wip #56 start implementing CatalyticReactionComplex

src/conformational_sampling/metal_complexes.py

@@ -1,8 +1,13 @@
+from dataclasses import dataclass
 from math import cos, pi, sin
+import stk
 from stk.molecular.topology_graphs import Edge
 from stk.molecular.topology_graphs.metal_complex import MetalComplex
 from stk.molecular.topology_graphs.metal_complex.vertices import BiDentateLigandVertex, MonoDentateLigandVertex, MetalVertex
 
+from conformational_sampling.main import bind_ligands
+from conformational_sampling.utils import stk_metal
+
 class TwoMonoOneBidentateSquarePlanar(MetalComplex):
 
     _metal_vertex_prototypes = (
@@ -75,3 +80,54 @@ class OneLargeTwoSmallMonodentateTrigonalPlanar(MetalComplex):
             position=(cos(4*pi/3), sin(4*pi/3), 0),
         ),
     )
+
+
+@dataclass
+class CatalyticReactionComplex:
+    metal: stk.Molecule
+    ancillary_ligand: stk.Molecule
+    reactive_ligand_1: stk.Molecule
+    reactive_ligand_2: stk.Molecule
+
+
+    def __post_init__(self) -> None:
+        'create a complex with ane ancillary ligand and two reactive ligands, like bind_ligands'
+        self.complex = bind_ligands(
+            self.metal,
+            self.ancillary_ligand,
+            self.reactive_ligand_1,
+            self.reactive_ligand_2,
+        )
+
+
+    def gen_reductive_elim_drive_coords(self):
+        'generate reductive elimination driving coordinates for this complex'
+        atom_infos = list(self.complex.get_atom_infos())
+        driving_coordinates = []
+
+        def is_metal_reactive_ligand_bond(atom_info_1: stk.AtomInfo, atom_info_2: stk.AtomInfo) -> bool:
+            building_block_1 = atom_info_1.get_building_block()
+            building_block_2 = atom_info_2.get_building_block()
+            return (building_block_1 is self.metal
+                    and building_block_2 in (self.reactive_ligand_1, self.reactive_ligand_2))
+
+        # determine driving coordinates to break
+        for bond_info in self.complex.get_bond_infos():
+            if bond_info.get_building_block() is None:
+                bond = bond_info.get_bond()
+                atom_id_1, atom_id_2 = bond.get_atom1().get_id(), bond.get_atom2().get_id()
+                atom_info_1 = next(self.complex.get_atom_infos(atom_id_1))
+                atom_info_2 = next(self.complex.get_atom_infos(atom_id_2))
+                if (is_metal_reactive_ligand_bond(atom_info_1, atom_info_2)
+                    or is_metal_reactive_ligand_bond(atom_info_2, atom_info_1)):
+                    # this bond is broken in reductive elimination
+                    driving_coordinates += ('BREAK', atom_id_1, atom_id_2)
+
+        # CHECK THAT THERE ARE TWO BREAKING DRIVING COORDS
+
+
+
+        # go from zero-indexed to one-indexed
+        return [(type, i+1, j+1) for (type, i, j) in driving_coordinates]
+
+