BonDNet

updated the molecule wrapper to use the helper. This way features  are correctly stored for later use in the featurizer

HiPRGen/species_filter.py

@@ -15,10 +15,12 @@
 from pymatgen.core.sites import Site
 from pymatgen.core.structure import Molecule
 from pymatgen.analysis.graphs import MoleculeGraph
+
 from bondnet.model.training_utils import get_grapher
 from bondnet.core.molwrapper import MoleculeWrapper
 from bondnet.data.transformers import HeteroGraphFeatureStandardScaler
-
+from bondnet.core.molwrapper import create_wrapper_mol_from_atoms_and_bonds
+from bondnet.utils import int_atom
 
 """
 Phase 1: species filtering
@@ -221,34 +223,77 @@ def collapse_isomorphism_group(g):
 
     log_message(str(len(fragment_dict.keys())) + " unique fragments found")
 
+
     # Make DGL Molecule graphs via BonDNet functions
     log_message("creating dgl molecule graphs")
     dgl_molecules_dict = {}
     dgl_molecules = []
     extra_keys = []
-
+
+    # BONDNET EDITS # BONDNET EDITS # BONDNET EDITS # BONDNET EDITS # BONDNET EDITS
     for mol in mol_entries:
         # print(f"mol: {mol.mol_graph}")
-        molecule_grapher = get_grapher(extra_keys)
-
-        non_metal_bonds = [ (i, j) for i, j, _ in mol.covalent_graph.edges.data()]
+        molecule_grapher = get_grapher(
+            features = extra_keys,
+            allowed_charges=[-2,-1,0,1,2],
+            global_feats=["charge"],
+            ) # same
+        non_metal_bonds = [ (i, j) for i, j, _ in mol.covalent_graph.edges.data()] # same
+
         # print(f"non metal bonds: {non_metal_bonds}")
-        mol_wrapper = MoleculeWrapper(mol_graph = mol.mol_graph, free_energy = None, id = mol.entry_id, non_metal_bonds = non_metal_bonds)
+        # use create molecule wrapper instead here
+        #mol_wrapper = MoleculeWrapper(
+        #    mol_graph = mol.mol_graph, 
+        #    free_energy = None, id = mol.entry_id, 
+        #    non_metal_bonds = non_metal_bonds,
+        #    extra_keys = extra_keys
+        #)
+        #print(mol.mol_graph.molecule.sites)
+        #print(mol.mol_graph.graph)
+        #print(mol.mol_graph.graph.edges())
+
+        species = [i.specie for i in mol.mol_graph.molecule.sites]
+        coords =  [i.coords for i in mol.mol_graph.molecule.sites]
+
+        bonds = [
+             [i[0], i[1]] for i in mol.mol_graph.graph.edges()
+        ]
+
+        mol_wrapper = create_wrapper_mol_from_atoms_and_bonds(
+            species, 
+            coords, 
+            bonds, 
+            charge = mol.charge,
+            functional_group=None, 
+            identifier=mol.entry_id,
+            original_atom_ind=None,
+            original_bond_ind=None,
+            atom_features=None,
+            bond_features=None,
+            global_features={"charge": mol.charge}
+        )
+        mol_wrapper.nonmetal_bonds = non_metal_bonds
         feature = {'charge': mol.charge}
-        dgl_molecule_graph = molecule_grapher.build_graph_and_featurize(mol_wrapper, extra_feats_info = feature, dataset_species = elements)
+        dgl_molecule_graph = molecule_grapher.build_graph_and_featurize(
+            mol_wrapper, 
+            extra_feats_info = feature, 
+            element_set = elements
+        )
         dgl_molecules.append(dgl_molecule_graph)
         for nt in ["global", "atom", "bond"]:
             print(f"nt: {nt}")
             fts = dgl_molecule_graph.nodes[nt].data["feat"]
             print(f"features: {fts}")
         dgl_molecules_dict[mol.entry_id] = mol.ind
+    print(molecule_grapher.feature_name)
     grapher_features= {'feature_size':molecule_grapher.feature_size, 'feature_name': molecule_grapher.feature_name}
     #mol_wrapper_dict[mol.entry_id] = mol_wrapper
 
     # Normalize DGL molecule graphs
     scaler = HeteroGraphFeatureStandardScaler(mean = None, std = None)
     normalized_graphs = scaler(dgl_molecules)
-
+    # BONDNET EDITS # BONDNET EDITS # BONDNET EDITS # BONDNET EDITS # BONDNET EDITS # BONDNET EDITS 
+
     # print(f"mean: {scaler._mean}")
     # print(f"std: {scaler._std}")
 
@@ -307,4 +352,4 @@ def add_electron_species(
     mol_entries.append(electron_entry)
     with open(mol_entries_pickle_location, "wb") as f:
         pickle.dump(mol_entries, f)
-    return mol_entries
+    return mol_entries