.find_conformers(
+            self.smiles, 
+            self.ligcoordList,
+            self.corecoordList,
+            metal=self.metal,
+            ligtype=self.geo,
+            ca_metal_dist_constraints=self.ca_metal_dist_constraints,
+            covrad_metal=covrad_metal,
+            vdwrad_metal=vdwrad_metal,
+            enforce_symmetry=self.enforce_symmetry,
+            debug=debug
+        )
         if len(conformers) > 0:
             self.conformerList = conformers
             self.conformerRotScore = rotscores
             self.rotList = rotlist
             self.out_ligcoordLists = tligcoordList
             self.selectedConformer = self.conformerList[0]
-            self.exists = True 
+            self.exists = True
             self.relax = relax
             self.BO_dict = bo_dict
             self.atom_types = atypes
@@ -238,10 +245,10 @@ def compute_conformer_efficacy(self,conformerList,rot_vals,ligand):
             elif (not out_eval.successful) and (self.parameters['debug']):
                 print('Ligand {} failed xtb/uff or overlapped.'.format(i))
         return bestConformer, assembled
-            
+
     def final_eval(self, single_point=False):
         """final_eval perform final evaulation of full complex conformer with XTB.
-        
+
         Involves either a relaxation or not for each "sane" conformer.
 
         Parameters
@@ -366,7 +373,9 @@ def gen_aligned_complex(newLigInputDicts,
                 lig_ca_metal_dist_constraints,
                 covrad_metal=inputDict['parameters']['covrad_metal'],
                 vdwrad_metal=inputDict['parameters']['vdwrad_metal'],
-                debug=inputDict['parameters']['debug']
+                enforce_symmetry=inputDict['parameters'].get(
+                    'enforce_ligand_internal_symmetry', False),
+                debug=inputDict['parameters']['debug'],
                                 )
             # Store results
             ligandDict[ligid] = ligandClass

architector/io_arch_dock.py

@@ -30,7 +30,7 @@
     # e.g. Reduce to allow for closer molecule-species distances
     'species_location_method': 'default',  # Default attempts a basic colomb repulsion placement, targeted
     # Only other option is 'random' at the moment.
-    'species_add_copies': 1,  # Number of species addition orientations to build 
+    'species_add_copies': 1,  # Number of species addition orientations to build
     'species_method': 'GFN2-xTB',  # Method to use on full species - right now only GFN2-xTB really works
     'species_relax': True,  # Whether or not to relax the generated secondary solvation structures.
     'species_intermediate_method': 'GFN-FF',  # Method to use for intermediate species screening - Suggested GFN-FF

architector/io_calc.py

@@ -208,7 +208,7 @@ def __init__(self, structure, parameters={}, init_sanity_check=False,
         self.detect_spin_charge = detect_spin_charge
         if len(parameters) > 0:
             for key,val in parameters.items():
-                setattr(self,key,val)
+                setattr(self, key, val)
         if assembly:
             self.init_sanity_check = True
             self.relax = False